Skip to main content

Epigenetics in Cancer Biology

  • Chapter
  • First Online:
Cancer Research: An Interdisciplinary Approach

Part of the book series: Interdisciplinary Cancer Research ((ICR,volume 1))

Abstract

The term epigenetics dates back to the 1940s, when Conrad Waddington introduced it to refer to gene expression changes that occur during development and do not involve alterations in the DNA sequence. Subsequently the definition expanded beyond development, and the field became one of the most rapidly developing ones in life sciences. Advances in epigenetics transformed our understanding of cellular and molecular events that occur during development, homeostasis, and disease and helped explain processes that have long fascinated and puzzled scientists, such as the link between inflammation and disease, the intricacies of memory formation and maintenance, and the connection between the social environment/social adversity and chronic disease risk. Epigenetically mediated gene expression changes were described in a broad group of medical conditions, including cancer and neurodegenerative, metabolic, autoimmune, psychiatric, and cardiovascular diseases and, of these, the most advanced understanding of their contribution, so far, has occurred for cancer. Changes in DNA methylation, histone posttranslational modifications, and microRNA alterations, described in a broad group of human cancers, were implicated in all stages of carcinogenesis, including initiation, progression, invasion, and metastasis. The discovery of epigenetic biomarkers facilitated novel strategies for the early detection of disease, helped better monitor progression, therapeutic response, and prognosis, and revolutionized personalized medicine. Moreover, the reversible nature of epigenetic marks opened the possibility to therapeutically reverse aberrant gene expression patterns and catalyzed the emergence of epigenetic drugs. Besides their promise as monotherapies, epigenetic drugs show considerable interest thanks to the possibility to combine them with other cancer therapeutic modalities, such as chemotherapy, hormone therapy, and radiation therapy.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Ackloo S, Brown PJ, Müller S (2017) Chemical probes targeting epigenetic proteins: applications beyond oncology. Epigenetics 12:378–400

    PubMed  PubMed Central  Google Scholar 

  • Adams D, Gonzalez-Duarte A, O’Riordan WD, Yang CC, Ueda M, Kristen AV, Tournev I, Schmidt HH, Coelho T, Berk JL, Lin KP, Vita G, Attarian S, Planté-Bordeneuve V, Mezei MM, Campistol JM, Buades J, Brannagan TH 3rd, Kim BJ, Oh J, Parman Y, Sekijima Y, Hawkins PN, Solomon SD, Polydefkis M, Dyck PJ, Gandhi PJ, Goyal S, Chen J, Strahs AL, Nochur SV, Sweetser MT, Garg PP, Vaishnaw AK, Gollob JA, Suhr OB (2018) Patisiran, an RNAi therapeutic, for hereditary transthyretin amyloidosis. N Engl J Med 379:11–21

    CAS  PubMed  Google Scholar 

  • Adeegbe DO, Freeman GJ, Wong K-K (2016) BET bromodomain inhibition synergizes with immune checkpoint blockade to facilitate anti-tumor response in a murine model of non-small cell lung cancer harboring activating KRAS mutation. J Immunol 196:74.10

    Google Scholar 

  • Agarwal S, Simon AR, Goel V, Habtemariam BA, Clausen VA, Kim JB, Robbie GJ (2020) Pharmacokinetics and pharmacodynamics of the small interfering ribonucleic acid, Givosiran, in patients with acute hepatic porphyria. Clin Pharmacol Ther 108:63–72

    CAS  PubMed  Google Scholar 

  • Agostini F, Zagalak J, Attig J, Ule J, Luscombe NM (2021) Intergenic RNA mainly derives from nascent transcripts of known genes. Genome Biol 22:136

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ahmad K, Henikoff S (2002) The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 9:1191–1200

    CAS  PubMed  Google Scholar 

  • Ahmad W, Shabbiri K, Nazar N, Nazar S, Qaiser S, Shabbir Mughal MA (2011) Human linker histones: interplay between phosphorylation and O-β-GlcNAc to mediate chromatin structural modifications. Cell Div 6:15

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ahuja N, Sharma AR, Baylin SB (2016) Epigenetic therapeutics: a new weapon in the war against cancer. Annu Rev Med 67:73–89

    CAS  PubMed  PubMed Central  Google Scholar 

  • Al Shaer D, Al Musaimi O, Albericio F, de la Torre BG (2022) 2021 FDA TIDES (peptides and oligonucleotides) harvest. Pharmaceuticals (Basel) 15:222

    PubMed  Google Scholar 

  • Alam H, Gu B, Lee MG (2015) Histone methylation modifiers in cellular signaling pathways. Cell Mol Life Sci 72:4577–4592

    CAS  PubMed  PubMed Central  Google Scholar 

  • Alberts BJA, Lewis J et al (2002) Molecular biology of the cell, 4th edn. Garland Science, New York. An Overview of Gene Control. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26885/

    Google Scholar 

  • Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci U S A 51:786–794

    CAS  PubMed  PubMed Central  Google Scholar 

  • Allis CD, Richman R, Gorovsky MA, Ziegler YS, Touchstone B, Bradley WA, Cook RG (1986) hv1 is an evolutionarily conserved H2A variant that is preferentially associated with active genes. J Biol Chem 261:1941–1948

    CAS  PubMed  Google Scholar 

  • Anderson C, Stern CD (2016) Organizers in Development. Curr Top Dev Biol 117:435–454

    PubMed  Google Scholar 

  • Angeloni A, Bogdanovic O (2021) Sequence determinants, function, and evolution of CpG islands. Biochem Soc Trans 49:1109–1119

    CAS  PubMed  PubMed Central  Google Scholar 

  • Anghel SA, Ioniță-Mîndrican CB, Luca I, Pop AL (2021) Promising epigenetic biomarkers for the early detection of colorectal cancer: a systematic review. Cancers (Basel) 13:4965

    CAS  PubMed  Google Scholar 

  • Aran D, Toperoff G, Rosenberg M, Hellman A (2011) Replication timing-related and gene body-specific methylation of active human genes. Hum Mol Genet 20:670–680

    CAS  PubMed  Google Scholar 

  • Ardekani AM, Naeini MM (2010) The role of MicroRNAs in human diseases. Avicenna J Med Biotechnol 2:161–179

    CAS  PubMed  PubMed Central  Google Scholar 

  • Asangani IA, Wilder-Romans K, Dommeti VL, Krishnamurthy PM, Apel IJ, Escara-Wilke J, Plymate SR, Navone NM, Wang S, Feng FY, Chinnaiyan AM (2016) BET Bromodomain inhibitors enhance efficacy and disrupt resistance to AR antagonists in the treatment of prostate cancer. Mol Cancer Res 14:324–331

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bagherani N, Smoller BR (2016) An overview of cutaneous T cell lymphomas. F1000Res 5. https://doi.org/10.12688/f1000research.8829.1

  • Bai Y, Zhou BR (2021) Structures of native-like nucleosomes: one step closer toward understanding the structure and function of chromatin. J Mol Biol 433:166648

    CAS  PubMed  Google Scholar 

  • Baldan F, Mio C, Allegri L, Conzatti K, Toffoletto B, Puppin C, Radovic S, Vascotto C, Russo D, Di Loreto C, Damante G (2016) Identification of tumorigenesis-related mRNAs associated with RNA-binding protein HuR in thyroid cancer cells. Oncotarget 7:63388–63407

    PubMed  PubMed Central  Google Scholar 

  • Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27:361–368

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ballman KV (2015) Biomarker: predictive or prognostic? J Clin Oncol 33:3968–3971

    CAS  PubMed  Google Scholar 

  • Balzeau J, Menezes MR, Cao S, Hagan JP (2017) The LIN28/let-7 pathway in cancer. Front Genet 8:31

    PubMed  PubMed Central  Google Scholar 

  • Banach M, Kaźmierczak J, Mitkowski P, Wita K, Broncel M, Gąsior M, Gierlotka M, Gil R, Jankowski P, Niewada M, Witkowski A (2022) Which patients at risk of cardiovascular disease might benefit the most from inclisiran? Polish experts’ opinion. The compromise between EBM and possibilities in healthcare. Arch Med Sci 18:569–576

    CAS  PubMed  PubMed Central  Google Scholar 

  • Banaszynski LA, Wen D, Dewell S, Whitcomb SJ, Lin M, Diaz N, Elsässer SJ, Chapgier A, Goldberg AD, Canaani E, Rafii S, Zheng D, Allis CD (2013) Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 155:107–120

    CAS  PubMed  Google Scholar 

  • Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bao Y, Konesky K, Park YJ, Rosu S, Dyer PN, Rangasamy D, Tremethick DJ, Laybourn PJ, Luger K (2004) Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. EMBO J 23:3314–3324

    CAS  PubMed  PubMed Central  Google Scholar 

  • Barbarotta L, Hurley K (2015) Romidepsin for the treatment of peripheral T-cell lymphoma. J Adv Pract Oncol 6:22–36

    PubMed  PubMed Central  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    CAS  PubMed  Google Scholar 

  • Baud’huin M, Lamoureux F, Jacques C, Rodriguez Calleja L, Quillard T, Charrier C, Amiaud J, Berreur M, Brounais-LeRoyer B, Owen R, Reilly GC, Bradner JE, Heymann D, Ory B (2017) Inhibition of BET proteins and epigenetic signaling as a potential treatment for osteoporosis. Bone 94:10–21

    PubMed  Google Scholar 

  • Baylin SB, Jones PA (2011) A decade of exploring the cancer epigenome – biological and translational implications. Nat Rev Cancer 11:726–734

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bellazzo A, Di Minin G, Collavin L (2017) Block one, unleash a hundred. Mechanisms of DAB2IP inactivation in cancer. Cell Death Differ 24:15–25

    CAS  PubMed  Google Scholar 

  • Beltrán-García J, Osca-Verdegal R, Mena-Mollá S, García-Giménez JL (2019) Epigenetic IVD tests for personalized precision medicine in cancer. Front Genet 10:621

    PubMed  PubMed Central  Google Scholar 

  • Berdeja JG, Laubach JP, Richter J, Stricker S, Spencer A, Richardson PG, Chari A (2021) Panobinostat from bench to bedside: rethinking the treatment paradigm for multiple myeloma. Clin Lymphoma Myeloma Leuk 21:752–765

    CAS  PubMed  Google Scholar 

  • Berger NA (2018a) Young adult cancer: influence of the obesity pandemic. Obesity (Silver Spring) 26:641–650

    PubMed  Google Scholar 

  • Berger NA (2018b) Young adult cancer: influence of the obesity pandemic. Obesity 26:641–650

    PubMed  Google Scholar 

  • Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A (2009) An operational definition of epigenetics. Genes Dev 23:781–783

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bian C, Yu X (2014) PGC7 suppresses TET3 for protecting DNA methylation. Nucleic Acids Res 42:2893–2905

    CAS  PubMed  Google Scholar 

  • Blum R (2015) Stepping inside the realm of epigenetic modifiers. Biomol Concepts 6:119–136

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bondarev AD, Attwood MM, Jonsson J, Chubarev VN, Tarasov VV, Schiöth HB (2021) Recent developments of HDAC inhibitors: emerging indications and novel molecules. Br J Clin Pharmacol 87:4577–4597

    PubMed  Google Scholar 

  • Bönisch C, Hake SB (2012) Histone H2A variants in nucleosomes and chromatin: more or less stable? Nucleic Acids Res 40:10719–10741

    PubMed  PubMed Central  Google Scholar 

  • Bonner WM, Redon CE, Dickey JS, Nakamura AJ, Sedelnikova OA, Solier S, Pommier Y (2008) GammaH2AX and cancer. Nat Rev Cancer 8:957–967

    CAS  PubMed  PubMed Central  Google Scholar 

  • Borchiellini M, Ummarino S, Di Ruscio A (2019) The bright and dark side of DNA methylation: a matter of balance. Cell 8:1243

    CAS  Google Scholar 

  • Branco MR, Ficz G, Reik W (2011) Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet 13:7–13

    PubMed  Google Scholar 

  • Browne TR (1980) Valproic Acid. N Engl J Med 302:661–666

    CAS  PubMed  Google Scholar 

  • Brownell JE, Allis CD (1995) An activity gel assay detects a single, catalytically active histone acetyltransferase subunit in Tetrahymena macronuclei. Proc Natl Acad Sci U S A 92:6364–6368

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brunner PM, Jonak C, Knobler R (2020) Recent advances in understanding and managing cutaneous T-cell lymphomas. F1000Res 9:F1000

    PubMed  PubMed Central  Google Scholar 

  • Bubna AK (2015) Vorinostat-An Overview. Indian J Dermatol 60:419

    PubMed  PubMed Central  Google Scholar 

  • Bukowski K, Kciuk M, Kontek R (2020) Mechanisms of multidrug resistance in cancer chemotherapy. Int J Mol Sci 21:3233

    CAS  PubMed  PubMed Central  Google Scholar 

  • Burge C, Campbell AM, Karlin S (1992) Over- and under-representation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci U S A 89:1358–1362

    CAS  PubMed  PubMed Central  Google Scholar 

  • Butler LM, Agus DB, Scher HI, Higgins B, Rose A, Cordon-Cardo C, Thaler HT, Rifkind RA, Marks PA, Richon VM (2000) Suberoylanilide hydroxamic acid, an inhibitor of histone deacetylase, suppresses the growth of prostate cancer cells in vitro and in vivo. Cancer Res 60:5165–5170

    CAS  PubMed  Google Scholar 

  • Califf RM (2018) Biomarker definitions and their applications. Exp Biol Med (Maywood) 243:213–221

    CAS  PubMed  Google Scholar 

  • Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM (2002) Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 99:15524–15529

    CAS  PubMed  PubMed Central  Google Scholar 

  • Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M, Croce CM (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A 101:2999–3004

    CAS  PubMed  PubMed Central  Google Scholar 

  • Calle EE, Rodriguez C, Walker-Thurmond K, Thun MJ (2003) Overweight, obesity, and mortality from cancer in a prospectively studied cohort of U.S. adults. N Engl J Med 348:1625–1638

    PubMed  Google Scholar 

  • Campos EI, Reinberg D (2009) Histones: annotating chromatin. Annu Rev Genet 43:559–599

    CAS  PubMed  Google Scholar 

  • Capp JP (2021) Interplay between genetic, epigenetic, and gene expression variability: considering complexity in evolvability. Evol Appl 14:893–901

    PubMed  PubMed Central  Google Scholar 

  • Carlomagno N, Incollingo P, Tammaro V, Peluso G, Rupealta N, Chiacchio G, Sandoval Sotelo ML, Minieri G, Pisani A, Riccio E, Sabbatini M, Bracale UM, Calogero A, Dodaro CA, Santangelo M (2017) Diagnostic, predictive, prognostic, and therapeutic molecular biomarkers in third millennium: a breakthrough in gastric cancer. Biomed Res Int 2017:7869802

    PubMed  PubMed Central  Google Scholar 

  • Catalanotto C, Cogoni C, Zardo G (2016) MicroRNA in control of gene expression: An overview of nuclear functions. Int J Mol Sci 17:1712

    PubMed  PubMed Central  Google Scholar 

  • Celeste A, Petersen S, Romanienko PJ, Fernandez-Capetillo O, Chen HT, Sedelnikova OA, Reina-San-Martin B, Coppola V, Meffre E, Difilippantonio MJ, Redon C, Pilch DR, Olaru A, Eckhaus M, Camerini-Otero RD, Tessarollo L, Livak F, Manova K, Bonner WM, Nussenzweig MC, Nussenzweig A (2002) Genomic instability in mice lacking histone H2AX. Science 296:922–927

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cervoni N, Szyf M (2001) Demethylase activity is directed by histone acetylation. J Biol Chem 276:40778–40787

    CAS  PubMed  Google Scholar 

  • Chadwick BP, Willard HF (2001) A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive X chromosome. J Cell Biol 152:375–384

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chadwick BP, Valley CM, Willard HF (2001) Histone variant macroH2A contains two distinct macrochromatin domains capable of directing macroH2A to the inactive X chromosome. Nucleic Acids Res 29:2699–2705

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chakravarthy S, Bao Y, Roberts VA, Tremethick D, Luger K (2004) Structural characterization of histone H2A variants. Cold Spring Harb Symp Quant Biol 69:227–234

    CAS  PubMed  Google Scholar 

  • Chan TS, Tse E, Kwong YL (2017) Chidamide in the treatment of peripheral T-cell lymphoma. Onco Targets Ther 10:347–352

    CAS  PubMed  PubMed Central  Google Scholar 

  • Changolkar LN, Singh G, Pehrson JR (2008) macroH2A1-dependent silencing of endogenous murine leukemia viruses. Mol Cell Biol 28:2059–2065

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chateauvieux S, Morceau F, Dicato M, Diederich M (2010) Molecular and therapeutic potential and toxicity of valproic acid. J Biomed Biotechnol 2010:479364

    PubMed  PubMed Central  Google Scholar 

  • Chédin F (2011) The DNMT3 family of mammalian de novo DNA methyltransferases. Prog Mol Biol Transl Sci 101:255–285

    PubMed  Google Scholar 

  • Chen H, Toyooka S, Gazdar AF, Hsieh JT (2003) Epigenetic regulation of a novel tumor suppressor gene (hDAB2IP) in prostate cancer cell lines. J Biol Chem 278:3121–3130

    CAS  PubMed  Google Scholar 

  • Chen H, Tu SW, Hsieh JT (2005) Down-regulation of human DAB2IP gene expression mediated by polycomb Ezh2 complex and histone deacetylase in prostate cancer. J Biol Chem 280:22437–22444

    CAS  PubMed  Google Scholar 

  • Chen Y, Sprung R, Tang Y, Ball H, Sangras B, Kim SC, Falck JR, Peng J, Gu W, Zhao Y (2007) Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics 6:812–819

    CAS  PubMed  Google Scholar 

  • Chen P, Zhao J, Wang Y, Wang M, Long H, Liang D, Huang L, Wen Z, Li W, Li X, Feng H, Zhao H, Zhu P, Li M, Wang QF, Li G (2013) H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin. Genes Dev 27:2109–2124

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chen K, Zhang J, Guo Z, Ma Q, Xu Z, Zhou Y, Xu Z, Li Z, Liu Y, Ye X, Li X, Yuan B, Ke Y, He C, Zhou L, Liu J, Ci W (2016) Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer. Cell Res 26:103–118

    CAS  PubMed  Google Scholar 

  • Chen R, Zhang Q, Duan X, York P, Chen GD, Yin P, Zhu H, Xu M, Chen P, Wu Q, Li D, Samarut J, Xu G, Zhang P, Cao X, Li J, Wong J (2017) The 5-Hydroxymethylcytosine (5hmC) reader UHRF2 is required for Normal levels of 5hmC in mouse adult brain and spatial learning and memory. J Biol Chem 292:4533–4543

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng Y, Li Z, Manupipatpong S, Lin L, Li X, Xu T, Jiang YH, Shu Q, Wu H, Jin P (2018) 5-Hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder. Hum Mol Genet 27:2955–2964

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chern YJ, Tai IT (2020) Adaptive response of resistant cancer cells to chemotherapy. Cancer Biol Med 17:842–863

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chew YC, Camporeale G, Kothapalli N, Sarath G, Zempleni J (2006) Lysine residues in N-terminal and C-terminal regions of human histone H2A are targets for biotinylation by biotinidase. J Nutr Biochem 17:225–233

    CAS  PubMed  Google Scholar 

  • Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A, Sarthy J (2021) Short H2A histone variants are expressed in cancer. Nat Commun 12:490

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chi P, Allis CD, Wang GG (2010) Covalent histone modifications–miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 10:457–469

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chinaranagari S, Sharma P, Bowen NJ, Chaudhary J (2015) Prostate cancer epigenome. Methods Mol Biol 1238:125–140

    PubMed  PubMed Central  Google Scholar 

  • Chirshev E, Oberg KC, Ioffe YJ, Unternaehrer JJ (2019) Let-7 as biomarker, prognostic indicator, and therapy for precision medicine in cancer. Clin Transl Med 8:24

    PubMed  PubMed Central  Google Scholar 

  • Choghaei E, Khamisipour G, Falahati M, Naeimi B, Mossahebi-Mohammadi M, Tahmasebi R, Hasanpour M, Shamsian S, Hashemi ZS (2016) Knockdown of microRNA-29a changes the expression of heat shock proteins in breast carcinoma MCF-7 cells. Oncol Res 23:69–78

    PubMed  PubMed Central  Google Scholar 

  • Choi JD, Lee JS (2013) Interplay between epigenetics and genetics in cancer. Genomics Inform 11:164–173

    PubMed  PubMed Central  Google Scholar 

  • Choi HS, Choi BY, Cho YY, Mizuno H, Kang BS, Bode AM, Dong Z (2005) Phosphorylation of histone H3 at serine 10 is indispensable for neoplastic cell transformation. Cancer Res 65:5818–5827

    CAS  PubMed  PubMed Central  Google Scholar 

  • Choi C, Lee GH, Son A, Yoo GS, Yu JI, Park HC (2021) Downregulation of Mcl-1 by Panobinostat potentiates proton beam therapy in hepatocellular carcinoma cells. Cell 10:554

    CAS  Google Scholar 

  • Chokkalla AK, Mehta SL, Vemuganti R (2022) Epitranscriptomic modifications modulate Normal and pathological functions in CNS. Transl Stroke Res 13:1–11

    PubMed  Google Scholar 

  • Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325:834–840

    CAS  PubMed  Google Scholar 

  • Ciechomska M, O’Reilly S (2016) Epigenetic modulation as a therapeutic Prospect for treatment of autoimmune rheumatic diseases. Mediat Inflamm 2016:9607946

    Google Scholar 

  • Cimmino A, Calin GA, Fabbri M, Iorio MV, Ferracin M, Shimizu M, Wojcik SE, Aqeilan RI, Zupo S, Dono M, Rassenti L, Alder H, Volinia S, Liu CG, Kipps TJ, Negrini M, Croce CM (2005) miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci U S A 102:13944–13949

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cloonan N (2015) Re-thinking miRNA-mRNA interactions: intertwining issues confound target discovery. BioEssays 37:379–388

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cobos SN, Bennett SA, Torrente MP (2019) The impact of histone post-translational modifications in neurodegenerative diseases. Biochim Biophys Acta Mol basis Dis 1865:1982–1991

    CAS  PubMed  Google Scholar 

  • Cohen LA, Amin S, Marks PA, Rifkind RA, Desai D, Richon VM (1999) Chemoprevention of carcinogen-induced mammary tumorigenesis by the hybrid polar cytodifferentiation agent, suberanilohydroxamic acid (SAHA). Anticancer Res 19:4999–5005

    CAS  PubMed  Google Scholar 

  • Cohen I, Poręba E, Kamieniarz K, Schneider R (2011) Histone modifiers in cancer: friends or foes? Genes Cancer 2:631–647

    CAS  PubMed  PubMed Central  Google Scholar 

  • Colino-Sanguino Y, Clark SJ, Valdes-Mora F (2016) H2A.Z acetylation and transcription: ready, steady, go! Epigenomics 8:583–586

    CAS  PubMed  Google Scholar 

  • Connolly DR, Zhou Z (2019) Genomic insights into MeCP2 function: a role for the maintenance of chromatin architecture. Curr Opin Neurobiol 59:174–179

    CAS  PubMed  PubMed Central  Google Scholar 

  • Coomer MA, Ham L, Stumpf MPH (2022) Noise distorts the epigenetic landscape and shapes cell-fate decisions. Cell Syst 13:83–102.e106

    CAS  PubMed  Google Scholar 

  • Cooper DN, Mort M, Stenson PD, Ball EV, Chuzhanova NA (2010) Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides. Hum Genomics 4:406–410

    CAS  PubMed  PubMed Central  Google Scholar 

  • Corujo D, Buschbeck M (2018) Post-translational modifications of H2A histone variants and their role in cancer. Cancers (Basel) 10:59

    PubMed  Google Scholar 

  • Costanzi C, Pehrson JR (1998) Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals. Nature 393:599–601

    CAS  PubMed  Google Scholar 

  • Costa-Pinheiro P, Montezuma D, Henrique R, Jerónimo C (2015) Diagnostic and prognostic epigenetic biomarkers in cancer. Epigenomics 7:1003–1015

    CAS  PubMed  Google Scholar 

  • Coussens LM, Werb Z (2002) Inflammation and cancer. Nature 420:860–867

    CAS  PubMed  PubMed Central  Google Scholar 

  • Daher-Reyes GS, Merchan BM, Yee KWL (2019) Guadecitabine (SGI-110): an investigational drug for the treatment of myelodysplastic syndrome and acute myeloid leukemia. Expert Opin Investig Drugs 28:835–849

    CAS  PubMed  Google Scholar 

  • Dai L, Xie X, Zhou Z (2018) Crystal structure of the histone heterodimer containing histone variant H2A.Bbd. Biochem Biophys Res Commun 503:1786–1791

    CAS  PubMed  Google Scholar 

  • Dalvai M, Bellucci L, Fleury L, Lavigne AC, Moutahir F, Bystricky K (2013) H2A.Z-dependent crosstalk between enhancer and promoter regulates cyclin D1 expression. Oncogene 32:4243–4251

    CAS  PubMed  Google Scholar 

  • Dantas Machado AC, Zhou T, Rao S, Goel P, Rastogi C, Lazarovici A, Bussemaker HJ, Rohs R (2015) Evolving insights on how cytosine methylation affects protein-DNA binding. Brief Funct Genomics 14:61–73

    CAS  PubMed  Google Scholar 

  • Das PM, Singal R (2004) DNA methylation and cancer. J Clin Oncol 22:4632–4642

    CAS  PubMed  Google Scholar 

  • Davis-Dusenbery BN, Hata A (2010) MicroRNA in cancer: the involvement of aberrant MicroRNA biogenesis regulatory pathways. Genes Cancer 1:1100–1114

    CAS  PubMed  PubMed Central  Google Scholar 

  • de Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustienes E, Gómez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O, Lister R (2021) The emergence of the brain non-CpG methylation system in vertebrates. Nat Ecol Evol 5:369–378

    PubMed  PubMed Central  Google Scholar 

  • De Pergola G, Silvestris F (2013) Obesity as a major risk factor for cancer. J Obes 2013:291546

    PubMed  PubMed Central  Google Scholar 

  • de Vos D, van Overveld W (2005) Decitabine: a historical review of the development of an epigenetic drug. Ann Hematol 84:3

    PubMed  PubMed Central  Google Scholar 

  • Deng T, Lyon CJ, Bergin S, Caligiuri MA, Hsueh WA (2016) Obesity, inflammation, and cancer. Annu Rev Pathol 11:421–449

    CAS  PubMed  Google Scholar 

  • Denissenko MF, Chen JX, Tang MS, Pfeifer GP (1997) Cytosine methylation determines hot spots of DNA damage in the human P53 gene. Proc Natl Acad Sci U S A 94:3893–3898

    CAS  PubMed  PubMed Central  Google Scholar 

  • Desrosiers R, Friderici K, Rottman F (1974) Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. Proc Natl Acad Sci U S A 71:3971–3975

    CAS  PubMed  PubMed Central  Google Scholar 

  • Diamantopoulos MA, Tsiakanikas P, Scorilas A (2018) Non-coding RNAs: the riddle of the transcriptome and their perspectives in cancer. Ann Transl Med 6:241

    PubMed  PubMed Central  Google Scholar 

  • Dickey JS, Redon CE, Nakamura AJ, Baird BJ, Sedelnikova OA, Bonner WM (2009) H2AX: functional roles and potential applications. Chromosoma 118:683–692

    CAS  PubMed  PubMed Central  Google Scholar 

  • Diesch J, Zwick A, Garz A-K, Palau A, Buschbeck M, Götze KS (2016) A clinical-molecular update on azanucleoside-based therapy for the treatment of hematologic cancers. Clin Epigenetics 8:71

    PubMed  PubMed Central  Google Scholar 

  • do Canto LM, Barros-Filho MC, Rainho CA, Marinho D, BEC K, Begnami M, Scapulatempo-Neto C, Havelund BM, Lindebjerg J, Marchi FA, Baumbach J, Aguiar S Jr, Rogatto SR (2020) Comprehensive analysis of DNA methylation and prediction of response to NeoadjuvantTherapy in locally advanced rectal cancer. Cancers (Basel) 12:3079

    CAS  PubMed  Google Scholar 

  • Dong E, Chen Y, Gavin DP, Grayson DR, Guidotti A (2010) Valproate induces DNA demethylation in nuclear extracts from adult mouse brain. Epigenetics 5:730–735

    CAS  PubMed  Google Scholar 

  • Dryhurst D, Ishibashi T, Rose KL, Eirín-López JM, McDonald D, Silva-Moreno B, Veldhoen N, Helbing CC, Hendzel MJ, Shabanowitz J, Hunt DF, Ausió J (2009) Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates. BMC Biol 7:86

    PubMed  PubMed Central  Google Scholar 

  • Duan Q, Chen H, Costa M, Dai W (2008) Phosphorylation of H3S10 blocks the access of H3K9 by specific antibodies and histone methyltransferase. Implication in regulating chromatin dynamics and epigenetic inheritance during mitosis. J Biol Chem 283:33585–33590

    CAS  PubMed  PubMed Central  Google Scholar 

  • Duarte LF, Young AR, Wang Z, Wu HA, Panda T, Kou Y, Kapoor A, Hasson D, Mills NR, Ma’ayan A, Narita M, Bernstein E (2014) Histone H3.3 and its proteolytically processed form drive a cellular senescence programme. Nat Commun 5:5210

    CAS  PubMed  Google Scholar 

  • Duncan BK, Miller JH (1980) Mutagenic deamination of cytosine residues in DNA. Nature 287:560–561

    CAS  PubMed  Google Scholar 

  • Duncan EM, Muratore-Schroeder TL, Cook RG, Garcia BA, Shabanowitz J, Hunt DF, Allis CD (2008) Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell 135:284–294

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dürig J, Bug S, Klein-Hitpass L, Boes T, Jöns T, Martin-Subero JI, Harder L, Baudis M, Dührsen U, Siebert R (2007) Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32). Leukemia 21:2153–2163

    PubMed  Google Scholar 

  • Duvic M, Talpur R, Ni X, Zhang C, Hazarika P, Kelly C, Chiao JH, Reilly JF, Ricker JL, Richon VM, Frankel SR (2007) Phase 2 trial of oral vorinostat (suberoylanilide hydroxamic acid, SAHA) for refractory cutaneous T-cell lymphoma (CTCL). Blood 109:31–39

    CAS  PubMed  PubMed Central  Google Scholar 

  • Eleutherakis-Papaiakovou E, Kanellias N, Kastritis E, Gavriatopoulou M, Terpos E, Dimopoulos MA (2020) Efficacy of Panobinostat for the treatment of multiple myeloma. J Oncol 2020:7131802

    PubMed  PubMed Central  Google Scholar 

  • Elsheikh SE, Green AR, Rakha EA, Powe DG, Ahmed RA, Collins HM, Soria D, Garibaldi JM, Paish CE, Ammar AA, Grainge MJ, Ball GR, Abdelghany MK, Martinez-Pomares L, Heery DM, Ellis IO (2009) Global histone modifications in breast cancer correlate with tumor phenotypes, prognostic factors, and patient outcome. Cancer Res 69:3802–3809

    CAS  PubMed  Google Scholar 

  • Esquela-Kerscher A, Slack FJ (2006) Oncomirs — microRNAs with a role in cancer. Nat Rev Cancer 6:259–269

    CAS  PubMed  Google Scholar 

  • Esteller M, Toyota M, Sanchez-Cespedes M, Capella G, Peinado MA, Watkins DN, Issa JP, Sidransky D, Baylin SB, Herman JG (2000) Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is associated with G to A mutations in K-ras in colorectal tumorigenesis. Cancer Res 60:2368–2371

    CAS  PubMed  Google Scholar 

  • Faast R, Thonglairoam V, Schulz TC, Beall J, Wells JR, Taylor H, Matthaei K, Rathjen PD, Tremethick DJ, Lyons I (2001) Histone variant H2A.Z is required for early mammalian development. Curr Biol 11:1183–1187

    CAS  PubMed  Google Scholar 

  • Feinberg AP (2014) Epigenetic stochasticity, nuclear structure and cancer: the implications for medicine. J Intern Med 276:5–11

    CAS  PubMed  PubMed Central  Google Scholar 

  • Feinberg AP, Vogelstein B (1983a) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89–92

    CAS  PubMed  Google Scholar 

  • Feinberg AP, Vogelstein B (1983b) Hypomethylation of ras oncogenes in primary human cancers. Biochem Biophys Res Commun 111:47–54

    CAS  PubMed  Google Scholar 

  • Feng Y, Fan Y, Huiqing C, Zicai L, Quan D (2014) The emerging landscape of long non-coding RNAs. Yi Chuan 36:456–468

    PubMed  Google Scholar 

  • Ferrand J, Rondinelli B, Polo SE (2020) Histone variants: guardians of genome integrity. Cell 9:2424

    CAS  Google Scholar 

  • Festuccia C, Gravina GL, D’Alessandro AM, Muzi P, Millimaggi D, Dolo V, Ricevuto E, Vicentini C, Bologna M (2009) Azacitidine improves antitumor effects of docetaxel and cisplatin in aggressive prostate cancer models. Endocr Relat Cancer 16:401–413

    CAS  PubMed  Google Scholar 

  • Ficz G, Gribben JG (2014) Loss of 5-hydroxymethylcytosine in cancer: cause or consequence? Genomics 104:352–357

    CAS  PubMed  Google Scholar 

  • Fischle W, Tseng BS, Dormann HL, Ueberheide BM, Garcia BA, Shabanowitz J, Hunt DF, Funabiki H, Allis CD (2005) Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438:1116–1122

    CAS  PubMed  Google Scholar 

  • Flatmark K, Nome RV, Folkvord S, Bratland A, Rasmussen H, Ellefsen MS, Fodstad Ø, Ree AH (2006) Radiosensitization of colorectal carcinoma cell lines by histone deacetylase inhibition. Radiat Oncol 1:25

    PubMed  PubMed Central  Google Scholar 

  • Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, Bonaldi T, Haydon C, Ropero S, Petrie K, Iyer NG, Pérez-Rosado A, Calvo E, Lopez JA, Cano A, Calasanz MJ, Colomer D, Piris MA, Ahn N, Imhof A, Caldas C, Jenuwein T, Esteller M (2005) Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat Genet 37:391–400

    CAS  PubMed  Google Scholar 

  • Francescone R, Hou V, Grivennikov SI (2014) Microbiome, inflammation, and cancer. Cancer J 20:181–189

    CAS  PubMed  PubMed Central  Google Scholar 

  • Frey A, Listovsky T, Guilbaud G, Sarkies P, Sale JE (2014) Histone H3.3 is required to maintain replication fork progression after UV damage. Curr Biol 24:2195–2201

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fryxell KJ, Moon W-J (2004) CpG mutation rates in the human genome are highly dependent on local GC content. Mol Biol Evol 22:650–658

    PubMed  Google Scholar 

  • Fuks F, Hurd PJ, Wolf D, Nan X, Bird AP, Kouzarides T (2003) The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem 278:4035–4040

    CAS  PubMed  Google Scholar 

  • Furman D, Campisi J, Verdin E, Carrera-Bastos P, Targ S, Franceschi C, Ferrucci L, Gilroy DW, Fasano A, Miller GW, Miller AH, Mantovani A, Weyand CM, Barzilai N, Goronzy JJ, Rando TA, Effros RB, Lucia A, Kleinstreuer N, Slavich GM (2019) Chronic inflammation in the etiology of disease across the life span. Nat Med 25:1822–1832

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gama-Sosa MA, Slagel VA, Trewyn RW, Oxenhandler R, Kuo KC, Gehrke CW, Ehrlich M (1983) The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res 11:6883–6894

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gangopadhyay S, Gore KR (2022) Advances in siRNA therapeutics and synergistic effect on siRNA activity using emerging dual ribose modifications. RNA Biol 19:452–467

    CAS  PubMed  PubMed Central  Google Scholar 

  • Garcia JS, Jain N, Godley LA (2010) An update on the safety and efficacy of decitabine in the treatment of myelodysplastic syndromes. Onco Targets Ther 3:1–13

    CAS  PubMed  PubMed Central  Google Scholar 

  • García-Giménez JL, Seco-Cervera M, Tollefsbol TO, Romá-Mateo C, Peiró-Chova L, Lapunzina P, Pallardó FV (2017) Epigenetic biomarkers: current strategies and future challenges for their use in the clinical laboratory. Crit Rev Clin Lab Sci 54:529–550

    PubMed  PubMed Central  Google Scholar 

  • Garcia-Manero G, Roboz G, Walsh K, Kantarjian H, Ritchie E, Kropf P, O’Connell C, Tibes R, Lunin S, Rosenblat T, Yee K, Stock W, Griffiths E, Mace J, Podoltsev N, Berdeja J, Jabbour E, Issa JJ, Hao Y, Keer HN, Azab M, Savona MR (2019) Guadecitabine (SGI-110) in patients with intermediate or high-risk myelodysplastic syndromes: phase 2 results from a multicentre, open-label, randomised, phase 1/2 trial. Lancet Haematol 6:e317–e327

    PubMed  PubMed Central  Google Scholar 

  • Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196:261–282

    CAS  PubMed  Google Scholar 

  • Garnock-Jones KP (2015) Panobinostat: first global approval. Drugs 75:695–704

    CAS  PubMed  Google Scholar 

  • Gebeshuber CA, Zatloukal K, Martinez J (2009) miR-29a suppresses tristetraprolin, which is a regulator of epithelial polarity and metastasis. EMBO Rep 10:400–405

    CAS  PubMed  PubMed Central  Google Scholar 

  • Georgoulis A, Vorgias CE, Chrousos GP, Rogakou EP (2017) Genome instability and γH2AX. Int J Mol Sci 18:1979

    PubMed  PubMed Central  Google Scholar 

  • Gertz MA, Mauermann ML, Grogan M, Coelho T (2019) Advances in the treatment of hereditary transthyretin amyloidosis: a review. Brain Behav 9:e01371

    PubMed  PubMed Central  Google Scholar 

  • Gévry N, Hardy S, Jacques PE, Laflamme L, Svotelis A, Robert F, Gaudreau L (2009) Histone H2A.Z is essential for estrogen receptor signaling. Genes Dev 23:1522–1533

    PubMed  PubMed Central  Google Scholar 

  • Gielen GH, Gessi M, Hammes J, Kramm CM, Waha A, Pietsch T (2013) H3F3A K27M mutation in pediatric CNS tumors: a marker for diffuse high-grade astrocytomas. Am J Clin Pathol 139:345–349

    CAS  PubMed  Google Scholar 

  • Gilles ME, Slack FJ (2018) Let-7 microRNA as a potential therapeutic target with implications for immunotherapy. Expert Opin Ther Targets 22:929–939

    CAS  PubMed  PubMed Central  Google Scholar 

  • Globisch D, Münzel M, Müller M, Michalakis S, Wagner M, Koch S, Brückl T, Biel M, Carell T (2010) Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 5:e15367

    CAS  PubMed  PubMed Central  Google Scholar 

  • Goel S, Bhatia V, Biswas T, Ateeq B (2021) Epigenetic reprogramming during prostate cancer progression: a perspective from development. Semin Cancer Biol 83:136

    PubMed  PubMed Central  Google Scholar 

  • Goldberg AD, Allis CD, Bernstein E (2007) Epigenetics: a landscape takes shape. Cell 128:635–638

    CAS  PubMed  Google Scholar 

  • González-Romero R, Méndez J, Ausió J, Eirín-López JM (2008) Quickly evolving histones, nucleosome stability and chromatin folding: all about histone H2A.Bbd. Gene 413:1–7

    PubMed  Google Scholar 

  • Goossens N, Nakagawa S, Sun X, Hoshida Y (2015) Cancer biomarker discovery and validation. Transl Cancer Res 4:256–269

    CAS  PubMed  Google Scholar 

  • Gore SD, Jones C, Kirkpatrick P (2006) Decitabine. Nat Rev Drug Discov 5:891–892

    CAS  PubMed  Google Scholar 

  • Gorodilov Iu N (2001) Spemann’s organizer—it’s origin and derivatives (cellular-tissue and molecular-genetic aspects). Tsitologiia 43:182–203

    CAS  PubMed  Google Scholar 

  • Göttlicher M, Minucci S, Zhu P, Krämer OH, Schimpf A, Giavara S, Sleeman JP, Lo Coco F, Nervi C, Pelicci PG, Heinzel T (2001) Valproic acid defines a novel class of HDAC inhibitors inducing differentiation of transformed cells. EMBO J 20:6969–6978

    PubMed  PubMed Central  Google Scholar 

  • Gowher H, Jeltsch A (2018) Mammalian DNA methyltransferases: new discoveries and open questions. Biochem Soc Trans 46:1191–1202

    CAS  PubMed  PubMed Central  Google Scholar 

  • Grippo P, Iaccarino M, Parisi E, Scarano E (1968) Methylation of DNA in developing sea urchin embryos. J Mol Biol 36:195–208

    CAS  PubMed  Google Scholar 

  • Grivennikov SI, Greten FR, Karin M (2010) Immunity, inflammation, and cancer. Cell 140:883–899

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gromova M, Vaggelas A, Dallmann G, Seimetz D (2020) Biomarkers: opportunities and challenges for drug development in the current regulatory landscape. Biomark Insights 15:1177271920974652

    PubMed  PubMed Central  Google Scholar 

  • Group BDW (2001) Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin Pharmacol Ther 69:89–95

    Google Scholar 

  • Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming GL, Gao Y, Song H (2011) Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci 14:1345–1351

    CAS  PubMed  PubMed Central  Google Scholar 

  • Guo R, Zheng L, Park JW, Lv R, Chen H, Jiao F, Xu W, Mu S, Wen H, Qiu J, Wang Z, Yang P, Wu F, Hui J, Fu X, Shi X, Shi YG, Xing Y, Lan F, Shi Y (2014a) BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Mol Cell 56:298–310

    CAS  PubMed  PubMed Central  Google Scholar 

  • Guo W, Chung WY, Qian M, Pellegrini M, Zhang MQ (2014b) Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Res 42:3009–3016

    CAS  PubMed  Google Scholar 

  • Gurdon JB, Uehlinger V (1966) “Fertile” intestine nuclei. Nature 210:1240–1241

    CAS  PubMed  Google Scholar 

  • Hake SB, Garcia BA, Kauer M, Baker SP, Shabanowitz J, Hunt DF, Allis CD (2005) Serine 31 phosphorylation of histone variant H3.3 is specific to regions bordering centromeres in metaphase chromosomes. Proc Natl Acad Sci U S A 102:6344–6349

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hall BK (2015) Waddington’s legacy in development and Evolution1. Am Zool 32:113–122

    Google Scholar 

  • Hamamoto R, Furukawa Y, Morita M, Iimura Y, Silva FP, Li M, Yagyu R, Nakamura Y (2004) SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells. Nat Cell Biol 6:731–740

    CAS  PubMed  Google Scholar 

  • Hamm CA, Costa FF (2015) Epigenomes as therapeutic targets. Pharmacol Ther 151:72–86

    CAS  PubMed  Google Scholar 

  • Han L, Chen C, Lu X, Song Y, Zhang Z, Zeng C, Chiu R, Li L, Xu M, He C, Zhang W, Duan S (2021) Alterations of 5-hydroxymethylcytosines in circulating cell-free DNA reflect retinopathy in type 2 diabetes. Genomics 113:79–87

    CAS  PubMed  Google Scholar 

  • Hangauer MJ, Vaughn IW, McManus MT (2013) Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet 9:e1003569

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hatch CL, Bonner WM (1990) The human histone H2A.Z gene. Sequence and regulation. J Biol Chem 265:15211–15218

    CAS  PubMed  Google Scholar 

  • Hayashi-Takanaka Y, Yamagata K, Nozaki N, Kimura H (2009) Visualizing histone modifications in living cells: spatiotemporal dynamics of H3 phosphorylation during interphase. J Cell Biol 187:781–790

    CAS  PubMed  PubMed Central  Google Scholar 

  • He PC, He C (2021) M(6) a RNA methylation: from mechanisms to therapeutic potential. EMBO J 40:e105977

    CAS  PubMed  PubMed Central  Google Scholar 

  • He RZ, Jiang J, Luo DX (2020a) The functions of N6-methyladenosine modification in lncRNAs. Genes Dis 7:598–605

    CAS  PubMed  PubMed Central  Google Scholar 

  • He Y, Chen D, Yi Y, Zeng S, Liu S, Li P, Xie H, Yu P, Jiang G, Liu H (2020b) Histone deacetylase inhibitor sensitizes ERCC1-high non-small-cell lung cancer cells to cisplatin via regulating miR-149. Mol Ther Oncolytics 17:448–459

    CAS  PubMed  PubMed Central  Google Scholar 

  • Héberlé É, Bardet AF (2019) Sensitivity of transcription factors to DNA methylation. Essays Biochem 63:727–741

    PubMed  PubMed Central  Google Scholar 

  • Hermann A, Gowher H, Jeltsch A (2004) Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 61:2571–2587

    CAS  PubMed  Google Scholar 

  • Hirayama F, Takagi S, Yokoyama Y, Yamamoto K, Iwao E, Haga K (2002) Long-term effects of helicobacter pylori eradication in Mongolian gerbils. J Gastroenterol 37:779–784

    CAS  PubMed  Google Scholar 

  • Holliday R, Pugh JE (1975) DNA modification mechanisms and gene activity during development. Science 187:226–232

    CAS  PubMed  Google Scholar 

  • Hollstein M, Sidransky D, Vogelstein B, Harris CC (1991) p53 mutations in human cancers. Science 253:49–53

    CAS  PubMed  Google Scholar 

  • Hollstein M, Shomer B, Greenblatt M, Soussi T, Hovig E, Montesano R, Harris CC (1996) Somatic point mutations in the p53 gene of human tumors and cell lines: updated compilation. Nucleic Acids Res 24:141–146

    CAS  PubMed  PubMed Central  Google Scholar 

  • Holmila R, Sklias A, Muller DC, Degli Esposti D, Guilloreau P, McKay J, Sangrajrang S, Srivatanakul P, Hainaut P, Merle P, Herceg Z, Nogueira da Costa A (2017) Targeted deep sequencing of plasma circulating cell-free DNA reveals vimentin and Fibulin 1 as potential epigenetic biomarkers for hepatocellular carcinoma. PLoS One 12:e0174265

    PubMed  PubMed Central  Google Scholar 

  • Holoch D, Moazed D (2015) RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet 16:71–84

    CAS  PubMed  PubMed Central  Google Scholar 

  • Honda S, Fujioka T, Tokieda M, Satoh R, Nishizono A, Nasu M (1998) Development of helicobacter pylori-induced gastric carcinoma in Mongolian gerbils. Cancer Res 58:4255–4259

    CAS  PubMed  Google Scholar 

  • Hoque MO, Begum S, Topaloglu O, Jeronimo C, Mambo E, Westra WH, Califano JA, Sidransky D (2004) Quantitative detection of promoter hypermethylation of multiple genes in the tumor, urine, and serum DNA of patients with renal cancer. Cancer Res 64:5511–5517

    CAS  PubMed  Google Scholar 

  • Horwitz GA, Zhang K, McBrian MA, Grunstein M, Kurdistani SK, Berk AJ (2008) Adenovirus small e1a alters global patterns of histone modification. Science 321:1084–1085

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hosseinahli N, Aghapour M, Duijf PHG, Baradaran B (2018) Treating cancer with microRNA replacement therapy: a literature review. J Cell Physiol 233:5574–5588

    CAS  PubMed  Google Scholar 

  • Hotchkiss RD (1948) The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J Biol Chem 175:315–332

    CAS  PubMed  Google Scholar 

  • Hoy SM (2020) Tazemetostat: First Approval. Drugs 80:513–521

    PubMed  Google Scholar 

  • Hsu CC, Shi J, Yuan C, Zhao D, Jiang S, Lyu J, Wang X, Li H, Wen H, Li W, Shi X (2018) Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer. Genes Dev 32:58–69

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hsu CJ, Meers O, Buschbeck M, Heidel FH (2021) The role of MacroH2A histone variants in cancer. Cancers (Basel) 13:3003

    CAS  PubMed  Google Scholar 

  • Hu S, Wan J, Su Y, Song Q, Zeng Y, Nguyen HN, Shin J, Cox E, Rho HS, Woodard C, Xia S, Liu S, Lyu H, Ming GL, Wade H, Song H, Qian J, Zhu H (2013) DNA methylation presents distinct binding sites for human transcription factors. elife 2:e00726

    PubMed  PubMed Central  Google Scholar 

  • Hu C, Liu T, Xu Y, Han C, Yang S, Yang K (2022) METTL14 promotes the proliferation and migration of cervical cancer cells by up-regulating m(6)a Myc expression. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 38:131–137

    PubMed  Google Scholar 

  • Hua S, Kallen CB, Dhar R, Baquero MT, Mason CE, Russell BA, Shah PK, Liu J, Khramtsov A, Tretiakova MS, Krausz TN, Olopade OI, Rimm DL, White KP (2008) Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. Mol Syst Biol 4:188

    PubMed  PubMed Central  Google Scholar 

  • Hussain SP, Harris CC (2007) Inflammation and cancer: an ancient link with novel potentials. Int J Cancer 121:2373–2380

    CAS  PubMed  Google Scholar 

  • Hutt DM, Roth DM, Vignaud H, Cullin C, Bouchecareilh M (2014) The histone deacetylase inhibitor, Vorinostat, represses hypoxia inducible factor 1 alpha expression through translational inhibition. PLoS One 9:e106224

    PubMed  PubMed Central  Google Scholar 

  • Iliopoulos D, Hirsch HA, Struhl K (2009) An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell 139:693–706

    CAS  PubMed  PubMed Central  Google Scholar 

  • Iliopoulos D, Jaeger SA, Hirsch HA, Bulyk ML, Struhl K (2010) STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer. Mol Cell 39:493–506

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ilse P, Biesterfeld S, Pomjanski N, Wrobel C, Schramm M (2014) Analysis of SHOX2 methylation as an aid to cytology in lung cancer diagnosis. Cancer Genomics Proteomics 11:251–258

    PubMed  Google Scholar 

  • Inoue A, Fujimoto D (1969) Enzymatic deacetylation of histone. Biochem Biophys Res Commun 36:146–150

    CAS  PubMed  Google Scholar 

  • Irizarry RA, Wu H, Feinberg AP (2009) A species-generalized probabilistic model-based definition of CpG islands. Mamm Genome 20:674–680

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ishibashi T, Li A, Eirín-López JM, Zhao M, Missiaen K, Abbott DW, Meistrich M, Hendzel MJ, Ausió J (2009) H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis. Nucleic Acids Res 38:1780–1789

    PubMed  PubMed Central  Google Scholar 

  • Issa JP, Kantarjian H (2005) Azacitidine. Nat Rev Drug Discov 4(Suppl S6–7):275

    CAS  PubMed  Google Scholar 

  • Issa JJ, Roboz G, Rizzieri D, Jabbour E, Stock W, O’Connell C, Yee K, Tibes R, Griffiths EA, Walsh K, Daver N, Chung W, Naim S, Taverna P, Oganesian A, Hao Y, Lowder JN, Azab M, Kantarjian H (2015) Safety and tolerability of guadecitabine (SGI-110) in patients with myelodysplastic syndrome and acute myeloid leukaemia: a multicentre, randomised, dose-escalation phase 1 study. Lancet Oncol 16:1099–1110

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jabbour E, Issa JP, Garcia-Manero G, Kantarjian H (2008) Evolution of decitabine development: accomplishments, ongoing investigations, and future strategies. Cancer 112:2341–2351

    CAS  PubMed  Google Scholar 

  • Jain K, Fraser CS, Marunde MR, Parker MM, Sagum C, Burg JM, Hall N, Popova IK, Rodriguez KL, Vaidya A, Krajewski K, Keogh MC, Bedford MT, Strahl BD (2020) Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions. Epigenetics Chromatin 13:3

    CAS  PubMed  PubMed Central  Google Scholar 

  • James SJ, Shpyleva S, Melnyk S, Pavliv O, Pogribny IP (2014) Elevated 5-hydroxymethylcytosine in the Engrailed-2 (EN-2) promoter is associated with increased gene expression and decreased MeCP2 binding in autism cerebellum. Transl Psychiatry 4:e460

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jang CW, Shibata Y, Starmer J, Yee D, Magnuson T (2015) Histone H3.3 maintains genome integrity during mammalian development. Genes Dev 29:1377–1392

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jang HS, Shin WJ, Lee JE, Do JT (2017) CpG and non-CpG methylation in epigenetic gene regulation and brain function. Genes (Basel) 8:148

    PubMed  Google Scholar 

  • Jankowski J, Holst MI, Liebig C, Oberdick J, Baader SL (2004) Engrailed-2 negatively regulates the onset of perinatal Purkinje cell differentiation. J Comp Neurol 472:87–99

    CAS  PubMed  Google Scholar 

  • Jeffery NN, Davidson C, Peslak SA, Kingsley PD, Nakamura Y, Palis J, Bulger M (2021) Histone H2A.X phosphorylation and caspase-initiated chromatin condensation in late-stage erythropoiesis. Epigenetics Chromatin 14:37

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang X, Wen J, Paver E, Wu Y-H, Sun G, Bullman A, Dahlstrom Jane E, Tremethick DJ, Soboleva TA (2021) H2A.B is a cancer/testis factor involved in the activation of ribosome biogenesis in Hodgkin lymphoma. EMBO Rep 22:e52462

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jin Z, Liu Y (2018) DNA methylation in human diseases. Genes Dis 5:1–8

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jin B, Li Y, Robertson KD (2011a) DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer 2:607–617

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jin S-G, Jiang Y, Qiu R, Rauch TA, Wang Y, Schackert G, Krex D, Lu Q, Pfeifer GP (2011b) 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels Do not correlate with IDH1 mutations. Cancer Res 71:7360–7365

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jirtle RL (2009) Epigenome: the program for human health and disease. Epigenomics 1:13–16

    CAS  PubMed  Google Scholar 

  • Johansen KM, Johansen J (2006) Regulation of chromatin structure by histone H3S10 phosphorylation. Chromosom Res 14:393–404

    CAS  Google Scholar 

  • Johnson TB, Coghill RD (1925) Researches on pyrimidines. C111. The discovery of 5-methyl-cytosine in Tuberculinic acid, the nucleic acid of the tubercle Bacillus1. J Am Chem Soc 47:2838–2844

    CAS  Google Scholar 

  • Jones PA, Taylor SM (1980) Cellular differentiation, cytidine analogs and DNA methylation. Cell 20:85–93

    CAS  PubMed  Google Scholar 

  • Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP (1998) Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 19:187–191

    CAS  PubMed  Google Scholar 

  • Jueliger S, Lyons J, Cannito S, Pata I, Pata P, Shkolnaya M, Lo Re O, Peyrou M, Villarroya F, Pazienza V, Rappa F, Cappello F, Azab M, Taverna P, Vinciguerra M (2016) Efficacy and epigenetic interactions of novel DNA hypomethylating agent guadecitabine (SGI-110) in preclinical models of hepatocellular carcinoma. Epigenetics 11:709–720

    PubMed  PubMed Central  Google Scholar 

  • Julia E, Salles G (2021) EZH2 inhibition by tazemetostat: mechanisms of action, safety and efficacy in relapsed/refractory follicular lymphoma. Future Oncol 17:2127–2140

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jung S, Yi L, Kim J, Jeong D, Oh T, Kim CH, Kim CJ, Shin J, An S, Lee MS (2011) The role of vimentin as a methylation biomarker for early diagnosis of cervical cancer. Mol Cells 31:405–411

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jurkowska RZ, Jurkowski TP, Jeltsch A (2011) Structure and function of mammalian DNA methyltransferases. Chembiochem 12:206–222

    CAS  PubMed  Google Scholar 

  • Jutras S, Bachvarova M, Keita M, Bascands J-L, Mes-Masson A-M, Stewart JM, Bachvarov D (2010) Strong cytotoxic effect of the bradykinin antagonist BKM-570 in ovarian cancer cells – analysis of the molecular mechanisms of its antiproliferative action. FEBS J 277:5146–5160

    CAS  PubMed  Google Scholar 

  • Kaczmarek JV, Bogan CM, Pierce JM, Tao YK, Chen SC, Liu Q, Liu X, Boyd KL, Calcutt MW, Bridges TM, Lindsley CW, Friedman DL, Richmond A, Daniels AB (2021) Intravitreal HDAC inhibitor Belinostat effectively eradicates vitreous seeds without retinal toxicity in vivo in a rabbit retinoblastoma model. Invest Ophthalmol Vis Sci 62:8

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kalari S, Pfeifer GP (2010a) Chapter 10: identification of driver and passenger DNA methylation in cancer by Epigenomic analysis. In: Herceg Z, Ushijima T (eds) Advances in genetics, vol 70. Academic, pp 277–308

    Google Scholar 

  • Kalari S, Pfeifer GP (2010b) Identification of driver and passenger DNA methylation in cancer by epigenomic analysis. Adv Genet 70:277–308

    CAS  PubMed  Google Scholar 

  • Kallappagoudar S, Yadav RK, Lowe BR, Partridge JF (2015) Histone H3 mutations--a special role for H3.3 in tumorigenesis? Chromosoma 124:177–189

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kamińska K, Nalejska E, Kubiak M, Wojtysiak J, Żołna Ł, Kowalewski J, Lewandowska MA (2019) Prognostic and predictive epigenetic biomarkers in oncology. Mol Diagn Ther 23:83–95

    PubMed  Google Scholar 

  • Kaminskas E, Farrell AT, Wang YC, Sridhara R, Pazdur R (2005) FDA drug approval summary: azacitidine (5-azacytidine, Vidaza) for injectable suspension. Oncologist 10:176–182

    CAS  PubMed  Google Scholar 

  • Kanai Y, Ushijima S, Nakanishi Y, Sakamoto M, Hirohashi S (2003) Mutation of the DNA methyltransferase (DNMT) 1 gene in human colorectal cancers. Cancer Lett 192:75–82

    CAS  PubMed  Google Scholar 

  • Kantarjian H, Issa JP, Rosenfeld CS, Bennett JM, Albitar M, DiPersio J, Klimek V, Slack J, de Castro C, Ravandi F, Helmer R 3rd, Shen L, Nimer SD, Leavitt R, Raza A, Saba H (2006) Decitabine improves patient outcomes in myelodysplastic syndromes: results of a phase III randomized study. Cancer 106:1794–1803

    CAS  PubMed  Google Scholar 

  • Kapoor A, Goldberg MS, Cumberland LK, Ratnakumar K, Segura MF, Emanuel PO, Menendez S, Vardabasso C, Leroy G, Vidal CI, Polsky D, Osman I, Garcia BA, Hernando E, Bernstein E (2010) The histone variant macroH2A suppresses melanoma progression through regulation of CDK8. Nature 468:1105–1109

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kato S, Alsafar A, Walavalkar V, Hainsworth J, Kurzrock R (2021) Cancer of unknown primary in the molecular era. Trends Cancer 7:465–477

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC (2014) Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A 111:6131–6138

    CAS  PubMed  PubMed Central  Google Scholar 

  • Khan C, Pathe N, Fazal S, Lister J, Rossetti JM (2012) Azacitidine in the management of patients with myelodysplastic syndromes. Ther Adv Hematol 3:355–373

    CAS  PubMed  PubMed Central  Google Scholar 

  • Khan SA, Reddy D, Gupta S (2015) Global histone post-translational modifications and cancer: biomarkers for diagnosis, prognosis and treatment? World J Biol Chem 6:333–345

    PubMed  PubMed Central  Google Scholar 

  • Khan SA, Amnekar R, Khade B, Barreto SG, Ramadwar M, Shrikhande SV, Gupta S (2016) p38-MAPK/MSK1-mediated overexpression of histone H3 serine 10 phosphorylation defines distance-dependent prognostic value of negative resection margin in gastric cancer. Clin Epigenetics 8:88

    PubMed  PubMed Central  Google Scholar 

  • Khuong-Quang DA, Buczkowicz P, Rakopoulos P, Liu XY, Fontebasso AM, Bouffet E, Bartels U, Albrecht S, Schwartzentruber J, Letourneau L, Bourgey M, Bourque G, Montpetit A, Bourret G, Lepage P, Fleming A, Lichter P, Kool M, von Deimling A, Sturm D, Korshunov A, Faury D, Jones DT, Majewski J, Pfister SM, Jabado N, Hawkins C (2012) K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol 124:439–447

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kim K, Punj V, Choi J, Heo K, Kim JM, Laird PW, An W (2013) Gene dysregulation by histone variant H2A.Z in bladder cancer. Epigenetics Chromatin 6:34

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kim K, Skora AD, Li Z, Liu Q, Tam AJ, Blosser RL, Diaz LA Jr, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S (2014) Eradication of metastatic mouse cancers resistant to immune checkpoint blockade by suppression of myeloid-derived cells. Proc Natl Acad Sci U S A 111:11774–11779

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kimura H, Shiota K (2003) Methyl-CpG-binding protein, MeCP2, is a target molecule for maintenance DNA methyltransferase, Dnmt1. J Biol Chem 278:4806–4812

    CAS  PubMed  Google Scholar 

  • Komar D, Juszczynski P (2020) Rebelled epigenome: histone H3S10 phosphorylation and H3S10 kinases in cancer biology and therapy. Clin Epigenetics 12:147

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kota J, Chivukula RR, O’Donnell KA, Wentzel EA, Montgomery CL, Hwang HW, Chang TC, Vivekanandan P, Torbenson M, Clark KR, Mendell JR, Mendell JT (2009) Therapeutic microRNA delivery suppresses tumorigenesis in a murine liver cancer model. Cell 137:1005–1017

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705

    CAS  PubMed  Google Scholar 

  • Kozlowski M, Corujo D, Hothorn M, Guberovic I, Mandemaker IK, Blessing C, Sporn J, Gutierrez-Triana A, Smith R, Portmann T, Treier M, Scheffzek K, Huet S, Timinszky G, Buschbeck M, Ladurner AG (2018) MacroH2A histone variants limit chromatin plasticity through two distinct mechanisms. EMBO Rep 19:e44445

    PubMed  PubMed Central  Google Scholar 

  • Kriaucionis S, Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324:929–930

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kroeze LI, Aslanyan MG, van Rooij A, Koorenhof-Scheele TN, Massop M, Carell T, Boezeman JB, Marie JP, Halkes CJ, de Witte T, Huls G, Suciu S, Wevers RA, van der Reijden BA, Jansen JH (2014) Characterization of acute myeloid leukemia based on levels of global hydroxymethylation. Blood 124:1110–1118

    CAS  PubMed  Google Scholar 

  • Krug RM, Morgan MA, Shatkin AJ (1976) Influenza viral mRNA contains internal N6-methyladenosine and 5′-terminal 7-methylguanosine in cap structures. J Virol 20:45–53

    CAS  PubMed  PubMed Central  Google Scholar 

  • Krützfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, Manoharan M, Stoffel M (2005) Silencing of microRNAs in vivo with ‘antagomirs’. Nature 438:685–689

    PubMed  Google Scholar 

  • Kumar S, Mohapatra T (2021) Deciphering Epitranscriptome: modification of mRNA bases provides a new perspective for post-transcriptional regulation of gene expression. Front Cell Dev Biol 9:628415

    PubMed  PubMed Central  Google Scholar 

  • Laganà A, Russo F, Sismeiro C, Giugno R, Pulvirenti A, Ferro A (2010) Variability in the incidence of miRNAs and genes in fragile sites and the role of repeats and CpG islands in the distribution of genetic material. PLoS One 5:e11166

    PubMed  PubMed Central  Google Scholar 

  • Lagger S, Connelly JC, Schweikert G, Webb S, Selfridge J, Ramsahoye BH, Yu M, He C, Sanguinetti G, Sowers LC, Walkinshaw MD, Bird A (2017) MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain. PLoS Genet 13:e1006793

    PubMed  PubMed Central  Google Scholar 

  • Lakshminarasimhan R, Liang G (2016) The role of DNA methylation in cancer. Adv Exp Med Biol 945:151–172

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lamaa A, Humbert J, Aguirrebengoa M, Cheng X, Nicolas E, Côté J, Trouche D (2020) Integrated analysis of H2A.Z isoforms function reveals a complex interplay in gene regulation. elife 9:e53375

    PubMed  PubMed Central  Google Scholar 

  • Lamb YN (2021) Inclisiran: first approval. Drugs 81:389–395

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    CAS  PubMed  Google Scholar 

  • Laubach JP, Schjesvold F, Mariz M, Dimopoulos MA, Lech-Maranda E, Spicka I, Hungria VTM, Shelekhova T, Abdo A, Jacobasch L, Polprasert C, Hájek R, Illés Á, Wróbel T, Sureda A, Beksac M, Gonçalves IZ, Bladé J, Rajkumar SV, Chari A, Lonial S, Spencer A, Maison-Blanche P, Moreau P, San-Miguel JF, Richardson PG (2021) Efficacy and safety of oral panobinostat plus subcutaneous bortezomib and oral dexamethasone in patients with relapsed or relapsed and refractory multiple myeloma (PANORAMA 3): an open-label, randomised, phase 2 study. Lancet Oncol 22:142–154

    CAS  PubMed  Google Scholar 

  • Ledford H (2018) Gene-silencing technology gets first drug approval after 20-year wait. Nature 560:291–292

    CAS  PubMed  Google Scholar 

  • Lee YS, Dutta A (2009) MicroRNAs in cancer. Annu Rev Pathol 4:199–227

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee MS, Sanoff HK (2020) Cancer of unknown primary. BMJ 371:m4050

    PubMed  Google Scholar 

  • Lee J, Stephanie Huang R (2013) Cancer epigenetics: mechanisms and crosstalk of a HDAC inhibitor, Vorinostat. Chemotherapy (Los Angel) 2:14934

    PubMed  Google Scholar 

  • Lee AS, Seo YC, Chang A, Tohari S, Eu KW, Seow-Choen F, McGee JO (2000) Detailed deletion mapping at chromosome 11q23 in colorectal carcinoma. Br J Cancer 83:750–755

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee HZ, Kwitkowski VE, Del Valle PL, Ricci MS, Saber H, Habtemariam BA, Bullock J, Bloomquist E, Li Shen Y, Chen XH, Brown J, Mehrotra N, Dorff S, Charlab R, Kane RC, Kaminskas E, Justice R, Farrell AT, Pazdur R (2015) FDA approval: Belinostat for the treatment of patients with relapsed or refractory peripheral T-cell lymphoma. Clin Cancer Res 21:2666–2670

    CAS  PubMed  Google Scholar 

  • Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ (2019) Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 143:573–593

    CAS  PubMed  PubMed Central  Google Scholar 

  • Leone G, D’Alò F, Zardo G, Voso MT, Nervi C (2008) Epigenetic treatment of myelodysplastic syndromes and acute myeloid leukemias. Curr Med Chem 15:1274–1287

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li M, Chen SS (2011) The tendency to recreate ancestral CG dinucleotides in the human genome. BMC Evol Biol 11:3

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li W, Liu M (2011) Distribution of 5-hydroxymethylcytosine in different human tissues. J Nucleic Acids 2011:870726

    PubMed  PubMed Central  Google Scholar 

  • Li Y, Seto E (2016) HDACs and HDAC inhibitors in cancer development and therapy. Cold Spring Harb Perspect Med 6:a026831

    PubMed  PubMed Central  Google Scholar 

  • Li E, Zhang Y (2014) DNA methylation in mammals. Cold Spring Harb Perspect Biol 6:a019133

    PubMed  PubMed Central  Google Scholar 

  • Li B, Huang G, Zhang X, Li R, Wang J, Dong Z, He Z (2013a) Increased phosphorylation of histone H3 at serine 10 is involved in Epstein-Barr virus latent membrane protein-1-induced carcinogenesis of nasopharyngeal carcinoma. BMC Cancer 13:124

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li S, Liu L, Zhuang X, Yu Y, Liu X, Cui X, Ji L, Pan Z, Cao X, Mo B, Zhang F, Raikhel N, Jiang L, Chen X (2013b) MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell 153:562–574

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li J, Jin H, Wang X (2014) Epigenetic biomarkers: potential applications in gastrointestinal cancers. ISRN Gastroenterol 2014:464015

    PubMed  PubMed Central  Google Scholar 

  • Lian CG, Xu Y, Ceol C, Wu F, Larson A, Dresser K, Xu W, Tan L, Hu Y, Zhan Q, Lee CW, Hu D, Lian BQ, Kleffel S, Yang Y, Neiswender J, Khorasani AJ, Fang R, Lezcano C, Duncan LM, Scolyer RA, Thompson JF, Kakavand H, Houvras Y, Zon LI, Mihm MC Jr, Kaiser UB, Schatton T, Woda BA, Murphy GF, Shi YG (2012) Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 150:1135–1146

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liang G, Weisenberger DJ (2017) DNA methylation aberrancies as a guide for surveillance and treatment of human cancers. Epigenetics 12:416–432

    PubMed  PubMed Central  Google Scholar 

  • Lin CJ, Koh FM, Wong P, Conti M, Ramalho-Santos M (2014) Hira-mediated H3.3 incorporation is required for DNA replication and ribosomal RNA transcription in the mouse zygote. Dev Cell 30:268–279

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lin G, Wang H, Wu Y, Wang K, Li G (2021) Hub Long noncoding RNAs with m6A modification for signatures and prognostic values in kidney renal clear cell carcinoma. Front Mol Biosci 8:682471

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu BL, Cheng JX, Zhang X, Wang R, Zhang W, Lin H, Xiao X, Cai S, Chen XY, Cheng H (2010) Global histone modification patterns as prognostic markers to classify glioma patients. Cancer Epidemiol Biomark Prev 19:2888–2896

    CAS  Google Scholar 

  • Liu C, Liu L, Chen X, Shen J, Shan J, Xu Y, Yang Z, Wu L, Xia F, Bie P, Cui Y, Bian XW, Qian C (2013) Decrease of 5-hydroxymethylcytosine is associated with progression of hepatocellular carcinoma through downregulation of TET1. PLoS One 8:e62828

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu L, Xu C, Hsieh JT, Gong J, Xie D (2016) DAB2IP in cancer. Oncotarget 7:3766–3776

    PubMed  Google Scholar 

  • Liu J, Eckert MA, Harada BT, Liu SM, Lu Z, Yu K, Tienda SM, Chryplewicz A, Zhu AC, Yang Y, Huang JT, Chen SM, Xu ZG, Leng XH, Yu XC, Cao J, Zhang Z, Liu J, Lengyel E, He C (2018a) M(6)a mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer. Nat Cell Biol 20:1074–1083

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu X, Lv X, Yang Q, Jin H, Zhou W, Fan Q (2018b) MicroRNA-29a functions as a tumor suppressor and increases cisplatin sensitivity by targeting NRAS in lung cancer. Technol Cancer Res Treat 17:1533033818758905

    PubMed  PubMed Central  Google Scholar 

  • Locke WJ, Guanzon D, Ma C, Liew YJ, Duesing KR, Fung KYC, Ross JP (2019) DNA methylation cancer biomarkers: translation to the clinic. Front Genet 10:1150

    CAS  PubMed  PubMed Central  Google Scholar 

  • Long MD, Smiraglia DJ, Campbell MJ (2017) The genomic impact of DNA CpG methylation on gene expression; Relationships in prostate cancer. Biomolecules 7:15

    PubMed  PubMed Central  Google Scholar 

  • Long M, Sun X, Shi W, Yanru A, Leung STC, Ding D, Cheema MS, MacPherson N, Nelson CJ, Ausio J, Yan Y, Ishibashi T (2019) A novel histone H4 variant H4G regulates rDNA transcription in breast cancer. Nucleic Acids Res 47:8399–8409

    CAS  PubMed  PubMed Central  Google Scholar 

  • Loppin B, Bonnefoy E, Anselme C, Laurençon A, Karr TL, Couble P (2005) The histone H3.3 chaperone HIRA is essential for chromatin assembly in the male pronucleus. Nature 437:1386–1390

    CAS  PubMed  Google Scholar 

  • Lord RV, Brabender J, Gandara D, Alberola V, Camps C, Domine M, Cardenal F, Sánchez JM, Gumerlock PH, Tarón M, Sánchez JJ, Danenberg KD, Danenberg PV, Rosell R (2002) Low ERCC1 expression correlates with prolonged survival after cisplatin plus gemcitabine chemotherapy in non-small cell lung cancer. Clin Cancer Res 8:2286–2291

    CAS  PubMed  Google Scholar 

  • Lorincz AT (2011) The promise and the problems of epigenetics biomarkers in cancer. Expert Opin Med Diagn 5:375–379

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lu R, Wang GG (2013) Tudor: a versatile family of histone methylation ‘readers’. Trends Biochem Sci 38:546–555

    CAS  PubMed  Google Scholar 

  • Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR (2005) MicroRNA expression profiles classify human cancers. Nature 435:834–838

    CAS  PubMed  Google Scholar 

  • Lu Y, Cao M, Gao K, Jiang J, Shi X (2015) The role of O(6)-methylguanine-DNA methyltransferase polymorphisms in colorectal cancer susceptibility: a meta analysis. Int J Clin Exp Med 8:791–799

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lu X, Ning Z, Li Z, Cao H, Wang X (2016) Development of chidamide for peripheral T-cell lymphoma, the first orphan drug approved in China. Intractable Rare Dis Res 5:185–191

    PubMed  PubMed Central  Google Scholar 

  • Lu Y, Chan YT, Tan HY, Li S, Wang N, Feng Y (2020) Epigenetic regulation in human cancer: the potential role of epi-drug in cancer therapy. Mol Cancer 19:79

    PubMed  PubMed Central  Google Scholar 

  • Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–260

    CAS  PubMed  Google Scholar 

  • Luger K, Dechassa ML, Tremethick DJ (2012) New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 13:436–447

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lunke S, Maxwell S, Khurana I, Harikrishnan KN, Okabe J, Al-Hasani K, El-Osta A (2021) Epigenetic evidence of an ac/dc axis by VPA and SAHA. Clin Epigenetics 13:58

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ma Y, Shen N, Wicha MS, Luo M (2021) The roles of the Let-7 family of MicroRNAs in the regulation of cancer Stemness. Cell 10:2415

    CAS  Google Scholar 

  • MacArthur BD (2022) The geometry of cell fate. Cell Syst 13:1–3

    CAS  PubMed  Google Scholar 

  • Maeda K, Kawakami K, Ishida Y, Ishiguro K, Omura K, Watanabe G (2003) Hypermethylation of the CDKN2A gene in colorectal cancer is associated with shorter survival. Oncol Rep 10:935–938

    CAS  PubMed  Google Scholar 

  • Majchrzak-Celińska A, Baer-Dubowska W (2017) Pharmacoepigenetics: an element of personalized therapy? Expert Opin Drug Metab Toxicol 13:387–398

    PubMed  Google Scholar 

  • Majchrzak-Celińska A, Warych A, Szoszkiewicz M (2021) Novel approaches to epigenetic therapies: from drug combinations to epigenetic editing. Genes (Basel) 12:208

    PubMed  Google Scholar 

  • Malik P, Cashen AF (2014) Decitabine in the treatment of acute myeloid leukemia in elderly patients. Cancer Manag Res 6:53–61

    PubMed  PubMed Central  Google Scholar 

  • Mann BS, Johnson JR, Cohen MH, Justice R, Pazdur R (2007) FDA approval summary: vorinostat for treatment of advanced primary cutaneous T-cell lymphoma. Oncologist 12:1247–1252

    CAS  PubMed  Google Scholar 

  • Manuyakorn A, Paulus R, Farrell J, Dawson NA, Tze S, Cheung-Lau G, Hines OJ, Reber H, Seligson DB, Horvath S, Kurdistani SK, Guha C, Dawson DW (2010) Cellular histone modification patterns predict prognosis and treatment response in resectable pancreatic adenocarcinoma: results from RTOG 9704. J Clin Oncol 28:1358–1365

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mariño-Ramírez L, Kann MG, Shoemaker BA, Landsman D (2005) Histone structure and nucleosome stability. Expert Rev Proteomics 2:719–729

    PubMed  PubMed Central  Google Scholar 

  • Marks PA, Xu WS (2009) Histone deacetylase inhibitors: potential in cancer therapy. J Cell Biochem 107:600–608

    CAS  PubMed  PubMed Central  Google Scholar 

  • Marriott L, Charbonneau A, Moss B, Shannon J, Thornburg K, Turker M (2016) Epigenetics: a new science for middle school – and why you should teach it. Sci Scope (Wash, DC) 39:6–11

    Google Scholar 

  • Matei D, Fang F, Shen C, Schilder J, Arnold A, Zeng Y, Berry WA, Huang T, Nephew KP (2012) Epigenetic resensitization to platinum in ovarian cancer. Cancer Res 72:2197–2205

    CAS  PubMed  PubMed Central  Google Scholar 

  • Matilainen O, Quirós PM, Auwerx J (2017) Mitochondria and epigenetics – crosstalk in homeostasis and stress. Trends Cell Biol 27:453–463

    CAS  PubMed  Google Scholar 

  • Mayeux R (2004) Biomarkers: potential uses and limitations. NeuroRx 1:182–188

    PubMed  PubMed Central  Google Scholar 

  • McGraw AL (2013) Romidepsin for the treatment of T-cell lymphomas. Am J Health Syst Pharm 70:1115–1122

    CAS  PubMed  Google Scholar 

  • Medina PP, Nolde M, Slack FJ (2010) OncomiR addiction in an in vivo model of microRNA-21-induced pre-B-cell lymphoma. Nature 467:86–90

    CAS  PubMed  Google Scholar 

  • Méndez-Acuña L, Di Tomaso MV, Palitti F, Martínez-López W (2010) Histone post-translational modifications in DNA damage response. Cytogenet Genome Res 128:28–36

    PubMed  Google Scholar 

  • Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, Pestova TV, Qian SB, Jaffrey SR (2015) 5′ UTR m(6)a promotes cap-independent translation. Cell 163:999–1010

    CAS  PubMed  PubMed Central  Google Scholar 

  • Milutinovic S, D’Alessio AC, Detich N, Szyf M (2007) Valproate induces widespread epigenetic reprogramming which involves demethylation of specific genes. Carcinogenesis 28:560–571

    CAS  PubMed  Google Scholar 

  • Mitalipov S, Wolf D (2009) Totipotency, pluripotency and nuclear reprogramming. Adv Biochem Eng Biotechnol 114:185–199

    CAS  PubMed  PubMed Central  Google Scholar 

  • Moen EL, Stark AL, Zhang W, Dolan ME, Godley LA (2014) The role of gene body cytosine modifications in MGMT expression and sensitivity to temozolomide. Mol Cancer Ther 13:1334–1344

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mogilyansky E, Rigoutsos I (2013) The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. Cell Death Diff 20:1603–1614

    CAS  Google Scholar 

  • Molaro A, Wood AJ, Janssens D, Kindelay SM, Eickbush MT, Wu S, Singh P, Muller CH, Henikoff S, Malik HS (2020) Biparental contributions of the H2A.B histone variant control embryonic development in mice. PLoS Biol 18:e3001001

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mongan NP, Emes RD, Archer N (2019) Detection and analysis of RNA methylation. F1000Res 8:F1000

    PubMed  PubMed Central  Google Scholar 

  • Moore D (2016) Panobinostat (Farydak): a novel option for the treatment of relapsed or relapsed and refractory multiple myeloma. P T 41:296–300

    PubMed  PubMed Central  Google Scholar 

  • Moore LD, Le T, Fan G (2013) DNA methylation and its basic function. Neuropsychopharmacology 38:23–38

    CAS  PubMed  Google Scholar 

  • Moosavi A, Motevalizadeh Ardekani A (2016) Role of epigenetics in biology and human diseases. Iran Biomed J 20:246–258

    PubMed  PubMed Central  Google Scholar 

  • Moran S, Martínez-Cardús A, Sayols S, Musulén E, Balañá C, Estival-Gonzalez A, Moutinho C, Heyn H, Diaz-Lagares A, de Moura MC, Stella GM, Comoglio PM, Ruiz-Miró M, Matias-Guiu X, Pazo-Cid R, Antón A, Lopez-Lopez R, Soler G, Longo F, Guerra I, Fernandez S, Assenov Y, Plass C, Morales R, Carles J, Bowtell D, Mileshkin L, Sia D, Tothill R, Tabernero J, Llovet JM, Esteller M (2016) Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis. Lancet Oncol 17:1386–1395

    PubMed  Google Scholar 

  • Morena F, Argentati C, Bazzucchi M, Emiliani C, Martino S (2018) Above the Epitranscriptome: RNA modifications and stem cell identity. Genes (Basel) 9:329

    PubMed  Google Scholar 

  • Mouhieddine TH, El Houjeiri L, Sabra M, Hayes RL, Mondello S (2015) Frontiers in Neuroengineering CNS trauma biomarkers and surrogate endpoints pipeline from bench to bedside: a translational perspective. In: Kobeissy FH (ed) Brain Neurotrauma: molecular, neuropsychological, and rehabilitation aspects. CRC Press/Taylor & Francis © 2015 by Taylor & Francis Group, LLC, Boca Raton

    Google Scholar 

  • Mulero-Navarro S, Esteller M (2008) Epigenetic biomarkers for human cancer: the time is now. Crit Rev Oncol Hematol 68:1–11

    PubMed  Google Scholar 

  • Mullard A (2009) Epigenomic colon cancer kit. Nat Biotechnol 27:1066–1066

    CAS  Google Scholar 

  • Multhoff G, Molls M, Radons J (2011) Chronic inflammation in cancer development. Front Immunol 2:98

    PubMed  Google Scholar 

  • Munari E, Chaux A, Vaghasia AM, Taheri D, Karram S, Bezerra SM, Gonzalez Roibon N, Nelson WG, Yegnasubramanian S, Netto GJ, Haffner MC (2016) Global 5-Hydroxymethylcytosine levels are profoundly reduced in multiple genitourinary malignancies. PLoS One 11:e0146302

    PubMed  PubMed Central  Google Scholar 

  • Munn LL (2017) Cancer and inflammation. Wiley Interdiscip Rev Syst Biol Med 9:e1370

    Google Scholar 

  • Munshi A, Tanaka T, Hobbs ML, Tucker SL, Richon VM, Meyn RE (2006) Vorinostat, a histone deacetylase inhibitor, enhances the response of human tumor cells to ionizing radiation through prolongation of gamma-H2AX foci. Mol Cancer Ther 5:1967–1974

    CAS  PubMed  Google Scholar 

  • Munster PN, Thurn KT, Thomas S, Raha P, Lacevic M, Miller A, Melisko M, Ismail-Khan R, Rugo H, Moasser M, Minton SE (2011) A phase II study of the histone deacetylase inhibitor vorinostat combined with tamoxifen for the treatment of patients with hormone therapy-resistant breast cancer. Br J Cancer 104:1828–1835

    CAS  PubMed  PubMed Central  Google Scholar 

  • Murata M (2018) Inflammation and cancer. Environ Health Prev Med 23:50

    PubMed  PubMed Central  Google Scholar 

  • Musselman CA, Lalonde ME, Côté J, Kutateladze TG (2012) Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol 19:1218–1227

    CAS  PubMed  PubMed Central  Google Scholar 

  • Muthurajan UM, McBryant SJ, Lu X, Hansen JC, Luger K (2011) The linker region of macroH2A promotes self-association of nucleosomal arrays. J Biol Chem 286:23852–23864

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nabel CS, Manning SA, Kohli RM (2012) The curious chemical biology of cytosine: deamination, methylation, and oxidation as modulators of genomic potential. ACS Chem Biol 7:20–30

    CAS  PubMed  Google Scholar 

  • Nacev BA, Feng L, Bagert JD, Lemiesz AE, Gao J, Soshnev AA, Kundra R, Schultz N, Muir TW, Allis CD (2019) The expanding landscape of ‘oncohistone’ mutations in human cancers. Nature 567:473–478

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nagelkerke A, van Kuijk SJ, Sweep FC, Nagtegaal ID, Hoogerbrugge N, Martens JW, Timmermans MA, van Laarhoven HW, Bussink J, Span PN (2011) Constitutive expression of γ-H2AX has prognostic relevance in triple negative breast cancer. Radiother Oncol 101:39–45

    CAS  PubMed  Google Scholar 

  • Nakayama T, Watanabe M, Yamanaka M, Hirokawa Y, Suzuki H, Ito H, Yatani R, Shiraishi T (2001) The role of epigenetic modifications in retinoic acid receptor beta2 gene expression in human prostate cancers. Lab Investig 81:1049–1057

    CAS  PubMed  Google Scholar 

  • Nan P, Niu Y, Wang X, Li Q (2019) MiR-29a function as tumor suppressor in cervical cancer by targeting SIRT1 and predict patient prognosis. Onco Targets Ther 12:6917–6925

    PubMed  PubMed Central  Google Scholar 

  • Napoli C, Grimaldi V, De Pascale MR, Sommese L, Infante T, Soricelli A (2016) Novel epigenetic-based therapies useful in cardiovascular medicine. World J Cardiol 8:211–219

    PubMed  PubMed Central  Google Scholar 

  • Napoli C, Bontempo P, Palmieri V, Coscioni E, Maiello C, Donatelli F, Benincasa G (2021) Epigenetic therapies for heart failure: current insights and future potential. Vasc Health Risk Manag 17:247–254

    PubMed  PubMed Central  Google Scholar 

  • Needham J, Waddington CH, Needham DMM, Hopkins FG (1934) Physico-chemical experiments on the amphibian organizer. Proc R Soc London Ser B Containing Papers Biol Character 114:393–422

    CAS  Google Scholar 

  • Nepali K, Liou J-P (2021) Recent developments in epigenetic cancer therapeutics: clinical advancement and emerging trends. J Biomed Sci 28:27

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nestor CE, Ottaviano R, Reddington J, Sproul D, Reinhardt D, Dunican D, Katz E, Dixon JM, Harrison DJ, Meehan RR (2012) Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res 22:467–477

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ng CS, Zhang J, Wan S, Lee TW, Arifi AA, Mok T, Lo DY, Yim AP (2002) Tumor p16M is a possible marker of advanced stage in non-small cell lung cancer. J Surg Oncol 79:101–106

    PubMed  Google Scholar 

  • Ni W-J, Leng X-M (2015) Dynamic miRNA–mRNA paradigms: new faces of miRNAs. Biochem Biophy Rep 4:337–341

    Google Scholar 

  • Nichols JL (1979) N6-methyladenosine in maize poly(a)-containing RNA. Plant Sci Lett 15:357–361

    CAS  Google Scholar 

  • Nicodeme E, Jeffrey KL, Schaefer U, Beinke S, Dewell S, Chung CW, Chandwani R, Marazzi I, Wilson P, Coste H, White J, Kirilovsky J, Rice CM, Lora JM, Prinjha RK, Lee K, Tarakhovsky A (2010) Suppression of inflammation by a synthetic histone mimic. Nature 468:1119–1123

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nicoglou A (2018) Waddington’s epigenetics or the pictorial meetings of development and genetics. Hist Philos Life Sci 40:61

    PubMed  Google Scholar 

  • Ning B, Li W, Zhao W, Wang R (2016) Targeting epigenetic regulations in cancer. Acta Biochim Biophys Sin Shanghai 48:97–109

    CAS  PubMed  Google Scholar 

  • Nishibuchi I, Suzuki H, Kinomura A, Sun J, Liu NA, Horikoshi Y, Shima H, Kusakabe M, Harata M, Fukagawa T, Ikura T, Ishida T, Nagata Y, Tashiro S (2014) Reorganization of damaged chromatin by the exchange of histone variant H2A.Z-2. Int J Radiat Oncol Biol Phys 89:736–744

    CAS  PubMed  Google Scholar 

  • Nishioka C, Ikezoe T, Yang J, Takeuchi S, Koeffler HP, Yokoyama A (2008) MS-275, a novel histone deacetylase inhibitor with selectivity against HDAC1, induces degradation of FLT3 via inhibition of chaperone function of heat shock protein 90 in AML cells. Leuk Res 32:1382–1392

    CAS  PubMed  Google Scholar 

  • Niwa T, Tsukamoto T, Toyoda T, Mori A, Tanaka H, Maekita T, Ichinose M, Tatematsu M, Ushijima T (2010a) Inflammatory processes triggered by helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells. Cancer Res 70:1430–1440

    CAS  PubMed  Google Scholar 

  • Niwa T, Tsukamoto T, Toyoda T, Mori A, Tanaka H, Maekita T, Ichinose M, Tatematsu M, Ushijima T (2010b) Inflammatory processes triggered by helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells. Cancer Res 70:1430–1440

    CAS  PubMed  Google Scholar 

  • Niwa T, Toyoda T, Tsukamoto T, Mori A, Tatematsu M, Ushijima T (2013) Prevention of helicobacter pylori-induced gastric cancers in gerbils by a DNA demethylating agent. Cancer Prev Res (Phila) 6:263–270

    CAS  PubMed  Google Scholar 

  • O’Brien J, Hayder H, Zayed Y, Peng C (2018) Overview of MicroRNA biogenesis, mechanisms of actions, and circulation. Front Endocrinol 9:402

    Google Scholar 

  • O’Connor OA, Horwitz S, Masszi T, Van Hoof A, Brown P, Doorduijn J, Hess G, Jurczak W, Knoblauch P, Chawla S, Bhat G, Choi MR, Walewski J, Savage K, Foss F, Allen LF, Shustov A (2015) Belinostat in patients with relapsed or refractory peripheral T-cell lymphoma: results of the pivotal phase II BELIEF (CLN-19) study. J Clin Oncol 33:2492–2499

    PubMed  PubMed Central  Google Scholar 

  • Olsen EA, Kim YH, Kuzel TM, Pacheco TR, Foss FM, Parker S, Frankel SR, Chen C, Ricker JL, Arduino JM, Duvic M (2007) Phase IIb multicenter trial of vorinostat in patients with persistent, progressive, or treatment refractory cutaneous T-cell lymphoma. J Clin Oncol 25:3109–3115

    CAS  PubMed  Google Scholar 

  • Oronsky B, Oronsky N, Scicinski J, Fanger G, Lybeck M, Reid T (2014) Rewriting the epigenetic code for tumor resensitization: a review. Transl Oncol 7:626–631

    PubMed  PubMed Central  Google Scholar 

  • Pacaud R, Cheray M, Nadaradjane A, Vallette FM, Cartron PF (2015) Histone H3 phosphorylation in GBM: a new rational to guide the use of kinase inhibitors in anti-GBM therapy. Theranostics 5:12–22

    PubMed  PubMed Central  Google Scholar 

  • Palazzo AF, Gregory TR (2014) The case for junk DNA. PLoS Genet 10:e1004351

    PubMed  PubMed Central  Google Scholar 

  • Pan H, Renaud L, Chaligne R, Bloehdorn J, Tausch E, Mertens D, Fink AM, Fischer K, Zhang C, Betel D, Gnirke A, Imielinski M, Moreaux J, Hallek M, Meissner A, Stilgenbauer S, Wu CJ, Elemento O, Landau DA (2021) Discovery of candidate DNA methylation cancer driver genes. Cancer Discov 11:2266–2281

    CAS  PubMed  PubMed Central  Google Scholar 

  • Panchin AY, Makeev VJ, Medvedeva YA (2016) Preservation of methylated CpG dinucleotides in human CpG islands. Biol Direct 11:11

    PubMed  PubMed Central  Google Scholar 

  • Pang AP, Sugai C, Maunakea AK (2016) High-throughput sequencing offers new insights into 5-hydroxymethylcytosine. Biomol Concepts 7:169–178

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pang MYH, Sun X, Ausió J, Ishibashi T (2020) Histone H4 variant, H4G, drives ribosomal RNA transcription and breast cancer cell proliferation by loosening nucleolar chromatin structure. J Cell Physiol 235:9601–9608

    CAS  PubMed  Google Scholar 

  • Papale LA, Madrid A, Zhang Q, Chen K, Sak L, Keleş S, Alisch RS (2022) Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders. Genome Res 32:266–279

    PubMed  PubMed Central  Google Scholar 

  • Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT (2021) Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer 2:1002–1017

    CAS  PubMed  PubMed Central  Google Scholar 

  • Parbin S, Kar S, Shilpi A, Sengupta D, Deb M, Rath SK, Patra SK (2014) Histone deacetylases: a saga of perturbed acetylation homeostasis in cancer. J Histochem Cytochem 62:11–33

    PubMed  PubMed Central  Google Scholar 

  • Park S-Y, Kim J-S (2020) A short guide to histone deacetylases including recent progress on class II enzymes. Exp Mol Med 52:204–212

    CAS  PubMed  PubMed Central  Google Scholar 

  • Park YS, Jin MY, Kim YJ, Yook JH, Kim BS, Jang SJ (2008) The global histone modification pattern correlates with cancer recurrence and overall survival in gastric adenocarcinoma. Ann Surg Oncol 15:1968–1976

    PubMed  Google Scholar 

  • Park JL, Kim HJ, Seo EH, Kwon OH, Lim B, Kim M, Kim SY, Song KS, Kang GH, Kim HJ, Choi BY, Kim YS (2015) Decrease of 5hmC in gastric cancers is associated with TET1 silencing due to with DNA methylation and bivalent histone marks at TET1 CpG island 3′-shore. Oncotarget 6:37647–37662

    PubMed  PubMed Central  Google Scholar 

  • Patil V, Ward RL, Hesson LB (2014) The evidence for functional non-CpG methylation in mammalian cells. Epigenetics 9:823–828

    PubMed  PubMed Central  Google Scholar 

  • Pavlidis N, Fizazi K (2005) Cancer of unknown primary (CUP). Crit Rev Oncol Hematol 54:243–250

    PubMed  Google Scholar 

  • Peng J, Yuan C, Hua X, Zhang Z (2020) Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures. Epigenetics Chromatin 13:28

    CAS  PubMed  PubMed Central  Google Scholar 

  • Peng Q, Weng K, Li S, Xu R, Wang Y, Wu Y (2021) A perspective of epigenetic regulation in radiotherapy. Front Cell Dev Biol 9:624312

    PubMed  PubMed Central  Google Scholar 

  • Penn NW, Suwalski R, O’Riley C, Bojanowski K, Yura R (1972) The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem J 126:781–790

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pertea M (2012) The human transcriptome: an unfinished story. Genes (Basel) 3:344–360

    CAS  PubMed  Google Scholar 

  • Pértille F, Da Silva VH, Johansson AM, Lindström T, Wright D, Coutinho LL, Jensen P, Guerrero-Bosagna C (2019) Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification. Epigenetics 14:685–707

    PubMed  PubMed Central  Google Scholar 

  • Peserico A, Germani A, Sanese P, Barbosa AJ, Di Virgilio V, Fittipaldi R, Fabini E, Bertucci C, Varchi G, Moyer MP, Caretti G, Del Rio A, Simone C (2015) A SMYD3 small-molecule inhibitor impairing cancer cell growth. J Cell Physiol 230:2447–2460

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pfeifer GP (2018) Defining driver DNA methylation changes in human cancer. Int J Mol Sci 19:1166

    PubMed  PubMed Central  Google Scholar 

  • Pfeifer GP, Xiong W, Hahn MA, Jin SG (2014) The role of 5-hydroxymethylcytosine in human cancer. Cell Tissue Res 356:631–641

    CAS  PubMed  PubMed Central  Google Scholar 

  • Phiel CJ, Zhang F, Huang EY, Guenther MG, Lazar MA, Klein PS (2001) Histone deacetylase is a direct target of valproic acid, a potent anticonvulsant, mood stabilizer, and teratogen. J Biol Chem 276:36734–36741

    CAS  PubMed  Google Scholar 

  • Phillips DM (1963) The presence of acetyl groups of histones. Biochem J 87:258–263

    CAS  PubMed  PubMed Central  Google Scholar 

  • Piljić Burazer M, Mladinov S, Matana A, Kuret S, Bezić J, Glavina Durdov M (2019) Low ERCC1 expression is a good predictive marker in lung adenocarcinoma patients receiving chemotherapy based on platinum in all TNM stages – a single-center study. Diagn Pathol 14:105

    PubMed  PubMed Central  Google Scholar 

  • Pískala AŠF (1964) Nucleic acids components and their analogues. LI. Synthesis of 1-glycosyl derivatives of 5-azauracil and 5-azacytosine. Coll Czech Chem Commun 29:2060–2076

    Google Scholar 

  • Pliml JŠF (1964) Synthesis of 2′-deoxy-D-ribofuranosyl-5-azacytosine. Coll Czech Chem Commun 29:2576–2577

    CAS  Google Scholar 

  • Plotnik JP, Hollenhorst PC (2017) Interaction with ZMYND11 mediates opposing roles of Ras-responsive transcription factors ETS1 and ETS2. Nucleic Acids Res 45:4452–4462

    CAS  PubMed  PubMed Central  Google Scholar 

  • Podhorecka M, Skladanowski A, Bozko P (2010) H2AX phosphorylation: its role in DNA damage response and cancer therapy. J Nucleic Acids 2010:920161

    PubMed  PubMed Central  Google Scholar 

  • Ponnusamy L, Mahalingaiah PKS, Chang YW, Singh KP (2018) Reversal of epigenetic aberrations associated with the acquisition of doxorubicin resistance restores drug sensitivity in breast cancer cells. Eur J Pharm Sci 123:56–69

    CAS  PubMed  Google Scholar 

  • Powis G, Kirkpatrick L (2004) Hypoxia inducible factor-1alpha as a cancer drug target. Mol Cancer Ther 3:647–654

    CAS  PubMed  Google Scholar 

  • Pulido HA, Fakruddin MJ, Chatterjee A, Esplin ED, Beleño N, Martinez G, Posso H, Evans GA, Murty VV (2000) Identification of a 6-cM minimal deletion at 11q23.1-23.2 and exclusion of PPP2R1B gene as a deletion target in cervical cancer. Cancer Res 60:6677–6682

    CAS  PubMed  Google Scholar 

  • Pulitzer M (2017) Cutaneous T-cell lymphoma. Clin Lab Med 37:527–546

    PubMed  PubMed Central  Google Scholar 

  • Qaseem A, Usman N, Jayaraj JS, Janapala RN, Kashif T (2019) Cancer of unknown primary: a review on clinical guidelines in the development and targeted Management of Patients with the unknown primary site. Cureus 11:e5552

    PubMed  PubMed Central  Google Scholar 

  • Quagliano A, Gopalakrishnapillai A, Barwe SP (2020a) Understanding the mechanisms by which epigenetic modifiers avert therapy resistance in cancer. Front Oncol 10:992

    PubMed  PubMed Central  Google Scholar 

  • Quagliano A, Gopalakrishnapillai A, Barwe SP (2020b) Understanding the mechanisms by which epigenetic modifiers avert therapy resistance in cancer. Front Oncol 10:992

    PubMed  PubMed Central  Google Scholar 

  • Quénet D (2018) Histone variants and disease. Int Rev Cell Mol Biol 335:1–39

    PubMed  Google Scholar 

  • Ramazi S, Allahverdi A, Zahiri J (2020) Evaluation of post-translational modifications in histone proteins: a review on histone modification defects in developmental and neurological disorders. J Biosci 45:135

    CAS  PubMed  Google Scholar 

  • Rando OJ (2012) Combinatorial complexity in chromatin structure and function: revisiting the histone code. Curr Opin Genet Dev 22:148–155

    CAS  PubMed  PubMed Central  Google Scholar 

  • Raynal NJ, Da Costa EM, Lee JT, Gharibyan V, Ahmed S, Zhang H, Sato T, Malouf GG, Issa JJ (2017) Repositioning FDA-approved drugs in combination with epigenetic drugs to reprogram colon cancer epigenome. Mol Cancer Ther 16:397–407

    CAS  PubMed  Google Scholar 

  • Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901–906

    CAS  PubMed  Google Scholar 

  • Ren M, Leng Y, Jeong M, Leeds PR, Chuang DM (2004) Valproic acid reduces brain damage induced by transient focal cerebral ischemia in rats: potential roles of histone deacetylase inhibition and heat shock protein induction. J Neurochem 89:1358–1367

    CAS  PubMed  Google Scholar 

  • Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X (2018) Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 53:88–99

    CAS  PubMed  PubMed Central  Google Scholar 

  • Richon VM (2010) Targeting histone deacetylases: development of vorinostat for the treatment of cancer. Epigenomics 2:457–465

    CAS  PubMed  Google Scholar 

  • Richon VM, Sandhoff TW, Rifkind RA, Marks PA (2000) Histone deacetylase inhibitor selectively induces p21WAF1 expression and gene-associated histone acetylation. Proc Natl Acad Sci U S A 97:10014–10019

    CAS  PubMed  PubMed Central  Google Scholar 

  • Riggs AD (1975) X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet 14:9–25

    CAS  PubMed  Google Scholar 

  • Roberti A, Valdes AF, Torrecillas R, Fraga MF, Fernandez AF (2019) Epigenetics in cancer therapy and nanomedicine. Clin Epigenetics 11:81

    PubMed  PubMed Central  Google Scholar 

  • Robinson EL, Anene-Nzelu CG, Rosa-Garrido M, Foo RSY (2021) Cardiac epigenetics: driving signals to the cardiac epigenome in development and disease. J Mol Cell Cardiol 151:88

    CAS  PubMed  Google Scholar 

  • Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM (1998) DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J Biol Chem 273:5858–5868

    CAS  PubMed  Google Scholar 

  • Rogakou EP, Boon C, Redon C, Bonner WM (1999) Megabase chromatin domains involved in DNA double-strand breaks in vivo. J Cell Biol 146:905–916

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roundtree IA, Evans ME, Pan T, He C (2017a) Dynamic RNA modifications in gene expression regulation. Cell 169:1187–1200

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roundtree IA, Luo GZ, Zhang Z, Wang X, Zhou T, Cui Y, Sha J, Huang X, Guerrero L, Xie P, He E, Shen B, He C (2017b) YTHDC1 mediates nuclear export of N(6)-methyladenosine methylated mRNAs. elife 6:e31311

    PubMed  PubMed Central  Google Scholar 

  • Ruefli AA, Ausserlechner MJ, Bernhard D, Sutton VR, Tainton KM, Kofler R, Smyth MJ, Johnstone RW (2001) The histone deacetylase inhibitor and chemotherapeutic agent suberoylanilide hydroxamic acid (SAHA) induces a cell-death pathway characterized by cleavage of Bid and production of reactive oxygen species. Proc Natl Acad Sci U S A 98:10833–10838

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rutnam ZJ, Yang BB (2012) The involvement of microRNAs in malignant transformation. Histol Histopathol 27:1263–1270

    CAS  PubMed  Google Scholar 

  • Saba HI (2007) Decitabine in the treatment of myelodysplastic syndromes. Ther Clin Risk Manag 3:807–817

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sakabe K, Wang Z, Hart GW (2010) Beta-N-acetylglucosamine (O-GlcNAc) is part of the histone code. Proc Natl Acad Sci U S A 107:19915–19920

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sakai A, Schwartz BE, Goldstein S, Ahmad K (2009) Transcriptional and developmental functions of the H3.3 histone variant in drosophila. Curr Biol 19:1816–1820

    CAS  PubMed  PubMed Central  Google Scholar 

  • Saleh K, Michot JM, Ribrag V (2021) Updates in the treatment of peripheral T-cell lymphomas. J Exp Pharmacol 13:577–591

    PubMed  PubMed Central  Google Scholar 

  • Sales-Gil R, Kommer DC, de Castro IJ, Amin HA, Vinciotti V, Sisu C, Vagnarelli P (2021) Non-redundant functions of H2A.Z.1 and H2A.Z.2 in chromosome segregation and cell cycle progression. EMBO Rep 22:e52061

    CAS  PubMed  PubMed Central  Google Scholar 

  • San-Miguel JF, Hungria VT, Yoon SS, Beksac M, Dimopoulos MA, Elghandour A, Jedrzejczak WW, Günther A, Nakorn TN, Siritanaratkul N, Schlossman RL, Hou J, Moreau P, Lonial S, Lee JH, Einsele H, Sopala M, Bengoudifa BR, Binlich F, Richardson PG (2016) Overall survival of patients with relapsed multiple myeloma treated with panobinostat or placebo plus bortezomib and dexamethasone (the PANORAMA 1 trial): a randomised, placebo-controlled, phase 3 trial. Lancet Haematol 3:e506–e515

    PubMed  Google Scholar 

  • Sansoni V, Casas-Delucchi CS, Rajan M, Schmidt A, Bönisch C, Thomae AW, Staege MS, Hake SB, Cardoso MC, Imhof A (2014) The histone variant H2A.Bbd is enriched at sites of DNA synthesis. Nucleic Acids Res 42:6405–6420

    CAS  PubMed  PubMed Central  Google Scholar 

  • Saravi S, Katsuta E, Jeyaneethi J, Amin HA, Kaspar M, Takabe K, Pados G, Drenos F, Hall M, Karteris E (2020) H2A histone family member X (H2AX) is upregulated in ovarian cancer and demonstrates utility as a prognostic biomarker in terms of overall survival. J Clin Med 9:2844

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sarg B, Lopez R, Lindner H, Ponte I, Suau P, Roque A (2015) Identification of novel post-translational modifications in linker histones from chicken erythrocytes. J Proteome 113:162–177

    CAS  Google Scholar 

  • Sarver AE, Li L, Kartha RV, Subramanian S (2015) microRNAs in the malignant transformation process. Adv Exp Med Biol 889:1–21

    CAS  PubMed  Google Scholar 

  • Sassa A, Kanemaru Y, Kamoshita N, Honma M, Yasui M (2016) Mutagenic consequences of cytosine alterations site-specifically embedded in the human genome. Genes Environ 38:17

    PubMed  Google Scholar 

  • Sawas A, Radeski D, O’Connor OA (2015) Belinostat in patients with refractory or relapsed peripheral T-cell lymphoma: a perspective review. Ther Adv Hematol 6:202–208

    CAS  PubMed  PubMed Central  Google Scholar 

  • Saxonov S, Berg P, Brutlag DL (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103:1412–1417

    CAS  PubMed  PubMed Central  Google Scholar 

  • Schiffer CA (2018) “Epigenetic” modification as therapy for acute myeloid leukemia. Cancer 124:242–244

    PubMed  Google Scholar 

  • Schneider BG, Piazuelo MB, Sicinschi LA, Mera R, Peng DF, Roa JC, Romero-Gallo J, Delgado AG, de Sablet T, Bravo LE, Wilson KT, El-Rifai W, Peek RM Jr, Correa P (2013) Virulence of infecting helicobacter pylori strains and intensity of mononuclear cell infiltration are associated with levels of DNA hypermethylation in gastric mucosae. Epigenetics 8:1153–1161

    CAS  PubMed  PubMed Central  Google Scholar 

  • Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DA, Tönjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jäger N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Frühwald MC, Roggendorf W, Kramm C, Dürken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N (2012) Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 482:226–231

    CAS  PubMed  Google Scholar 

  • Scott LJ (2020) Givosiran: First Approval. Drugs 80:335–339

    PubMed  Google Scholar 

  • Scott LJ, Keam SJ (2021) Lumasiran: first approval. Drugs 81:277–282

    CAS  PubMed  Google Scholar 

  • Seligson DB, Horvath S, Shi T, Yu H, Tze S, Grunstein M, Kurdistani SK (2005) Global histone modification patterns predict risk of prostate cancer recurrence. Nature 435:1262–1266

    CAS  PubMed  Google Scholar 

  • Seligson DB, Horvath S, McBrian MA, Mah V, Yu H, Tze S, Wang Q, Chia D, Goodglick L, Kurdistani SK (2009) Global levels of histone modifications predict prognosis in different cancers. Am J Pathol 174:1619–1628

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma S, Kelly TK, Jones PA (2010) Epigenetics in cancer. Carcinogenesis 31:27–36

    CAS  PubMed  Google Scholar 

  • Shen JC, Rideout WM 3rd, Jones PA (1994) The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res 22:972–976

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shen L, Kondo Y, Rosner GL, Xiao L, Hernandez NS, Vilaythong J, Houlihan PS, Krouse RS, Prasad AR, Einspahr JG, Buckmeier J, Alberts DS, Hamilton SR, Issa JP (2005) MGMT promoter methylation and field defect in sporadic colorectal cancer. J Natl Cancer Inst 97:1330–1338

    CAS  PubMed  Google Scholar 

  • Shi Y, Dong M, Hong X, Zhang W, Feng J, Zhu J, Yu L, Ke X, Huang H, Shen Z, Fan Y, Li W, Zhao X, Qi J, Huang H, Zhou D, Ning Z, Lu X (2015) Results from a multicenter, open-label, pivotal phase II study of chidamide in relapsed or refractory peripheral T-cell lymphoma. Ann Oncol 26:1766–1771

    CAS  PubMed  Google Scholar 

  • Shi W, Palmer JD, Werner-Wasik M, Andrews DW, Evans JJ, Glass J, Kim L, Bar-Ad V, Judy K, Farrell C, Simone N, Liu H, Dicker AP, Lawrence YR (2016) Phase I trial of panobinostat and fractionated stereotactic re-irradiation therapy for recurrent high grade gliomas. J Neuro-Oncol 127:535–539

    CAS  Google Scholar 

  • Shi D-Q, Ali I, Tang J, Yang W-C (2017a) New insights into 5hmC DNA modification: generation, distribution and function. Front Genet 8:100

    PubMed  PubMed Central  Google Scholar 

  • Shi L, Wen H, Shi X (2017b) The histone variant H3.3 in transcriptional regulation and human disease. J Mol Biol 429:1934–1945

    CAS  PubMed  Google Scholar 

  • Shimony S, Horowitz N, Ribakovsky E, Rozovski U, Avigdor A, Zloto K, Berger T, Avivi I, Perry C, Abadi U, Raanani P, Gafter-Gvili A, Gurion R (2019) Romidepsin treatment for relapsed or refractory peripheral and cutaneous T-cell lymphoma: real-life data from a national multicenter observational study. Hematol Oncol 37:569–577

    CAS  PubMed  Google Scholar 

  • Shin YJ, Kim JH (2012) The role of EZH2 in the regulation of the activity of matrix metalloproteinases in prostate cancer cells. PLoS One 7:e30393

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H (2013) Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet 9:e1003439

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shirley M (2020) Epi proColon(®) for colorectal cancer screening: a profile of its use in the USA. Mol Diagn Ther 24:497–503

    CAS  PubMed  Google Scholar 

  • Shojaei F, Goodenow B, Lee G, Kabbinavar F, Gillings M (2021) HBI-8000, HUYABIO Lead clinical program, is a selective histone deacetylase inhibitor with therapeutic benefits in leukemia and in solid tumors. Front Oncol 11:768685

    CAS  PubMed  Google Scholar 

  • Shoji M, Ninomiya I, Makino I, Kinoshita J, Nakamura K, Oyama K, Nakagawara H, Fujita H, Tajima H, Takamura H, Kitagawa H, Fushida S, Harada S, Fujimura T, Ohta T (2012) Valproic acid, a histone deacetylase inhibitor, enhances radiosensitivity in esophageal squamous cell carcinoma. Int J Oncol 40:2140–2146

    CAS  PubMed  Google Scholar 

  • Siew-Gek Lee A, Rudduck-Sivaswaren C, Khun-Hong Lie D, Li-Ming Chua C, Tien SL, Morsberger L, Griffin CA (2004) Overlapping deletion regions at 11q23 in myelodysplastic syndrome and chronic lymphocytic leukemia, characterized by a novel BAC probe set. Cancer Genet Cytogenet 153:151–157

    CAS  PubMed  Google Scholar 

  • Silva G, Cardoso BA, Belo H, Almeida AM (2013) Vorinostat induces apoptosis and differentiation in myeloid malignancies: genetic and molecular mechanisms. PLoS One 8:e53766

    CAS  PubMed  PubMed Central  Google Scholar 

  • Silverman L (1994) Azacitidine (Aza C) in myelodysplastic syndromes (MDS), CALGB studies 8421 and 8921. Ann Hematol 68:A12

    Google Scholar 

  • Silverman L, Holland J, Ellison R (1990) Low dose continuous infusion azacytidine is an effective therapy for patients with myelodysplastic syndromes, a study of cancer and leukemia Group B. J Cancer Res Clin Oncol 116:816

    Google Scholar 

  • Silverman LR, Demakos EP, Peterson BL, Kornblith AB, Holland JC, Odchimar-Reissig R, Stone RM, Nelson D, Powell BL, DeCastro CM, Ellerton J, Larson RA, Schiffer CA, Holland JF (2002) Randomized controlled trial of azacitidine in patients with the myelodysplastic syndrome: a study of the cancer and leukemia group B. J Clin Oncol 20:2429–2440

    CAS  PubMed  Google Scholar 

  • Singh N, Baby D, Rajguru JP, Patil PB, Thakkannavar SS, Pujari VB (2019) Inflammation and cancer. Ann Afr Med 18:121–126

    PubMed  PubMed Central  Google Scholar 

  • Skaland I, Janssen EA, Gudlaugsson E, Klos J, Kjellevold KH, Søiland H, Baak JP (2007) Phosphohistone H3 expression has much stronger prognostic value than classical prognosticators in invasive lymph node-negative breast cancer patients less than 55 years of age. Mod Pathol 20:1307–1315

    CAS  PubMed  Google Scholar 

  • Slupianek A, Yerrum S, Safadi FF, Monroy MA (2010) The chromatin remodeling factor SRCAP modulates expression of prostate specific antigen and cellular proliferation in prostate cancer cells. J Cell Physiol 224:369–375

    CAS  PubMed  Google Scholar 

  • Smith E, Jones ME, Drew PA (2009) Quantitation of DNA methylation by melt curve analysis. BMC Cancer 9:123

    PubMed  PubMed Central  Google Scholar 

  • Smolewski P, Robak T (2017) The discovery and development of romidepsin for the treatment of T-cell lymphoma. Expert Opin Drug Discov 12:859–873

    CAS  PubMed  Google Scholar 

  • Soboleva TA, Parker BJ, Nekrasov M, Hart-Smith G, Tay YJ, Tng W-Q, Wilkins M, Ryan D, Tremethick DJ (2017) A new link between transcriptional initiation and pre-mRNA splicing: the RNA binding histone variant H2A.B. PLoS Genet 13:e1006633

    PubMed  PubMed Central  Google Scholar 

  • Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, Li Y, Chen CH, Zhang W, Jian X, Wang J, Zhang L, Looney TJ, Zhang B, Godley LA, Hicks LM, Lahn BT, Jin P, He C (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 29:68–72

    CAS  PubMed  Google Scholar 

  • Sotero-Caio CG, de Souza MJ, Cabral-de-Mello DC, Brasileiro-Vidal AC, Guerra M (2011) Phosphorylation of histone H3S10 in animal chromosomes: is there a uniform pattern? Cytogenet Genome Res 135:111–117

    CAS  PubMed  Google Scholar 

  • Spemann H, Mangold H (1924) über Induktion von Embryonalanlagen durch Implantation artfremder Organisatoren. Archiv für mikroskopische Anatomie und Entwicklungsmechanik 100:599–638

    Google Scholar 

  • Spiers H, Hannon E, Schalkwyk LC, Bray NJ, Mill J (2017) 5-hydroxymethylcytosine is highly dynamic across human fetal brain development. BMC Genomics 18:738

    PubMed  PubMed Central  Google Scholar 

  • Spineti PPM (2019) Biomarkers in heart failure. Arq Bras Cardiol 113:205–206

    PubMed  PubMed Central  Google Scholar 

  • Sporn JC, Kustatscher G, Hothorn T, Collado M, Serrano M, Muley T, Schnabel P, Ladurner AG (2009) Histone macroH2A isoforms predict the risk of lung cancer recurrence. Oncogene 28:3423–3428

    CAS  PubMed  Google Scholar 

  • Stasik S, Middeke JM, Kramer M, Röllig C, Krämer A, Scholl S, Hochhaus A, Crysandt M, Brümmendorf TH, Naumann R, Steffen B, Kunzmann V, Einsele H, Schaich M, Burchert A, Neubauer A, Schäfer-Eckart K, Schliemann C, Krause S, Herbst R, Hänel M, Frickhofen N, Noppeney R, Kaiser U, Baldus CD, Kaufmann M, Rácil Z, Platzbecker U, Berdel WE, Mayer J, Serve H, Müller-Tidow C, Ehninger G, Bornhäuser M, Schetelig J, Thiede C (2020) EZH2 mutations and impact on clinical outcome: an analysis in 1,604 patients with newly diagnosed acute myeloid leukemia. Haematologica 105:e228–e231

    PubMed  PubMed Central  Google Scholar 

  • Steensma DP (2009) Decitabine treatment of patients with higher-risk myelodysplastic syndromes. Leuk Res 33(Suppl 2):S12–S17

    CAS  PubMed  Google Scholar 

  • Steffan JS, Bodai L, Pallos J, Poelman M, McCampbell A, Apostol BL, Kazantsev A, Schmidt E, Zhu YZ, Greenwald M, Kurokawa R, Housman DE, Jackson GR, Marsh JL, Thompson LM (2001) Histone deacetylase inhibitors arrest polyglutamine-dependent neurodegeneration in Drosophila. Nature 413:739–743

    CAS  PubMed  Google Scholar 

  • Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45

    CAS  PubMed  Google Scholar 

  • Straining R, Eighmy W (2022) Tazemetostat: EZH2 Inhibitor. J Adv Pract Oncol 13:158–163

    PubMed  PubMed Central  Google Scholar 

  • Strauss J, Figg WD (2016) Using epigenetic therapy to overcome chemotherapy resistance. Anticancer Res 36:1–4

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stresemann C, Lyko F (2008) Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine. Int J Cancer 123:8–13

    CAS  PubMed  Google Scholar 

  • Strimbu K, Tavel JA (2010) What are biomarkers? Curr Opin HIV AIDS 5:463–466

    PubMed  PubMed Central  Google Scholar 

  • Sun W, Sun Y, Zhu M, Wang Z, Zhang H, Xin Y, Jiang G, Guo X, Zhang Z, Liu Y (2014a) The role of plasma cell-free DNA detection in predicting preoperative chemoradiotherapy response in rectal cancer patients. Oncol Rep 31:1466–1472

    CAS  PubMed  Google Scholar 

  • Sun W, Zang L, Shu Q, Li X (2014b) From development to diseases: the role of 5hmC in brain. Genomics 104:347–351

    CAS  PubMed  Google Scholar 

  • Sun XJ, Liu BY, Yan S, Jiang TH, Cheng HQ, Jiang HS, Cao Y, Mao AW (2015) MicroRNA-29a promotes pancreatic cancer growth by inhibiting Tristetraprolin. Cell Physiol Biochem 37:707–718

    CAS  PubMed  Google Scholar 

  • Sun L, Yao Y, Lu T, Shang Z, Zhan S, Shi W, Pan G, Zhu X, He S (2018a) DAB2IP downregulation enhances the proliferation and metastasis of human gastric cancer cells by Derepressing the ERK1/2 pathway. Gastroenterol Res Pract 2018:2968252

    PubMed  PubMed Central  Google Scholar 

  • Sun X, Xu C, Xiao G, Meng J, Wang J, Tang SC, Qin S, Du N, Li G, Ren H, Liu D (2018b) Breast cancer stem-like cells are sensitized to tamoxifen induction of self-renewal inhibition with enforced let-7c dependent on Wnt blocking. Int J Mol Med 41:1967–1975

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sung H, Siegel RL, Rosenberg PS, Jemal A (2019) Emerging cancer trends among young adults in the USA: analysis of a population-based cancer registry. Lancet Public Health 4:e137–e147

    PubMed  Google Scholar 

  • Sved J, Bird A (1990) The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci U S A 87:4692–4696

    CAS  PubMed  PubMed Central  Google Scholar 

  • Szenker E, Ray-Gallet D, Almouzni G (2011) The double face of the histone variant H3.3. Cell Res 21:421–434

    CAS  PubMed  PubMed Central  Google Scholar 

  • Szulwach KE, Li X, Li Y, Song CX, Han JW, Kim S, Namburi S, Hermetz K, Kim JJ, Rudd MK, Yoon YS, Ren B, He C, Jin P (2011) Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet 7:e1002154

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–935

    CAS  PubMed  PubMed Central  Google Scholar 

  • Takahashi H, Ogata H, Nishigaki R, Broide DH, Karin M (2010) Tobacco smoke promotes lung tumorigenesis by triggering IKKbeta- and JNK1-dependent inflammation. Cancer Cell 17:89–97

    CAS  PubMed  PubMed Central  Google Scholar 

  • Talbert PB, Henikoff S (2010) Histone variants–ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol 11:264–275

    CAS  PubMed  Google Scholar 

  • Talbert PB, Henikoff S (2021) Histone variants at a glance. J Cell Sci 134:jcs244749

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tamaru H, Selker EU (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414:277–283

    CAS  PubMed  Google Scholar 

  • Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146:1016–1028

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tang S, Huang X, Wang X, Zhou X, Huang H, Qin L, Tao H, Wang Q, Tao Y (2020) Vital and distinct roles of H2A.Z isoforms in hepatocellular carcinoma. Onco Targets Ther 13:4319–4337

    CAS  PubMed  PubMed Central  Google Scholar 

  • Taryma-Leśniak O, Sokolowska KE, Wojdacz TK (2020) Current status of development of methylation biomarkers for in vitro diagnostic IVD applications. Clin Epigenetics 12:100

    PubMed  PubMed Central  Google Scholar 

  • Taunton J, Hassig CA, Schreiber SL (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272:408–411

    CAS  PubMed  Google Scholar 

  • Tepus M, Yau TO (2020) Non-invasive colorectal cancer screening: An overview. Gastrointest Tumors 7:62–73

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tiffon C, Adams J, van der Fits L, Wen S, Townsend P, Ganesan A, Hodges E, Vermeer M, Packham G (2011) The histone deacetylase inhibitors vorinostat and romidepsin downmodulate IL-10 expression in cutaneous T-cell lymphoma cells. Br J Pharmacol 162:1590–1602

    CAS  PubMed  PubMed Central  Google Scholar 

  • Titze-de-Almeida SS, Brandão PRP, Faber I, Titze-de-Almeida R (2020) Leading RNA interference therapeutics part 1: silencing hereditary transthyretin amyloidosis, with a focus on Patisiran. Mol Diagn Ther 24:49–59

    CAS  PubMed  Google Scholar 

  • Tolstorukov MY, Goldman Joseph A, Gilbert C, Ogryzko V, Kingston Robert E, Park Peter J (2012) Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. Mol Cell 47:596–607

    CAS  PubMed  PubMed Central  Google Scholar 

  • Torrezan GT, Ferreira EN, Nakahata AM, Barros BD, Castro MT, Correa BR, Krepischi AC, Olivieri EH, Cunha IW, Tabori U, Grundy PE, Costa CM, de Camargo B, Galante PA, Carraro DM (2014) Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour. Nat Commun 5:4039

    CAS  PubMed  Google Scholar 

  • Trang P, Medina PP, Wiggins JF, Ruffino L, Kelnar K, Omotola M, Homer R, Brown D, Bader AG, Weidhaas JB, Slack FJ (2010) Regression of murine lung tumors by the let-7 microRNA. Oncogene 29:1580–1587

    CAS  PubMed  Google Scholar 

  • Trosko JE, Upham BL (2005) The emperor wears no clothes in the field of carcinogen risk assessment: ignored concepts in cancer risk assessment. Mutagenesis 20:81–92

    CAS  PubMed  Google Scholar 

  • Trovato M, Patil V, Gehre M, Noh KM (2020) Histone variant H3.3 mutations in defining the chromatin function in mammals. Cell 9:2716

    CAS  Google Scholar 

  • Tsai C-H, Chen Y-J, Yu C-J, Tzeng S-R, Wu I-C, Kuo W-H, Lin M-C, Chan N-L, Wu K-J, Teng S-C (2016) SMYD3-mediated H2A.Z.1 methylation promotes cell cycle and cancer proliferation. Cancer Res 76:6043–6053

    CAS  PubMed  Google Scholar 

  • Turinetto V, Giachino C (2015) Multiple facets of histone variant H2AX: a DNA double-strand-break marker with several biological functions. Nucleic Acids Res 43:2489–2498

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tzao C, Tung HJ, Jin JS, Sun GH, Hsu HS, Chen BH, Yu CP, Lee SC (2009) Prognostic significance of global histone modifications in resected squamous cell carcinoma of the esophagus. Mod Pathol 22:252–260

    CAS  PubMed  Google Scholar 

  • Ueda H, Nakajima H, Hori Y, Fujita T, Nishimura M, Goto T, Okuhara M (1994) FR901228, a novel antitumor bicyclic depsipeptide produced by Chromobacterium violaceum no. 968. I. Taxonomy, fermentation, isolation, physico-chemical and biological properties, and antitumor activity. J Antibiot (Tokyo) 47:301–310

    CAS  PubMed  Google Scholar 

  • Uehara N, Yoshizawa K, Tsubura A (2012) Vorinostat enhances protein stability of p27 and p21 through negative regulation of Skp2 and Cks1 in human breast cancer cells. Oncol Rep 28:105–110

    CAS  PubMed  Google Scholar 

  • Uemura N, Okamoto S, Yamamoto S, Matsumura N, Yamaguchi S, Yamakido M, Taniyama K, Sasaki N, Schlemper RJ (2001) Helicobacter pylori infection and the development of gastric cancer. N Engl J Med 345:784–789

    CAS  PubMed  Google Scholar 

  • Ulirsch J, Fan C, Knafl G, Wu MJ, Coleman B, Perou CM, Swift-Scanlan T (2013) Vimentin DNA methylation predicts survival in breast cancer. Breast Cancer Res Treat 137:383–396

    CAS  PubMed  Google Scholar 

  • Vaisvila R, Ponnaluri VKC, Sun Z, Langhorst BW, Saleh L, Guan S, Dai N, Campbell MA, Sexton BS, Marks K, Samaranayake M, Samuelson JC, Church HE, Tamanaha E, Corrêa IR, Pradhan S, Dimalanta ET, Evans TC, Williams L, Davis TB (2021) Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res 31:1280–1289

    PubMed  PubMed Central  Google Scholar 

  • Valdés-Mora F, Song JZ, Statham AL, Strbenac D, Robinson MD, Nair SS, Patterson KI, Tremethick DJ, Stirzaker C, Clark SJ (2012) Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer. Genome Res 22:307–321

    PubMed  PubMed Central  Google Scholar 

  • van Daal A, White EM, Gorovsky MA, Elgin SC (1988) Drosophila has a single copy of the gene encoding a highly conserved histone H2A variant of the H2A.F/Z type. Nucleic Acids Res 16:7487–7497

    PubMed  PubMed Central  Google Scholar 

  • VanderMolen KM, McCulloch W, Pearce CJ, Oberlies NH (2011) Romidepsin (Istodax, NSC 630176, FR901228, FK228, depsipeptide): a natural product recently approved for cutaneous T-cell lymphoma. J Antibiot (Tokyo) 64:525–531

    CAS  PubMed  Google Scholar 

  • Vardabasso C, Hasson D, Ratnakumar K, Chung CY, Duarte LF, Bernstein E (2014) Histone variants: emerging players in cancer biology. Cell Mol Life Sci 71:379–404

    CAS  PubMed  Google Scholar 

  • Vardabasso C, Gaspar-Maia A, Hasson D, Pünzeler S, Valle-Garcia D, Straub T, Keilhauer EC, Strub T, Dong J, Panda T, Chung CY, Yao JL, Singh R, Segura MF, Fontanals-Cirera B, Verma A, Mann M, Hernando E, Hake SB, Bernstein E (2015) Histone variant H2A.Z.2 mediates proliferation and drug sensitivity of malignant melanoma. Mol Cell 59:75–88

    CAS  PubMed  PubMed Central  Google Scholar 

  • Varvara PV, Karaolanis G, Valavanis C, Stanc G, Tzaida O, Trihia H, Patapis P, Dimitroulis D, Perrea D (2019) Gamma-H2AX: a potential biomarker in breast cancer. Tumour Biol 41:1010428319878536

    CAS  PubMed  Google Scholar 

  • Vavouri T, Lehner B (2012) Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Genome Biol 13:R110

    PubMed  PubMed Central  Google Scholar 

  • Verma M (2012) Epigenetic biomarkers in cancer epidemiology. Methods Mol Biol 863:467–480

    CAS  PubMed  Google Scholar 

  • Veronezi GM, Felisbino MB, Gatti MS, Mello ML, Vidal BC (2017) DNA methylation changes in Valproic acid-treated HeLa cells as assessed by image analysis, immunofluorescence and vibrational microspectroscopy. PLoS One 12:e0170740

    PubMed  PubMed Central  Google Scholar 

  • Virchow R (1863) Cellular pathology as based upon physiological and pathological histology

    Google Scholar 

  • Vogler C, Huber C, Waldmann T, Ettig R, Braun L, Izzo A, Daujat S, Chassignet I, Lopez-Contreras AJ, Fernandez-Capetillo O, Dundr M, Rippe K, Längst G, Schneider R (2010) Histone H2A C-terminus regulates chromatin dynamics, remodeling, and histone H1 binding. PLoS Genet 6:e1001234

    PubMed  PubMed Central  Google Scholar 

  • Voigt P, Tee WW, Reinberg D (2013) A double take on bivalent promoters. Genes Dev 27:1318–1338

    CAS  PubMed  PubMed Central  Google Scholar 

  • Waddington CH (1940) Organisers and Genes. The Cambridge University Press, Cambridge

    Google Scholar 

  • Waddington CH (1942) The epigenotype. Endeavour 1:18–20

    Google Scholar 

  • Waddington CH (2012) The epigenotype. Int J Epidemiol 41:10–13

    CAS  PubMed  Google Scholar 

  • Waddington CH, Needham J, Needham DM (1933) Physico-chemical experiments on the amphibian Organiser. Nature 132:239–239

    CAS  Google Scholar 

  • Waddington CH, Needham J, Nowinski WW, Needham DM, Lemberg R (1934) Active principle of the amphibian organisation Centre. Nature 134:103–103

    CAS  Google Scholar 

  • Wagner RN, Piñón Hofbauer J, Wally V, Kofler B, Schmuth M, De Rosa L, De Luca M, Bauer JW (2021) Epigenetic and metabolic regulation of epidermal homeostasis. Exp Dermatol 30:1009–1022

    PubMed  PubMed Central  Google Scholar 

  • Walser JC, Furano AV (2010) The mutational spectrum of non-CpG DNA varies with CpG content. Genome Res 20:875–882

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang J, Tang J, Lai M, Zhang H (2014a) 5-Hydroxymethylcytosine and disease. Mutat Res Rev Mutat Res 762:167–175

    CAS  PubMed  Google Scholar 

  • Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C (2014b) N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505:117–120

    PubMed  Google Scholar 

  • Wang J, Zhu X, Hu J, He G, Li X, Wu P, Ren X, Wang F, Liao W, Liang L, Ding Y (2015a) The positive feedback between snail and DAB2IP regulates EMT, invasion and metastasis in colorectal cancer. Oncotarget 6:27427–27439

    PubMed  PubMed Central  Google Scholar 

  • Wang T, Wang G, Hao D, Liu X, Wang D, Ning N, Li X (2015b) Aberrant regulation of the LIN28A/LIN28B and let-7 loop in human malignant tumors and its effects on the hallmarks of cancer. Mol Cancer 14:125

    PubMed  PubMed Central  Google Scholar 

  • Wang T, Kong S, Tao M, Ju S (2020a) The potential role of RNA N6-methyladenosine in cancer progression. Mol Cancer 19:88

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Z, Du M, Yuan Q, Guo Y, Hutchinson JN, Su L, Zheng Y, Wang J, Mucci LA, Lin X, Hou L, Christiani DC (2020b) Epigenomic analysis of 5-hydroxymethylcytosine (5hmC) reveals novel DNA methylation markers for lung cancers. Neoplasia 22:154–161

    CAS  PubMed  PubMed Central  Google Scholar 

  • Watanabe T, Tada M, Nagai H, Sasaki S, Nakao M (1998) Helicobacter pylori infection induces gastric cancer in mongolian gerbils. Gastroenterology 115:642–648

    CAS  PubMed  Google Scholar 

  • Wei CM, Gershowitz A, Moss B (1975) Methylated nucleotides block 5′-terminus of HeLa cell messenger RNA. Cell 4:379–386

    CAS  PubMed  Google Scholar 

  • Wei CM, Gershowitz A, Moss B (1976) 5′-terminal and internal methylated nucleotide sequences in HeLa cell mRNA. Biochemistry 15:397–401

    CAS  PubMed  Google Scholar 

  • Wei Y, Mizzen CA, Cook RG, Gorovsky MA, Allis CD (1998) Phosphorylation of histone H3 at serine 10 is correlated with chromosome condensation during mitosis and meiosis in Tetrahymena. Proc Natl Acad Sci 95:7480–7484

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wei JW, Huang K, Yang C, Kang CS (2017) Non-coding RNAs as regulators in epigenetics (review). Oncol Rep 37:3–9

    PubMed  Google Scholar 

  • Weinberg DN, Papillon-Cavanagh S, Chen H, Yue Y, Chen X, Rajagopalan KN, Horth C, McGuire JT, Xu X, Nikbakht H, Lemiesz AE, Marchione DM, Marunde MR, Meiners MJ, Cheek MA, Keogh MC, Bareke E, Djedid A, Harutyunyan AS, Jabado N, Garcia BA, Li H, Allis CD, Majewski J, Lu C (2019) The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape. Nature 573:281–286

    CAS  PubMed  PubMed Central  Google Scholar 

  • Weinhold B (2006) Epigenetics: the science of change. Environ Health Perspect 114:A160–A167

    PubMed  PubMed Central  Google Scholar 

  • Weisenberger DJ, Liang G, Lenz HJ (2018) DNA methylation aberrancies delineate clinically distinct subsets of colorectal cancer and provide novel targets for epigenetic therapies. Oncogene 37:566–577

    CAS  PubMed  Google Scholar 

  • Wen D, Banaszynski LA, Liu Y, Geng F, Noh KM, Xiang J, Elemento O, Rosenwaks Z, Allis CD, Rafii S (2014a) Histone variant H3.3 is an essential maternal factor for oocyte reprogramming. Proc Natl Acad Sci U S A 111:7325–7330

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wen H, Li Y, Xi Y, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W, Li H, Shi X (2014b) ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature 508:263–268

    CAS  PubMed  PubMed Central  Google Scholar 

  • West MH, Bonner WM (1980) Histone 2A, a heteromorphous family of eight protein species. Biochemistry 19:3238–3245

    CAS  PubMed  Google Scholar 

  • Wigle TJ (2011) Promoting illiteracy in epigenetics: an emerging therapeutic strategy. Curr Chem Genomics 5:48–50

    PubMed  PubMed Central  Google Scholar 

  • Wijermans P, Lübbert M, Verhoef G, Bosly A, Ravoet C, Andre M, Ferrant A (2000) Low-dose 5-aza-2′-deoxycytidine, a DNA hypomethylating agent, for the treatment of high-risk myelodysplastic syndrome: a multicenter phase II study in elderly patients. J Clin Oncol 18:956–962

    CAS  PubMed  Google Scholar 

  • Wilkins OM, Johnson KC, Houseman EA, King JE, Marsit CJ, Christensen BC (2020) Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue. Epigenetics 15:398–418

    PubMed  Google Scholar 

  • Wolin KY, Carson K, Colditz GA (2010) Obesity and cancer. Oncologist 15:556–565

    PubMed  PubMed Central  Google Scholar 

  • Wratting D, Thistlethwaite A, Harris M, Zeef LA, Millar CB (2012) A conserved function for the H2A.Z C terminus. J Biol Chem 287:19148–19157

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu G, Broniscer A, McEachron TA, Lu C, Paugh BS, Becksfort J, Qu C, Ding L, Huether R, Parker M, Zhang J, Gajjar A, Dyer MA, Mullighan CG, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Ellison DW, Zhang J, Baker SJ (2012) Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat Genet 44:251–253

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu C, Du X, Tang L, Wu J, Zhao W, Guo X, Liu D, Hu W, Helmby H, Chen G, Wang Z (2020) Schistosoma japonicum SjE16.7 protein promotes tumor development via the receptor for advanced glycation end products (RAGE). Front Immunol 11:1767

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wyatt GR, Cohen SS (1952) A new Pyrimidine Base from bacteriophage nucleic acids. Nature 170:1072–1073

    CAS  PubMed  Google Scholar 

  • Wynder EL, Hoffmann D (1976) Tobacco and tobacco smoke. Semin Oncol 3:5–15

    CAS  PubMed  Google Scholar 

  • Xia J, Han L, Zhao Z (2012) Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. BMC Genomics 13(Suppl 8):S7

    PubMed  PubMed Central  Google Scholar 

  • Xiao C, Srinivasan L, Calado DP, Patterson HC, Zhang B, Wang J, Henderson JM, Kutok JL, Rajewsky K (2008) Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes. Nat Immunol 9:405–414

    CAS  PubMed  PubMed Central  Google Scholar 

  • Xiao W, Adhikari S, Dahal U, Chen YS, Hao YJ, Sun BF, Sun HY, Li A, Ping XL, Lai WY, Wang X, Ma HL, Huang CM, Yang Y, Huang N, Jiang GB, Wang HL, Zhou Q, Wang XJ, Zhao YL, Yang YG (2016) Nuclear m(6)a reader YTHDC1 regulates mRNA splicing. Mol Cell 61:507–519

    CAS  PubMed  Google Scholar 

  • Xu T, Gao H (2020) Hydroxymethylation and tumors: can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment? Hum Genomics 14:15

    PubMed  PubMed Central  Google Scholar 

  • Yan KS, Lin CY, Liao TW, Peng CM, Lee SC, Liu YJ, Chan WP, Chou RH (2017) EZH2 in cancer progression and potential application in cancer therapy: a friend or foe? Int J Mol Sci 18:1172

    PubMed  PubMed Central  Google Scholar 

  • Yang HD, Kim PJ, Eun JW, Shen Q, Kim HS, Shin WC, Ahn YM, Park WS, Lee JY, Nam SW (2016) Oncogenic potential of histone-variant H2A.Z.1 and its regulatory role in cell cycle and epithelial-mesenchymal transition in liver cancer. Oncotarget 7:11412–11423

    PubMed  PubMed Central  Google Scholar 

  • Yang SX, Polley EC, Nguyen D (2017) Association of γH2AX at diagnosis with chemotherapy outcome in patients with breast cancer. Theranostics 7:945–951

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Y, Zeng C, Lu X, Song Y, Nie J, Ran R, Zhang Z, He C, Zhang W, Liu SM (2019) 5-Hydroxymethylcytosines in circulating cell-free DNA reveal vascular complications of type 2 diabetes. Clin Chem 65:1414–1425

    CAS  PubMed  Google Scholar 

  • Yang YL, Chang YH, Li CJ, Huang YH, Tsai MC, Chu PY, Lin HY (2021) New insights into the role of miR-29a in hepatocellular carcinoma: implications in mechanisms and Theragnostics. J Pers Med 11:219

    PubMed  PubMed Central  Google Scholar 

  • Ye C, Li L (2014) 5-hydroxymethylcytosine: a new insight into epigenetics in cancer. Cancer Biol Ther 15:10–15

    CAS  PubMed  Google Scholar 

  • Yildirim O, Li R, Hung JH, Chen PB, Dong X, Ee LS, Weng Z, Rando OJ, Fazzio TG (2011) Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147:1498–1510

    CAS  PubMed  PubMed Central  Google Scholar 

  • You JS, Jones PA (2012) Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 22:9–20

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yu W, Zhang L, Wei Q, Shao A (2019) O(6)-Methylguanine-DNA methyltransferase (MGMT): challenges and new opportunities in glioma chemotherapy. Front Oncol 9:1547

    PubMed  Google Scholar 

  • Yuan EF, Yang Y, Cheng L, Deng X, Chen SM, Zhou X, Liu SM (2019) Hyperglycemia affects global 5-methylcytosine and 5-hydroxymethylcytosine in blood genomic DNA through upregulation of SIRT6 and TETs. Clin Epigenetics 11:63

    PubMed  PubMed Central  Google Scholar 

  • Zaina S, Pérez-Luque EL, Lund G (2010) Genetics talks to epigenetics? The interplay between sequence variants and chromatin structure. Curr Genomics 11:359–367

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zampieri M, Bacalini MG, Barchetta I, Scalea S, Cimini FA, Bertoccini L, Tagliatesta S, De Matteis G, Zardo G, Cavallo MG, Reale A (2021) Increased PARylation impacts the DNA methylation process in type 2 diabetes mellitus. Clin Epigenetics 13:114

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Jeltsch A (2010) The application of next generation sequencing in DNA methylation analysis. Genes (Basel) 1:85–101

    PubMed  Google Scholar 

  • Zhang C, Richon V, Ni X, Talpur R, Duvic M (2005) Selective induction of apoptosis by histone deacetylase inhibitor SAHA in cutaneous T-cell lymphoma cells: relevance to mechanism of therapeutic action. J Invest Dermatol 125:1045–1052

    CAS  PubMed  Google Scholar 

  • Zhang Y, Wu K, Shao Y, Sui F, Yang Q, Shi B, Hou P, Ji M (2016) Decreased 5-Hydroxymethylcytosine (5-hmC) predicts poor prognosis in early-stage laryngeal squamous cell carcinoma. Am J Cancer Res 6:1089–1098

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang P, Wu W, Chen Q, Chen M (2019a) Non-coding RNAs and their integrated networks. J Integr Bioinform 16:20190027

    PubMed  PubMed Central  Google Scholar 

  • Zhang Q, Han Q, Zi J, Ma J, Song H, Tian Y, McGrath M, Song C, Ge Z (2019b) Mutations in EZH2 are associated with poor prognosis for patients with myeloid neoplasms. Genes Dis 6:276–281

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang MM, Bahal R, Rasmussen TP, Manautou JE, Zhong XB (2021a) The growth of siRNA-based therapeutics: updated clinical studies. Biochem Pharmacol 189:114432

    CAS  PubMed  Google Scholar 

  • Zhang Y, Geng X, Xu J, Li Q, Hao L, Zeng Z, Xiao M, Song J, Liu F, Fang C, Wang H (2021b) Identification and characterization of N6-methyladenosine modification of circRNAs in glioblastoma. J Cell Mol Med 25:7204–7217

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao Z, Han L (2009) CpG islands: algorithms and applications in methylation studies. Biochem Biophys Res Commun 382:643–645

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou J, Fan JY, Rangasamy D, Tremethick DJ (2007) The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression. Nat Struct Mol Biol 14:1070–1076

    CAS  PubMed  Google Scholar 

  • Zhu ZM, Huo FC, Pei DS (2020) Function and evolution of RNA N6-methyladenosine modification. Int J Biol Sci 16:1929–1940

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zou C, He Q, Feng Y, Chen M, Zhang D (2022) A m(6)Avalue predictive of prostate cancer stemness, tumor immune landscape and immunotherapy response. NAR. Cancer 4:zcac010

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Richard A. Stein .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Stein, R.A., Deverakonda, A.N. (2022). Epigenetics in Cancer Biology. In: Rezaei, N. (eds) Cancer Research: An Interdisciplinary Approach. Interdisciplinary Cancer Research, vol 1. Springer, Cham. https://doi.org/10.1007/16833_2022_86

Download citation

Publish with us

Policies and ethics