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Long Non-Coding RNAs Profiling Using Microarray in Papillary Thyroid Carcinoma

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Papillary Thyroid Carcinoma

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2534))

Abstract

Long non-coding RNAs (lncRNAs) have been implicated in various cancers, including papillary thyroid carcinomas (PTCs). Genome-wide analysis (GWAS) of lncRNAs expression in PTC samples exhibited up and down regulation of lncRNAs, thus, acting as tumor promoting oncogenes or tumor suppressors in the pathogenesis of PTC by interacting with target genes. For example, lncRNAs such as HOTAIR, NEAT1, MALAT1, FAL1, HOXD-AS1, etc. are overexpressed in PTC in comparison to that of non-cancerous thyroid tissues, which stimulate the pathogenesis of PTC. On the other hand, lncRNAs such as MEG3, CASC2, PANDAR, LINC00271, NAMA, PTCSC3, etc. are down regulated in PTC tissues when compared to that of non-cancerous thyroid samples, suppressing formation of PTC. Also, several lncRNAs such as BANCR acts as oncogenic or tumor suppressor in PTC formation depending on which they are interacting with. In addition, lncRNAs expression in patients with PTC associated with clinicopathological parameters such as distance metastasis, lymph node metastasis, tumor size, pathological stage, and response to therapy. Thus, lncRNAs profiles could have the potential to be used as prognostic or predictive biomarker in patients with PTC. Therefore, we describe the microarray method to examine lncRNAs expression in PTC tissue samples, which could facilitate better management of patients with PTC. Furthermore, this method could be fabricated to examine lncRNAs expression in other biological and/or clinical samples.

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References

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

    Article  CAS  Google Scholar 

  2. Hombach S, Kretz M (2016) Non-coding RNAs: classification, biology and functioning. Adv Exp Med Biol 937:3–17

    Article  CAS  PubMed  Google Scholar 

  3. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Huarte M (2015) The emerging role of lncRNAs in cancer. Nat Med 21:1253–1261

    Article  CAS  PubMed  Google Scholar 

  5. Lan X, Zhang H, Wang Z, Dong W, Sun W, Shao L, Zhang T, Zhang D (2015) Genome-wide analysis of long noncoding RNA expression profile in papillary thyroid carcinoma. Gene 569:109–117

    Article  CAS  PubMed  Google Scholar 

  6. Liao D, Lv G, Wang T, Min J, Wang Y, Liu S (2018) Prognostic value of long non-coding RNA BLACAT1 in patients with papillary thyroid carcinoma. Cancer Cell Int 18:47

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Yang M, Tian J, Guo X, Yang Y, Guan R, Qiu M, Li Y, Sun X, Zhen Y, Zhang Y, Chen C, Li Y, Fang H (2016) Long noncoding RNA are aberrantly expressed in human papillary thyroid carcinoma. Oncol Lett 12:544–552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Wang Q, Yang H, Wu L, Yao J, Meng X, Jiang H, Xiao C, Wu F (2016) Identification of specific long non-coding RNA expression: profile and analysis of association with clinicopathologic characteristics and BRAF mutation in papillary thyroid cancer. Thyroid 26:1719–1732

    Article  CAS  PubMed  Google Scholar 

  9. Liyanarachchi S, Li W, Yan P, Bundschuh R, Brock P, Senter L, Ringel MD, de la Chapelle A, He H (2016) Genome-wide expression screening discloses long noncoding RNAs involved in thyroid carcinogenesis. J Clin Endocrinol Metab 101:4005–4013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Xu B, Shao Q, Xie K, Zhang Y, Dong T, Xia Y, Tang W (2016) The long non-coding RNA ENST00000537266 and ENST00000426615 influence papillary thyroid cancer cell proliferation and motility. Cell Physiol Biochem 38:368–378

    Article  CAS  PubMed  Google Scholar 

  11. Li T, Yang XD, Ye CX, Shen ZL, Yang Y, Wang B, Guo P, Gao ZD, Ye YJ, Jiang KW, Wang S (2017) Long noncoding RNA HIT000218960 promotes papillary thyroid cancer oncogenesis and tumor progression by upregulating the expression of high mobility group AT-hook 2 (HMGA2) gene. Cell Cycle 16:224–231

    Article  CAS  PubMed  Google Scholar 

  12. Braconi C, Kogure T, Valeri N, Huang N, Nuovo G, Costinean S, Negrini M, Miotto E, Croce CM, Patel T (2011) microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene 30:4750–4756

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Do H, Kim W (2018) Roles of oncogenic long non-coding RNAs in cancer development. Genomics Inform 16:e18

    Article  PubMed  PubMed Central  Google Scholar 

  14. Sun W, Lan X, Zhang H, Wang Z, Dong W, He L, Zhang T, Zhang P, Liu J, Qin Y (2018) NEAT1_2 functions as a competing endogenous RNA to regulate ATAD2 expression by sponging microRNA-106b-5p in papillary thyroid cancer. Cell Death Dis 9:380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Zhu H, Lv Z, An C, Shi M, Pan W, Zhou L, Yang W, Yang M (2016) Onco-lncRNA HOTAIR and its functional genetic variants in papillary thyroid carcinoma. Sci Rep 6:31969

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Di W, Li Q, Shen W, Guo H, Zhao S (2017) The long non-coding RNA HOTAIR promotes thyroid cancer cell growth, invasion and migration through the miR-1-CCND2 axis. Am J Cancer Res 7:1298–1309

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Chu R, van Hasselt A, Vlantis AC, Ng EK, Liu SY, Fan MD, Ng SK, Chan AB, Liu Z, Li XY, Chen GG (2014) The cross-talk between estrogen receptor and peroxisome proliferator-activated receptor gamma in thyroid cancer. Cancer 120:142–153

    Article  CAS  PubMed  Google Scholar 

  18. Guzel E, Okyay TM, Yalcinkaya B, Karacaoglu S, Gocmen M, Akcakuyu MH (2019) Tumor suppressor and oncogenic role of long non-coding RNAs in cancer. North Clin Istanb 7:81–86

    PubMed  PubMed Central  Google Scholar 

  19. Yoon H, He H, Nagy R, Davuluri R, Suster S, Schoenberg D, Pellegata N, Chapelle Ade L (2007) Identification of a novel noncoding RNA gene, NAMA, that is downregulated in papillary thyroid carcinoma with BRAF mutation and associated with growth arrest. Int J Cancer 121:767–775

    Article  CAS  PubMed  Google Scholar 

  20. Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, Davuluri RV, Nagy R, de la Chapelle A (2012) The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proc Natl Acad Sci U S A 109:8646–8651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Wang Y, He H, Li W, Phay J, Shen R, Yu L, Hancioglu B, de la Chapelle A (2017) MYH9 binds to lncRNA gene PTCSC2 and regulates FOXE1 in the 9q22 thyroid cancer risk locus. Proc Natl Acad Sci U S A 114:474–479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Wang C, Yan G, Zhang Y, Jia X, Bu P (2015) Long non-coding RNA MEG3 suppresses migration and invasion of thyroid carcinoma by targeting of Rac1. Neoplasma 62:541–549

    Article  CAS  PubMed  Google Scholar 

  23. Ma B, Liao T, Wen D, Dong C, Zhou L, Yang S, Wang Y, Ji Q (2016) Long intergenic non-coding RNA 271 is predictive of a poorer prognosis of papillary thyroid cancer. Sci Rep 6:36973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Murugan AK, Munirajan AK, Alzahrani AS (2018) Long noncoding RNAs: emerging players in thyroid cancer pathogenesis. Endocr Relat Cancer 25:R59–R82

    Article  CAS  PubMed  Google Scholar 

  25. Zheng H, Wang M, Jiang L, Chu H, Hu J, Ning J, Li B, Wang D, Xu J (2016) BRAF-activated long noncoding RNA modulates papillary thyroid carcinoma cell proliferation through regulating thyroid stimulating hormone receptor. Cancer Res Treat 48:698–707

    Article  CAS  PubMed  Google Scholar 

  26. Liao T, Qu N, Shi RL, Guo K, Ma B, Cao YM, Xiang J, Lu ZW, Zhu YX, Li DS, Ji QH (2017) BRAF-activated LncRNA functions as a tumor suppressor in papillary thyroid cancer. Oncotarget 8:238–247

    Article  PubMed  Google Scholar 

  27. Zhang Y, Yu S, Jiang L, Wang X, Song X (2017) HOTAIR is a promising novel biomarker in patients with thyroid cancer. Exp Ther Med 13:2274–2278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Li HM, Yang H, Wen DY, Luo YH, Liang CY, Pan DH, Ma W, Chen G, He Y, Chen JQ (2017) Overexpression of LncRNA HOTAIR is associated with poor prognosis in thyroid carcinoma: a study based on TCGA and GEO Data. Horm Metab Res 49:388–399

    Article  CAS  PubMed  Google Scholar 

  29. Xia S, Wang C, Ni X, Ni Z, Dong Y, Zhan W (2017) NONHSAT076754 aids ultrasonography in predicting lymph node metastasis and promotes migration and invasion of papillary thyroid cancer cells. Oncotarget 8:2293–2306

    Article  PubMed  Google Scholar 

  30. Li Q, Shen W, Li X, Zhang L, Jin X (2017) The lncRNA n340790 accelerates carcinogenesis of thyroid cancer by regulating miR-1254. Am J Transl Res 9:2181–2194

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Goedert L, Plaça JR, Fuziwara CS, Machado MCR, Plaça DR, Almeida PP, Sanches TP, Santos JFD, Corveloni AC, Pereira IEG, de Castro MM, Kimura ET, Silva WA Jr, Espreafico EM (2017) Identification of long noncoding RNAs deregulated in papillary thyroid cancer and correlated with BRAFV600E Mutation by bioinformatics integrative analysis. Sci Rep 7:1662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Du Y, Xia W, Zhang J, Wan D, Yang Z, Li X (2017) Comprehensive analysis of long noncoding RNA-mRNA co-expression patterns in thyroid cancer. Mol BioSyst 13:2107–2115

    Article  CAS  PubMed  Google Scholar 

  33. Zhang R, Hardin H, Huang W, Chen J, Asioli S, Righi A, Maletta F, Sapino A, Lloyd RV (2017) MALAT1 long non-coding RNA expression in thyroid tissues: analysis by in situ hybridization and real-time PCR. Endocr Pathol 28:7–12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Sun W, Lan X, Wang Z, Dong W, He L, Zhang T, Zhang H (2016) Overexpression of long non-coding RNA NR_036575.1 contributes to the proliferation and migration of papillary thyroid cancer. Med Oncol 33:102

    Article  CAS  PubMed  Google Scholar 

  35. Kim D, Lee WK, Jeong S, Seol MY, Kim H, Kim KS, Lee EJ, Lee J, Jo YS (2016) Upregulation of long noncoding RNA LOC100507661 promotes tumor aggressiveness in thyroid cancer. Mol Cell Endocrinol 431:36–45

    Article  CAS  PubMed  Google Scholar 

  36. Jeong S, Lee J, Kim D, Seol MY, Lee WK, Jeong JJ, Nam KH, Jung SG, Shin DY, Lee EJ, Chung WY, Jo YS (2016) Relationship of focally amplified long noncoding on chromosome 1 (FAL1) lncRNA with E2F transcription factors in thyroid cancer. Medicine (Baltimore) 95:e2592

    Article  CAS  PubMed Central  Google Scholar 

  37. Xiong X, Zhu H, Chen X (2017) Low expression of long noncoding RNA CASC2 indicates a poor prognosis and promotes tumorigenesis in thyroid carcinoma. Biomed Pharmacother 93:391–397

    Article  CAS  PubMed  Google Scholar 

  38. Li Z, Gao B, Hao S, Tian W, Chen Y, Wang L, Zhang X, Luo D (2017) Knockdown of lncRNA-PANDAR suppresses the proliferation, cell cycle and promotes apoptosis in thyroid cancer cells. EXCLI J 16:354–362

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Zhang D, Liu X, Wei B, Qiao G, Jiang T, Chen Z (2017) Plasma lncRNA GAS8-AS1 as a potential biomarker of papillary thyroid carcinoma in Chinese patients. Int J Endocrinol 2017:2645904

    PubMed  PubMed Central  Google Scholar 

  40. Pan W, Zhou L, Ge M, Zhang B, Yang X, Xiong X, Fu G, Zhang J, Nie X, Li H, Tang X, Wei J, Shao M, Zheng J, Yuan Q, Tan W, Wu C, Yang M, Lin D (2016) Whole exome sequencing identifies lncRNA GAS8-AS1 and LPAR4 as novel papillary thyroid carcinoma driver alternations. Hum Mol Genet 25:1875–1884

    Article  CAS  PubMed  Google Scholar 

  41. Lan X, Sun W, Zhang P, He L, Dong W, Wang Z, Liu S, Zhang H (2016) Downregulation of long noncoding RNA NONHSAT037832 in papillary thyroid carcinoma and its clinical significance. Tumour Biol 37:6117–6123

    Article  CAS  PubMed  Google Scholar 

  42. He H, Li W, Liyanarachchi S, Jendrzejewski J, Srinivas M, Davuluri RV, Nagy R, de la Chapelle A (2015) Genetic predisposition to papillary thyroid carcinoma: involvement of FOXE1, TSHR, and a novel lincRNA gene, PTCSC2. J Clin Endocrinol Metab 100:E164–E172

    Article  CAS  PubMed  Google Scholar 

  43. He H, Nagy R, Liyanarachchi S, Jiao H, Li W, Suster S, Kere J, de la Chapelle A (2009) A susceptibility locus for papillary thyroid carcinoma on chromosome 8q24. Cancer Res 69:625–631

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh

    Farhadul Islam

  2. Cancer Molecular Pathology of School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia

    Farhadul Islam & Alfred K. Lam

  3. Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China

    Yaoqi Zhou

  4. Pathology Queensland, Gold Coast University Hospital, Southport, QLD, Australia

    Alfred K. Lam

  5. Faculty of Medicine, University of Queensland, Herston, QLD, Australia

    Alfred K. Lam

Authors
  1. Farhadul Islam
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  2. Yaoqi Zhou
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  3. Alfred K. Lam
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Corresponding authors

Correspondence to Farhadul Islam or Alfred K. Lam .

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Editors and Affiliations

  1. School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia

    Alfred K. Lam

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Islam, F., Zhou, Y., Lam, A.K. (2022). Long Non-Coding RNAs Profiling Using Microarray in Papillary Thyroid Carcinoma. In: Lam, A.K. (eds) Papillary Thyroid Carcinoma. Methods in Molecular Biology, vol 2534. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2505-7_10

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  • DOI: https://doi.org/10.1007/978-1-0716-2505-7_10

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2504-0

  • Online ISBN: 978-1-0716-2505-7

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