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KLF6 Super-enhancer Regulates Cell Proliferation by Recruiting GATA2 and SOX10 in Human Hepatoma Cells

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Abstract

Super-enhancer consists of a large cluster of transcription enhancers that regulates the expression of genes playing an important role in the growth and development of malignant tumors. Recently, several attempts for the identification of super-enhancers have been made, but their functional role in tumor cells remains unclear. This paper aims at elucidating the functional properties of KLF6 super-enhancer related to the growth regulation of HepG2 cells, in relation to transcription factors (TFs). First, some TFs specifying KLF6 super enhancer were identified using CRISPR/Cas9 system and siRNA. Then, their effects on the expression of the target gene KLF6 were assessed. Last, their influence on the proliferation of tumor cells was considered using the MTT method. The study shows that the active enhancers of KLF6 super-enhancer recruit GATA2 and SOX10 TFs to control the expression of the target gene, KLF6. Our findings suggest that the activity of KLF6 super-enhancer is regulated by two TFs (GATA2 and SOX10), and its targeting may be a potential therapeutic strategy for the liver cancer therapy.

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REFERENCES

  1. Chen D., Zhao Z., Huang Z., Chen D.C., Zhu X.X., Wang Y.Z., Yan Y.-W., Tang S., Madhavan S., Ni W., Huang Z.-P., Li W., Ji W., Shen H., Lin S., Jiang Y.-Z. 2018. Super enhancer inhibitors suppress MYC driven transcriptional amplification and tumor progression in osteosarcoma. Bone Res. 6, 11.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Betancur P.A., Abraham B.J., Yiu Y.Y., Willingham S.B., Khameneh F., Zarnegar M., Kuo A.H., McKenna K., Kojima Y., Leeper N.J., Ho P., Gip P., Swigut T., Sherwood R.I., Clarke M.F., et al. 2017. A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer. Nat. Commun. 8, 14802.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Chen C., Zhou D., Gu Y., Wang C., Zhang M., Lin X., Xing J., Wang H., Zhang Y. 2020. SEA version 3.0: a comprehensive extension and update of the super-enhancer archive. Nucleic Acids Res. 48, D198–D203.

    CAS  PubMed  Google Scholar 

  4. Didych D.A., Tyulkina D.V., Pleshkan V.V., Alekseenko I.V. 2015. Are super-enhancers regulators of regulatory genes of development and cancer? Mol. Biol. 49 (6), 818–824. https://doi.org/10.1134/S0026893315060059

    Article  CAS  Google Scholar 

  5. Dav K., Su I., Yan J., Zhang J., Kaasinen E., Zhong F., Blaas L., Li X., Kharazi S., Gustafsson C. 2017. Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. eLife. 6, e23382.

    Article  Google Scholar 

  6. Hnisz D., Abraham B.J., Lee T.I., Lau A., Saint-André V., Sigova A.A., Hoke H.A., Young R.A. 2013. Super-enhancers in the control of cell identity and disease. Cell. 155, 934–947.

    Article  CAS  PubMed  Google Scholar 

  7. Gröschel S., Sanders M.A., Hoogenboezem R., de Wit E., Bouwman BA., Erpelinck C., van der Velden V.H.J., Havermans M., Avellino R., van Lom K., Rombouts E.J., van Duin M., Döhner K., Beverloo H.B., Bradner J.E., et al. 2014. A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia. Cell. 157, 369‒381.

    Article  PubMed  CAS  Google Scholar 

  8. Li Y., Rivera C.M., Ishii H., Jin F., Selvaraj S., Lee A.Y., Dixon J.R., Ren B. 2014. CRISPR reveals a distal super-enhancer required for SOX2 expression in mouse embryonic stem cells. PLoS One. 9, e114485.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Deng R., Huang J.H., Wang Y., Zhou L.H., Wang Z.-F., Hu B.-X., Chen Y.-H., Yang D., Mai J., Li Z.-L., Zhang H.-L., Huang Y., Peng X.-D., Feng G.-K., Zhu X.-F., Tang J. 2020. Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma. Mol. Cancer. 19, 122.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Hnisz D., Schuijers J., Lin C.Y., Weintraub A.S., Abraham B.J., Lee T.I., Bradner J.E., Young R.A. 2015. Convergence of developmental and oncogenic signaling pathways at transcriptional super- enhancers. Mol. Cell. 58, 1–9.

    Article  CAS  Google Scholar 

  11. Hnisz D., Abraham B., Lee T., Lau A., Saint-Andre V., Sigova A., Hoke H., Yong R. 2013. Super-enhancers in the control of cell identity and disease. Cell. 155, 934–947.

    Article  CAS  PubMed  Google Scholar 

  12. Yong J., Qian F., Bai X., Liu Y., Wang Q., Ai B., Han X., Shi S., Zhang J., Li X., Tang Z., Pan Q., Wang Y., Wang F., Li C. 2019. SEdb: a comprehensive human super-enhancer database. Nucleic Acids Res. 47, D235–D243.

    Article  CAS  Google Scholar 

  13. Kubota S., Tokunaga K., Umezu T., Yuqi Sun., Oshima M., KarTong Tan., Yang H., Kanai A., Lwanaga E., Asou N., Maeda T., Nakagata N., Iwama A., Ohyashiki K., Osato M., Sashida G. 2019. Lineage-specific RUNX2 super-enhancer activates MYC and promotes the development of blastic plasmacytoid dendritic cell neoplasm. Nat. Commun. 10, 1653.

  14. Lovén J., Hoke H.A., Lin C.Y., Lau A., Orlando D.A., Vakoc C.R., Bradner J.E., Lee T.I., Young R.A. 2013. Selective inhibition of tumor oncogenes by disruption of super enhancers. Cell. 153, 320–334.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. DiFeo A., Martignetti J.A., Narla G. 2009. The role of KLF6 and its splice variants in cancer therapy. Drug Resist. Updates. 12, 1–7.

    Article  CAS  Google Scholar 

  16. Chen C., Hyytinen E.-R., Sun X., Helin H.J., Koivisto P.A., Frierson H.F.Jr, Vessella R.L., Dong J.T. 2003. Deletion, mutation, and lloss of expression of KLF6 in human prostate cancer. Am. J. Pathol. 162, 1349–1354.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Narla G., Kremer-Tal S., Matsumoto N., Zhao X., Yao S., Kelley K., Tarocchi M., Friedman S.L. 2007. In vivo regulation of p21 by the Kruppel-like factor 6 tumor-suppressor gene in mouse liver and human hepatocellular carcinoma. Oncogene. 26, 4428–4434.

    Article  CAS  PubMed  Google Scholar 

  18. He A.-D., Xie W., Song W., Ma Y.-Y., Liu G., Liang M.-L., Da X.-W., Yao G.Q., Zhang B.-X., Gao C.-J., Xiang J.-Z., Ming Z.-Y. 2017. Platelet releasates promote the proliferation of hepatocellular carcinoma cells by suppressing the expression of KLF6. Sci. Rep. 7, 3989.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. León X., Venegas M., Pujol A., Bulboa C., Llansana A., Casasayas M., Quer M., Camacho M. 2021. Predictive value of transcriptional expression of krüppel-like factor-6 (klf6) in head and neck carcinoma patients treated with radiotherapy. Clin. Transl. Oncol. 23 (12), 2507–2512.

    Article  PubMed  CAS  Google Scholar 

  20. Ri K.C., Kim J.S., Kim C. 2017. Identification of KLF6-related super enhancer in human hepatoma (HepG2) cells by CRISPR technique. Genet. Mol. Res. 16 (4), gmr16039841.

    Article  CAS  Google Scholar 

  21. Ri K.C., Kim C., Pak C.J., Ri P.C., Om HC. 2020. The KLF6 super enhancer modulates cell proliferation via MiR-1301 in human hepatoma cells. MicroRNA. 9, 64‒69.

    Article  CAS  PubMed  Google Scholar 

  22. Ri K.C., Kim C., Choe S.I., So J.H., Hyok S. 2019. The KLF6-related super enhancer regulates KLF6-SV2 expression-mediated proliferation in human hepatoma (HepG2) cells. Beni-Suef Univ. J. Basic Appl. Sci. 8, 10.

    Google Scholar 

  23. Ri K.C., Kim K.C., Kong S.H., Ri J.H. 2018. The Disruption of KLF6-related super- enhancer induces growth inhibition and apoptosis in human HepG2 Cells. Genet. Mol. Res. 17 (1), gmr16039888.

    Google Scholar 

  24. Ri K.C., Ri M.R., Song Y.J., Kim K.H., Kim C. 2020. The KLF6 super-enhancer determines KLF6 sensitivity to BRD4 inhibitors in human hepatoma (HepG2) cells. Curr. Biotechnol. 9, 209‒218.

    Article  CAS  Google Scholar 

  25. Gong J., Qiu C., Huang D., Zhang Y., Zeng C. 2018. Integrative functional analysis of super enhancer SNPs for coronary artery disease. J. Hum. Genet. 63, 627–638.

    Article  CAS  PubMed  Google Scholar 

  26. Shin H.Y. 2018. Targeting super-enhancers for disease treatment and diagnosis. Mol. Cells. 41, 506‒514.

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Labun K., Montague T. G., Krause M., Torres Cleuren Y.N., Tjeldnes H., Valen E. 2019. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res. 47 (1), 171‒174.

    Article  CAS  Google Scholar 

  28. Montague T.G., Cruz J.M., Gagnon J.A., Church G.M., Valen E. 2014. CHOPCHOP: A CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 42, W401‒W407.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Stovicek V., Holkenbrink C., Borodina I. 2017. CRISPR/Cas system for yeast genome engineering: advances and applications. FEMS. Yeast Res. 17 (5), 1‒16.

    Article  CAS  Google Scholar 

  30. D’Astolfo D.S., Gehrau R.C., Bocco J.L., Koritschoner N.P. 2008. Silencing of the transcription factor KLF6 by siRNA leads to cell cycle arrest and sensitizes cells to apoptosis induced by DNA damage, Cell Death Differ. 15, 613–616.

    Article  PubMed  CAS  Google Scholar 

  31. Naito Y., Yoshimura J., Morishita S., Ui-Tei K. 2009. siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinform. 10, 392.

    Article  CAS  Google Scholar 

  32. Vert J.P., Foveau N., Lajaunie C., Vandenbrouck Y. 2006. An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinform. 7 (1), 520.

    Article  CAS  Google Scholar 

  33. Fornes O., Castro-Mondragon J.A., Khan A., van der Lee R., Zhang X., Richmond Ph.A., Modi B.P., Correard S., Gheorghe M., Baranašić D., Santana-Garcia W., Tan G., Chèneby J., Ballester B., Parcy F., et al. 2020. JASPAR 2020: Update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 48, 87‒92.

    CAS  Google Scholar 

  34. Lin L., Huang M., Shi X., Anand M., Hu K., Jiang Y.-Y., Guo X., Chen L., Pang B., Doan N., Said J.W., Xie J., Gery S., Cheng X., Lin Z., et al. 2019. Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1. Nucleic Acids Res. 47, 1255–1267.

    Article  CAS  PubMed  Google Scholar 

  35. Mansour M.R., Abraham B.J., Anders L., Berezov-skaya A., Gutierrez A., Durbin A.D., Etchin J., Lawton L., Sallan S.E., Silverman L.B., Loh M.L., Hunger S.P., Sanda T., Young R.A., Look A.T. 2014. Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science. 346, 1373–1377.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Wiese M., Hamdan F.H., Kubiak K., Diederichs C., Gielen G.H., Nussbaumer G., Carcaboso A.M., Hulleman E., Johnsen S.A., Kramm C.M. 2020. Combined treatment with CBP and BET inhibitors reverses inadvertent activation of detrimental super enhancer programs in DIPG cells. Cell Death Dis. 11, 673.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Dhar S.S., Zhao D., Lin T., Gu B., Pal K., Wu S.J., Alam H., Lv J., Yun K., Gopalakrishnan V., Flores E.R., Northcott P.A., Rajaram V., Li W., Shilatifard A., et al. 2018. MLL4 is required to maintain broad H3K4me3 peaks and super-enhancers at tumor suppressor genes. Mol. Cell. 7, 825‒841.

    Article  CAS  Google Scholar 

  38. Sloan C.A., Chan E.T., Davidson J.M., Malladi V.S., Strattan J.S., Hitz B.C., Gabdank I., Narayanan A.K., Ho M., Lee B.T., Rowe L.D., Dreszer T.R., Roe G., Podduturi N.R., Tanaka F., et al. 2016. ENCODE data at the ENCODE portal. Nucleic Acids Res. 44, 726–732.

    Article  CAS  Google Scholar 

  39. Narla G., Heath K.E., Reeves H.L., Li D., Giono L.E., Kimmelman A.C., Glucksman M.J., Narla J., Eng F.J., Chan A.M., Ferrari A.C., Martignetti J.A., Friedman S.L. 2001. KLF6, a candidate tumor suppressor gene mutated in prostate cancer. Science. 294, 2563–2566.

    Article  CAS  PubMed  Google Scholar 

  40. Reeves H.L., Narla G., Ogunbiyi O., Haq A.I., Katz A., Benzeno S., Hod E., Harpaz N., Goldberg S., Tal-Kremer S., Eng F.J., Arthur M.J.P., Martignetti J.A., Friedman S.L. 2004. Kruppel-like factor6 (KLF6) is a tumor-suppressor gene frequently inactivated in colorectal cancer. Gastroenterology. 126, 1090–1103.

    Article  CAS  PubMed  Google Scholar 

  41. Kremer-Tal S., Reeves H.L., Narla G., Thung S.N., Schwartz M., Difeo A., Katz A., Bruix J., Bioulac-Sage P., Martignetti J.A., Friedman S.L. 2004. Frequent inactivation of the tumor suppressor Kruppel-like factor 6 (KLF6) in hepatocellular carcinoma. Hepatology. 40, 1047–1052.

    Article  CAS  PubMed  Google Scholar 

  42. Ito G., Uchiyama M., Kondo M., Mori S., Usami N., Maeda O., Kawabe T., Hasegawa Y., Shimokata K., Sekido Y. 2004. Kruppel-like factor 6 is frequently down-regulated and induces apoptosis in non-small cell lung cancer cells. Cancer Res. 64, 3838–3843.

    Article  CAS  PubMed  Google Scholar 

  43. Kimmelman A.C., Qiao RF., Narla G., Banno A., Lau N., Bos P.D., Rodriguez N.N., Liang B.C., Guha A., Martignetti J.A., Friedman S.L., Chan A.M. 2004. Suppression of glioblastoma tumorigenicity by the Kruppel-like transcription factor KLF6. Oncogene. 23, 5077–5083.

    Article  CAS  PubMed  Google Scholar 

  44. Camacho-Vanegas O., Narla G., Teixeira MS., DiFeo A., Misra A., Singh G., A.M. Chan, Friedman S.L., Feuerstein B.G., Martignetti J.A. 2007. Functional inactivation of the KLF6 tumor suppressor gene by loss of heterozygosity and increased alternative splicing in glioblastoma. Int. J. Cancer. 121, 1390–1395.

    Article  CAS  PubMed  Google Scholar 

  45. Yao Y.L., Ma J., Wang P., Xue Y.X., Li Z., Zhao L.N., Li Z.-Q., Feng T.-D., Liu Y.-H. 2015. miR-101 acts as a tumor suppressor by targeting Kruppel-like factor 6 in glioblastoma stem cells. CNS Neurosci. Ther. 21, 40–51.

    Article  PubMed  CAS  Google Scholar 

  46. Raninga P.V., Di Trapani G., Vuckovic S., Tonissen K.F. 2016. Targeted knockdown of DJ-1 induces multiple myeloma cell death via KLF6 upregulation. Apoptosis. 21 (12), 1422‒1437.

    Article  CAS  PubMed  Google Scholar 

  47. Gallardo-Vara E., Blanco F.J., Roqué M., Friedman S.L., Suzuki T., Botella L.M., Bernabeu C. 2016. Transcription factor klf6 upregulates expression of metalloprotease mmp14 and subsequent release of soluble endoglin during vascular injury. Angiogenesis. 19 (2), 155‒171.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Syafruddin S.E., Rodrigues P., Vojtasova E., Patel S.A., Zaini M.N., Burge J., Warren A.Y., Stewart G.D., Eisen T., Bihary D., Samarajiwa S.A., Vanharanta S. 2019. A KLF6-driven transcriptional network links lipid homeostasis and tumour growth in renal carcinoma. Nat. Commun. 10, 1152.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Peng L., Jiang B., Yuan X., Qiu Y., Peng J., Huang Y., Zhang C., Zhang Y., Lin Z., Li J., Yao W., Deng W., Zhang Y., Meng M., Pan X., Li C., et al. 2019. Super- enhancer-associated long noncoding RNA HCCL5 is activated by ZEB1 and promotes the malignancy of hepatocellular carcinoma. Cancer Res. 79, 572–584.

    Article  CAS  PubMed  Google Scholar 

  50. Yang R., Wu Y., Ming Y., Xu Y., Wang S., Shen J., Wang C., Chen X., Wang Y., Mao R., Fan Y. 2018. A super-enhancer maintains homeostatic expression of regnase-1. Cell. 30 (669), 35‒41.

    Google Scholar 

  51. Zhang X., Choi Ps., Francis J.M., Imielinski M., Watanabe H., Cherniack A.D., Meyerson M. 2016. Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers. Nat. Genet. 48, 176–182.

    Article  CAS  PubMed  Google Scholar 

  52. Groschel S., Mathijs A., Sanders., Hoogenboezem R., de Wit E., Bouwman B.A.M., Erpelinck C., van der Velden V.H.J., Havermans M., Avellino R., van Lom K., Rombouts E.J., van Duin M., Döhner K., Beverloo H.B., et al. 2014. A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia. Cell. 157, 369–381.

    Article  CAS  PubMed  Google Scholar 

  53. Li Y., Liu B., Harmacek L., Long Z., Liang J., Lukin K., Leach S.M., O’Connor B., Gerber A.N., Hagman J., Roers A., Finkelman F.D., Huang H. 2018. The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis. J. Allergy Clin. Immunol. 142, 1173–1184.

    Article  CAS  PubMed  Google Scholar 

  54. Arter J., Wegner M. 2015. Transcription factors SOX10 and SOX2 functionally interact with positive transcription elongation factor b in Schwann cells. J. Neurochem. 132 (4), 384–393.

    Article  CAS  PubMed  Google Scholar 

  55. Fogarty E.A., Brewer M.H., Rodriguez-Molina J.F., Law W.D., Ma K.H., Steinberg N.M., Svaren J., Antonellis A. 2016. SOX10 regulates an alternative promoter at the Charcot-Marietooth disease locus MTMR2. Hum. Mol. Genet. 25 (18), 3925–3936.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Gopinath C., Law W.D., Rodríguez-Molina J.F., Prasad A.B., Song L., Crawford G.E., Mullikin J.C., Svaren J., Antonellis A. 2016. Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation. BMC Genomics. 17 (1), 887.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  57. Doddrell R.D., Dun X.P., Shivane A., Feltri M.L., Wrabetz L., Wegner M., Sock E., Hanemann C.O., Parkinson D.B. 2013. Loss of SOX10 function contributes to the phenotype of human Merlin-null schwannoma cells. Brain. 136 (Pt. 2), 549–563.

    Article  PubMed  PubMed Central  Google Scholar 

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ACKNOWLEDGMENTS

The authors gratefully acknowledge the support from University of Science of DPRK. The authors would also like to take the opportunity to express their heartfelt gratitude to all those who made contributions to the completion of this article.

Funding

This work was supported by National Natural Science Foundation of Korea (grant no. 54289562) and National Natural Science Foundation of China (grant no. 715773068).

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Correspondence to Kum Chol Ri.

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Kum Chol Ri, Ri, M.R., Kim, K.H. et al. KLF6 Super-enhancer Regulates Cell Proliferation by Recruiting GATA2 and SOX10 in Human Hepatoma Cells. Mol Biol 56, 443–452 (2022). https://doi.org/10.1134/S0026893322030116

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