Transcriptomic Profiles of MV4-11 and Kasumi 1 Acute Myeloid Leukemia Cell Lines Modulated by Epigenetic Modifiers Trichostatin A and 5-Azacytidine

  • Mat Jusoh Siti Asmaa ORCID Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
  • Hamid Ali Al-Jamal ORCID Diagnostic and Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, Kuala Nerus, 21300, Terengganu, Malaysia
  • Abdul Rahim Hussein ORCID Regenerative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Pulau Pinang, Malaysia
  • Badrul Hisham Yahaya ORCID Regenerative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Pulau Pinang, Malaysia
  • Azlan Husin ORCID Department of Internal Medicine, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
  • Rosline Hassan ORCID Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
  • Faezahtul Arbaeyah Hussain ORCID Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
  • Shaharum Shamsuddin ORCID School of Health Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia. AND Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
  • Muhammad Farid Johan ORCID Mail Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
Acute myeloid leukemia, Epigenetics, Histone deacetylase inhibitor, 5-Azacytidine, Gene expression


Background: Acute myeloid leukemia (AML) is the most common form of acute leukemias in adults which is clinically and molecularly heterogeneous. Several risk and genetic factors have been widely investigated to characterize AML. However, the concomitant epigenetic factors in controlling the gene expression lead to AML transformation was not fully understood. This study was aimed to identify epigenetically regulated genes in AML cell lines induced by epigenetic modulating agents, Trichostatin A (TSA) and 5-Azacytidine (5-Aza).
Methods: MV4-11 and Kasumi 1 were treated with TSA and/or 5-Aza at IC50concentration. Gene expression profiling by microarray was utilized using SurePrint G3 Human Gene Expression v3. Gene ontology and KEGG pathway annotations were analyzed by DAVID bioinformatics software using EASE enrichment score. mRNA expression of the differentially expressed genes were verified by quantitative real time PCR.
Results: Gene expression analysis revealed a significantchanges in the expression of 24,822, 15,720, 15,654 genes in MV4-11 and 12,598, 8828, 18,026 genes in Kasumi 1, in response to TSA, 5-Aza and combination treatments, respectively, compared to non-treated (p<0.05). 7 genes (SOCS3,TUBA1C, CCNA1, MAP3K6, PTPRC, STAT6and RUNX1) and 4 genes (ANGPTL4, TUBB2A, ADAM12and PTPN6) shown to be predominantly expressed in MV4-11 and Kasumi 1, respectively (EASE<0.1). The analysis also revealed phagosome pathway commonly activated in both cell lines.
Conclusion: Our data showed a distinct optimal biological characteristic and pathway in different types of leukemic cell lines. These finding may help in the identification of cell-specific epigenetic biomarker in the pathogenesis of AML.


1. Babon J, Nicola NA. The biology and mechanism of action of suppressor of cytokine signaling 3 (SOCS3). Growth Factors. 2012;30(4):207-19.
2. Arber DA, Orazi A, Hasserji RP, Brunning RD, Le Beau MM, Porwit A, et al. Introduction and overview of the classification of myeloid neoplasms. WHO classification of tumors of haematopoietic and lymphoid tissues. Revised 4th Edition ed. Geneva: World Health Organization (WHO) Press; 2017. p. 172-75.
3. American Cancer Society:Cancer Facts & Figures. Atlanta: American Cancer Society; c1913-2019 [updated 20 November 2018]. American Cancer Society. Available from: 24 October 2018.
4. Pollack JR. A perspective on DNA microarrays in pathology research and practice. Am J Pathol. 2007;171(2):375-85.
5. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, et al. Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. Science. 1999;286(5439):531-37.
6. Kumar CC. Genetic abnormalities and challenges in the treatment of acute myeloid leukemia. Genes Cancer. 2011;2(2):95-107.
7. Li S, Mason CE, Melnick A. Genetic and epigenetic heterogeneity in acute myeloid leukemia. Curr Opin Genet Dev. 2016;36:100-06.
8. You JS, Jones PA. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell. 2012;22(1):9-20.
9. Sharma S, Kelly TK, Jones PA. Epigenetics in cancer. Carcinogenesis. 2010;31(1):27-36.
10. Baylin SB, Jones PA. A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer. 2011;11(10):726-34.
11. Hatziapostolou M, Iliopoulos D. Epigenetic aberrations during oncogenesis. Cell Mol Life Sci. 2011;68(10):1681-702.
12. Nicolas D, Zoller B, Suter DM, Naef F. Modulation of transcriptional burst frequency by histone acetylation. Proc Natl Acad Sci USA. 2018;115(27):7153-58.
13. Hosack DA, Dennis G, Jr., Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE. Genome Biol. 2003;4(10):R70-R70.
14. Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, et al. Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. Brief Funct Genomics. 2017;17(1):49-63.
15. Xiao L, Huang Y, Zhen R, Chiao JW, Liu D, Ma X. Deficient Histone Acetylation in Acute Leukemia and the Correction by an Isothiocyanate. Acta Haematol. 2010;123(2):71-76.
16. Shankar S, Srivastava RK. Histone deacetylase inhibitors: mechanisms and clinical significance in cancer: HDAC inhibitor-induced apoptosis. Adv Exp Med Biol. 2008;615:261-98.
17. Agrawal S, Unterberg M, Koschmieder S, zur Stadt U, Brunnberg U, Verbeek W, et al. DNA methylation of tumor suppressor genes in clinical remission predicts the relapse risk in acute myeloid leukemia. Cancer Res. 2007;67(3):1370-7.
18. NCI Drug Dictionary: Azacitidine. Bethesda: US National Cancer Institute; [updated 1 August 2018]. Available from: 25 October 2018.
19. Leone G, D'Alo F, Zardo G, Voso MT, Nervi C. Epigenetic treatment of myelodysplastic syndromes and acute myeloid leukemias. Curr Med Chem. 2008;15(13):1274-87.
20. Asgari MM, Wang W, Ioannidis NM, Itnyre J, Hoffmann T, Jorgenson E, et al. Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma. J Invest Dermatol. 2016;136(5):930-37.
21. Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, et al. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res. 2006;16(1):55-65.
22. Harisankar A. Identification of novel genes with important functions in glioblastoma multiforme and acute myeloid leukemia. Huddinge: Institute för medicine; 2018.
23. Liao YP, Chen LY, Huang RL, Su PH, Chan Michael WY, Chang CC, et al. Hypomethylation signature of tumor-initiating cells predicts poor prognosis of ovarian cancer patients. Hum Mol Genet. 2014;23(7):1894-906.
24. Pérez ME, Rodríguez de LÁ, Ribalta T, Ruano Y, Campos MY, Pérez BG, et al. Differential expression profiling analyses identifies downregulation of 1p, 6q, and 14q genes and overexpression of 6p histone cluster 1 genes as markers of recurrence in meningiomas. Neuro Oncol. 2010;12(12):1278-90.
25. Efergan A, Azouz NP, Klein O, Noguchi K, Rothenberg ME, Fukuda M, et al. Rab12 Regulates Retrograde Transport of Mast Cell Secretory Granules by Interacting with the RILP–Dynein Complex. J Immunol. 2016;196(3):1091-101.
26. Yoshida T, Kobayashi T, Itoda M, Muto T, Miyaguchi K, Mogushi K, et al. Clinical omics analysis of colorectal cancer incorporating copy number aberrations and gene expression data. Cancer Inform. 2010;9:147-61.
27. Lapenna S, Giordano A. Cell cycle kinases as therapeutic targets for cancer. Nat Rev Drug Discov. 2009;8(7):547-66.
28. National Cancer for Biotechnology Information (NCBI) Gene ID: 8900. CCNA1 cyclin A1 [Homo sapiens (human)]. Bethesda: U.S. National Library of Medicine; c1988-2019 [updated updated 7 September 2018]. Available from: 7 October 2018.
29. Yang N, Eijsink JJH, Lendvai Á, Volders HH, Klip H, Buikema HJ, et al. Methylation Markers for CCNA1 & C13ORF18 Are Strongly Associated with High-Grade Cervical Intraepithelial Neoplasia and Cervical Cancer in Cervical Scrapings. Cancer Epidemiol Biomarkers Prev. 2009;18(11):3000.
30. Rivera A, Mavila A, Bayless KJ, Davis GE, Maxwell SA. Cyclin A1 is a p53-induced gene that mediates apoptosis, G2/M arrest, and mitotic catastrophe in renal, ovarian, and lung carcinoma cells. Cell Mol Life Sci. 2006;63(12):1425-39.
31. Ekberg J, Holm C, Jalili S, Richter J, Anagnostaki L, Landberg G, et al. Expression of cyclin A1 and cell cycle proteins in hematopoietic cells and acute myeloid leukemia and links to patient outcome. Eur J Haematol. 2005;75(2):106-15.
32. Federico M, Symonds CE, Bagella L, Rizzolio F, Fanale D, Russo A, et al. R-Roscovitine (Seliciclib) prevents DNA damage-induced cyclin A1 upregulation and hinders non-homologous end-joining (NHEJ) DNA repair. Mol Cancer. 2010;9:208-08.
33. Vainchenker W, Constantinescu SN. JAK/STAT signaling in hematological malignancies. Oncogene. 2013;32(21):2601-13.
34. Kazi JU, Ronnstrand L. Suppressor of cytokine signaling 2 (SOCS2) associates with FLT3 and negatively regulates downstream signaling. Mol Oncol. 2013;7(3):693-703.
35. Fourouclas N, Li J, Gilby DC, Campbell PJ, Beer PA, Boyd EM, et al. Methylation of the suppressor of cytokine signaling 3 gene in myeloproliferative disorders. Haematologica. 2008;93(11):1635.
36. Pierconti F, Martini M, Pinto F, Cenci T, Capodimonti S, Calarco A, et al. Epigenetic silencing of SOCS3 identifies a subset of prostate cancer with an aggressive behavior. The Prostate. 2010;71(3):318-25.
37. Wang J, Zhou H, Han Y. SOCS3 methylation in synergy with Reg3A overexpression promotes cell growth in pancreatic cancer. Int J Mol Med. 2014;92(12):1257-69.
38. Chen H, Zhang C, Sheng Y, Yao S, Liu Z, Zhang C, et al. Frequent SOCS3 and 3OST2 promoter methylation and their epigenetic regulation in endometrial carcinoma. American Journal of Cancer Research. 2015;5(1):180-90.
39. Zhang X, You Q, Zhang X, Chen X. SOCS3 Methylation Predicts a Poor Prognosis in HBV Infection-Related Hepatocellular Carcinoma. Int J Mol Sci. 2015;16(9).
40. Barclay JL, Anderson ST, Waters MJ, Curlewis JD. SOCS3 as a tumor suppressor in breast cancer cells, and its regulation by PRL. Int J Cancer. 2009;124(8):1756-66.
41. National Cancer for Biotechnology Information (NCBI) Gene ID: 84790. TUBA1C tubulin alpha 1c [Homo sapiens (human)]. Bethesda: U.S. National Library of Medicine; c1988-2019 [updated 7 September 2018]. Available from: 7 October 2018.
42. Wang J, Chen W, Wei W, Lou J. Oncogene TUBA1C promotes migration and proliferation in hepatocellular carcinoma and predicts a poor prognosis. Oncotarget. 2017;8(56):96215-24.
43. Chen D, Li Y, Wang L, Jiao K. SEMA6D Expression and Patient Survival in Breast Invasive Carcinoma. Int J Breast Cancer. 2015;2015:10.
44. Closa A, Cordero D, Sanz-Pamplona R, Solé X, Crous-Bou M, Paré-Brunet L, et al. Identification of candidate susceptibility genes for colorectal cancer through eQTL analysis. Carcinogenesis. 2014;35(9):2039-46.
45. Tang X, Chen S. Epigenetic Regulation of Cytochrome P450 Enzymes and Clinical Implication. Curr Drug Metab. 2015;16(2):86-96.
46. Park HJ, Choi YJ, Kim JW, Chun HS, Im I, Yoon S, et al. Differences in the Epigenetic Regulation of Cytochrome P450 Genes between Human Embryonic Stem Cell-Derived Hepatocytes and Primary Hepatocytes. PLoS One. 2015;10(7):e0132992-e92.
47. La Paglia L, Listi A, Caruso S, Amodeo V. Potential Role of ANGPTL4 in the Cross Talk between Metabolism and Cancer through PPAR Signaling Pathway. PPAR Res. 2017;2017:8187235.
48. Genecards Human gene Database (GCID:GC19P008363). ANGPTL4 Gene (Protein Coding). Israel: Weizmann Institute of Science; c1996-2019 [updated 10 September 2018]. Available from: 4 October 2018.
49. Tan MJ, Teo Z, Sng MK, Zhu P, Tan NS. Emerging roles of angiopoietin-like 4 in human cancer. Mol Cancer Res. 2012;10(6):677-88.
50. UniProtKB - Q13885 (TBB2A_HUMAN). Protein knowledgebase (UniProtKB) Bethesda: National Institute of Health; c2002-2019 [updated 16 March 2018]. Available from: 21 August 2018.
51. Cushion Thomas D, Paciorkowski Alex R, Pilz Daniela T, Mullins Jonathan GL, Seltzer Laurie E, Marion Robert W, et al. De Novo Mutations in the Beta-Tubulin Gene TUBB2A Cause Simplified Gyral Patterning and Infantile-Onset Epilepsy. Am J Hum Genet. 2014;94(4):634-41.
52. Romaniello R, Arrigoni F, Bassi MT, Borgatti R. Mutations in α- and β-tubulin encoding genes: Implications in brain malformations. Brain Dev. 2015;37(3):273-80.
53. The Human Protein Atlas: TUBB2A. Knut & Alice Wallenberg foundation 2018[Available from: 24 june 2018.
54. Zhong F, Ouyang Y, Wang Q, Ding L, He S. Upregulation of ADAM12 contributes to accelerated cell proliferation and cell adhesion-mediated drug resistance (CAM-DR) in Non-Hodgkin’s Lymphoma AU - Yin, Haibing. Hematology. 2017;22(9):527-35.
55. Rahmatpanah FB, Carstens S, Hooshmand SI, Welsh EC, Sjahputera O, Taylor KH, et al. Large-scale analysis of DNA methylation in chronic lymphocytic leukemia. Epigenomics. 2009;1(1):39-61.
56. Al-jamal H, Asmaa MJ, Sidek M, Hassan R, Johan M. Restoration of PRG2 Expression by 5-Azacytidine Involves in Sensitivity of PKC-412 (Midostaurin) Resistant FLT3-ITD Positive Acute Myeloid Leukaemia Cells. J Hematol & Thromboembolic Dis. 2015;3(186):2.
57. Wu C, Sun M, Liu L, Zhou GW. The function of the protein tyrosine phosphatase SHP-1 in cancer. Gene. 2003;306:1-12.
58. Wen LZ, Ding K, Wang ZR, Ding Ch, Lei Sj, Liu J-p, et al. SHP-1 acts as a Tumor Suppressor in Hepatocarcinogenesis and HCC Progression. Cancer Res. 2018:canres.3896.2017.
59. Wang H, Hu H, Zhang Q, Yang Y, Li Y, Hu Y, et al. Dynamic transcriptomes of human myeloid leukemia cells. Genomics. 2013;102(4):250-56.
How to Cite
Siti Asmaa MJ, Al-Jamal HA, Hussein AR, Yahaya BH, Husin A, Hassan R, Hussain FA, Shamsuddin S, Johan MF. Transcriptomic Profiles of MV4-11 and Kasumi 1 Acute Myeloid Leukemia Cell Lines Modulated by Epigenetic Modifiers Trichostatin A and 5-Azacytidine. Int J Hematol Oncol Stem Cell Res. 14(1):72-92.
Original Article(s)