THE GENOMIC LANDSCAPE OF THE SWITCH/SUCROSE NON-FERMENTABLE CHROMATIN REMODELING COMPLEX IN ACUTE MYLEOID LEUKEMIA

Abstract

The SWI/SNF chromatin remodeling complex is involved in the regulation of gene expression required for processes such as cell maintenance and differentiation in hematopoietic stem cells. Abnormalities in the SWI/SNF subunits involved in the homeostasis of hematologic processes contribute to the initiation or progression of hematologic malignancies, but the mechanisms underlying this phenotype are not yet fully understood. The aim of study is to comprehensively identify mutations and expression profiles in the genes forming the SWI/SNF complex using bioinformatics tools, with a focus on understanding the underlying mechanisms. Genomic sequences and expression profiles of an AML cohort (n:872) were obtained from using tools and subsequently analyzed. PolyPhen-2, SIFT, and Mutation Assessor tools were used to estimate the oncogenic/pathogenic effects of mutations identified in 9 genes encoding subunits of the complex ARID1A, ARID1B, SMARCA2, SMARCA4, SMARCE1, SMARCB1, DPF2, PMBR1, and BCL7A in AML pathogenesis. STRING analysis was performed to better understand the functional relationships of the mutant proteins in cellular processes. Furthermore, to the mutation profile, gene expression and survival profiles were also determined. A total of 17 genetic abnormalities were determined in 9 genes, including 9 missense, 6 frameshift mutations, 1 mutation in the splice region, and 1 fusion mutation. In the AML cohort, the expression levels of ARID1A, ARID1B, SMARCA2, and PMBR1 were significantly higher in the patient group compared to the healthy group (p<0.01). Survival analysis based on low and high gene expression profiles showed no significant difference in results. In STRING analysis, our genes were found to have functional relationships with the PHF10 protein, which is involved in cell cycle control. The results suggest that the mutations identified in the ARID1A, ARID1B, SMARCA2, SMARCA4, and PBRM1 may disrupt the function of SWI/SNF chromatin remodeling complexes, possibly inducing/activating different cellular pathways involving different chromatin environments during AML pathogenesis.

Keywords

• AML
• chromatin remodeling
• gene expression
• mutation
• SWI/SNF komplex

Supporting Institution

No funding was received.

Ethical Statement

The data used in our study were obtained from public database TCGA, therefore, ethical approval was not required.

Thanks

The data used in our study are obtained from public database the TCGA Research Network: https:// www.cancer.gov/tcga. We thank the TCGA, GEPIA, cbio Portal, and STRING databases for the availability of the data.

AKUT MİYELOİD LÖSEMİDE SWITCH/SUKROZ FERMENTE EDILEMEZ KROMATİN YENİDEN ŞEKİLLENDİRME KOMPLEKSİNİN GENOMİK GÖRÜNÜMÜ

Abstract

SWI/SNF kromatin yeniden modelleme kompleksi, hematopoietik kök hücrelerde hücre bakımı ve farklılaşma gibi süreçler için gerekli olan gen ekspresyonunun düzenlenmesinde görev alır. Hematolojik süreçlerin homeostazında yer alan SWI/SNF kompleksi alt birimlerindeki değişiklikler hematolojik malignitelerin başlamasına veya ilerlemesine katkıda bulunmaktadır, ancak bu fenotipin arkasındaki mekanizmalar tam olarak açıklanmamıştır. Çalışmada, SWI/SNF kompleksini oluşturan genlerde mutasyonların ve ekspresyon profilinin biyoinformatik araçları kullanılarak kapsamlı belirlenmesi amaçlanmıştır. AML kohortuna (n:872) ait genom dizileri ve ifade profillerine biyoinformatik araçlar aracılığı ile elde edilmiş ve analiz edilmiştir. Kompleksin alt ünitelerini kodlayan 9 gende ARID1A, ARID1B, SMARCA2, SMARCA4, SMARCE1, SMARCB1, DPF2, PMBR1 ve BCL7A belirlenen mutasyonların AML patogenezinde onkojenik/patojenik etkilerinin tahmini PolyPhen-2, SIFT ve Mutation Assessor araçları kullanılmıştır. Mutasyona uğrayan proteinlerinin fonksiyenel etkilerini anlamak için STRING aracı ile analiz gerçekleştirilmiştir. Mutasyon profili değil aynı zamanda mutasyon varlığının gen ifadesi ve sağ kalım üzerine etkileride değerlendirilmiştir. 9 gende 9 yanlış anlam, 6 çerçeve kayması mutasyon, 1 splize bölge ve 1 füzyon mutasyonu olmak üzere toplam 17 genetik anormallik belirlenmiştir. AML kohortunda ARID1A, ARID1B, SMARCA2 ve PMBR1 ekspresyon seviyelerin hasta grubunda sağlıklı gruba yüksek ve istatistiksel olarak anlamlıdır (p<0.01). Düşük ve yüksek gen ekspresyon profillerine göre yapılan sağ kalım analizi sonuçlarımızda bir farklılık görülmemiştir. STRING analizinde, hedef genlerimizin, hücre döngüsü kontrolünde görev alan PHF10 ile fonksiyonel ilişkileri bulunduğu belirlenmiştir. Sonuç olarak, sonuçlarımız, ARID1A, ARID1B, SMARCA2, SMARCA4 ve PBRM1’de tespit ettiğimiz mutasyonlarının, SWI/SNF kromatin yeniden modelleme komplekslerinin fonksiyonunu bozarak AML patogenezi sırasında farklı kromatin ortamlarını içeren farklı hücresel yolları indükleyebileceği/inaktive edebileceğini düşündürmektedir.

Keywords

• AML
• kromatin remodülasyonu
• gen ifadesi
• mutasyon
• SWI/SNF kompleksi

References

1. Chen K, Yuan J, Sia Y, Chen Z. Mechanism of action of the SWI/SNF family complexes. Nucleus. 2023;14(1):2165604. doi:10.1080/19491034.2023.2165604.
2. Centore RC, Sandoval GJ, Soares LMM, Kadoch C, Chan HM. Mammalian SWI/SNF chromatin remodeling complexes: Emerging mechanisms and therapeutic strategies. Trends Genet. 2020;36(12):936-950. doi:10.1016/j.tig.2020.07.011.
3. Reyes AA, Marcum RD, He Y. Structure and function of chromatin remodelers. J Mol Biol. 2021;433(14):166929.doi:10.1016/j.jmb.2021.166929.
4. Krishnamurthy N, Kato S, Lippman S, Kurzrock R. Chromatin remodeling (SWI/SNF) complexes, cancer, and response to immunotherapy. J Immunother Cancer. 2022;10(9):e004669. doi:10.1136/jitc-2022-004669.
5. Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus. 2022 (1):236-276. doi:10.1080/19491034.2022.2143106.
6. Mittal P, Roberts CWM. The SWI/SNF complex in cancer - biology, biomarkers and therapy. Nat Rev Clin Oncol. 2020;17(7):435-448. doi:10.1038/s41571-020-0357-3.
7. Andrades A, Peinado P, Alvarez-Perez JC, et al. SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities. Mol Cancer. 2023;22(1):39.doi:10.1186/s12943-023-01736-8.
8. Bayona-Feliu A, Aguilera A. The SWI/SNF complex, transcription-replication conflicts and cancer: a connection with high therapeutic potential. Mol Cell Oncol. 2021;8(4):1976582. doi:10.1080/23723556.2021.1976582.

9. Bieluszewski T, Prakash S, Roulé T, Wagner D. The role and activity of SWI/SNF chromatin remodelers. Annu Rev Plant Biol. 2023;74:139-163. doi:10.1146/annurev-arplant-102820-093218.
10. Schaefer IM, Qian X. The roles of the SWI/SNF complex in cancer. Cancer Cytopathol. 2023;131(7):410-414. doi:10.1002/cncy.22691.
11. Madan V, Shyamsunder P, Dakle P, et al. Dissecting the role of SWI/SNF component ARID1B in steady-state hematopoiesis. Blood Adv. 2023;7(21):6553-6566. doi:10.1182/bloodadvances.2023009946.
12. Shi J, Whyte WA, Zepeda-Mendoza CJ, et al. Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev. 2013;27(24):2648-2662. doi:10.1101/gad.232710.113.
13. Jones CA, Tansey WP, Weissmiller AM. Emerging themes in mechanisms of tumorigenesis by SWI/SNF subunit mutation. Epigenet Insights. 2022;15:25168657221115656. doi:10.1177/25168657221115656.
14. Helming KC, Wang X, Roberts CWM. Vulnerabilities of mutant SWI/SNF complexes in cancer. Cancer Cell. 2014;26(3):309-317.doi:10.1016/j.ccr.2014.07.018.
15. Li Y, Yang X, Zhu W, Xu Y, Ma J, He C, et al. SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases. Cancer Cell Int. 2022;22(1):347. doi:10.1186/s12935-022-02757-x.
16. Hohmann AF, Vakoc CR. A rationale to target the SWI/SNF complex for cancer therapy. Trends Genet. 2014;30(8):356-363. doi:10.1016/j.tig.2014.05.001.
17. Sahu RK, Singh S, Tomar RS. The mechanisms of action of chromatin remodelers and implications in development and disease. Biochem Pharmacol. 2020;180:114200. doi:10.1016/j.bcp.2020.114200.
18. Cerami E, Gao J, Dogrusoz U, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2(5):401-404. doi:10.1158/2159-8290.CD-12-0095.
19. Adzhubei I, Jordan DM, Sunyaev SR. Predicting functionaleffect of human missense mutations using PolyPhen-2. Curr Protoc in Hum Genet. 2013;07:20. doi:10.1002/0471142905.hg0720s76.
20. Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001;11(5):863-874. doi:10.1101/gr.176601.
21. Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011;39(17):e118.doi:10.1093/nar/gkr407.doi: 10.1093/nar/gkr407.
22. Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45(1):98-102. doi:10.1093/nar/gkx247.
23. Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(1):607-613. doi:10.1093/nar/gky1131.
24. Yao H, Huo L, Ping N, et al. Recurrent mutations in multiple components of the SWI/SNF complex in myelodysplastic syndromes and acute myeloid leukaemia. Br J Haematol. 2022;196(2):441-444. doi:10.1111/bjh.17795.
25. Astori A, Tingvall-Gustafsson J, Kuruvilla J, et al. ARID1a associates with lymphoid-restricted transcription factors and has an essential role in T cell development. J Immunol. 2020;205(5):1419-1432. doi: 10.4049/jimmunol.1900959. doi:10.4049/jimmunol.1900959.
26. Prasad P, Lennartsson A, Ekwall K. The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia. Biomed Res Int. 2015;2015:347571. doi:10.1155/2015/347571.
27. Mullen J, Kato S, Sicklick JK, Kurzrock R. Targeting ARID1A mutations in cancer. Cancer Treat Rev.2021;100:102287.doi:10.1016/j.ctrv.2021.102287.
28. Du Z, Lovly CM. Mechanisms of receptor tyrosine kinase activation in cancer. Mol Cancer. 2018;17(1):58. doi:10.1186/s12943-018-0782-4.
29. Sim JC, White SM, Lockhart PJ. ARID1B-mediated disorders: Mutations and possible mechanisms. Intractable Rare Dis Res. 2015;4(1):17-23. doi:10.5582/irdr.2014.01021.
30. Reddy D, Bhattacharya S, Levy M, et al. Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing. EMBO Rep. 2023;24(1):e55345. doi:10.15252/embr.202255345.
31. Xu S, Tang C. The role of ARID1A in tumors: Tumor initiation or tumor suppression? Front Oncol. 2021;11:745187. doi:10.3389/fonc.2021.745187.
32. Baldi S, He Y, Ivanov I, et al. Aberrantly hypermethylated ARID1B is a novel biomarker and potential therapeutic target of colon adenocarcinoma. Front Genet. 2022;13:914354. doi:10.3389/fgene.2022.914354.
33. Yang M, Sun Y, Ma L, et al. Complex alternative splicing of the smarca2 gene suggests the importance of smarca2-B variants. J Cancer. 2011;2:386-400. doi:10.7150/jca.2.386.
34. Guerrero-Martínez JA, Reyes JC. High expression of SMARCA4 or SMARCA2 is frequently associated with an opposite prognosis in cancer. Sci Rep. 2018;8(1):2043.doi:10.1038/s41598-018-20217-3.
35. Fernando TM, Piskol R, Bainer R, et al. Functional characterization of SMARCA4 variants identified by targeted exome-sequencing of 131,668 cancer patients. Nat Commun. 2020;11(1):5551.doi:10.1038/s41467-020-19402-8.
36. Zhang FL, Li DQ. Targeting chromatin-remodeling factors in cancer cells: Promising molecules in cancer therapy. Int J Mol Sci. 2022;23(21):12815. doi:10.3390/ijms232112815.
37. Tian Y, Xu L, Li X, Li H, Zhao M. SMARCA4: Current status and future perspectives in non-small-cell lung cancer. Cancer Lett. 2023;554:216022. doi:10.1016/j.canlet.2022.216022.
38. Cruickshank VA, Sroczynska P, Sankar A, et al. SWI/SNF subunits SMARCA4, SMARCD2 and DPF2 collaborate in MLL-rearranged leukaemia maintenance. PLoS One. 2015;10(11):e0142806. doi:10.1371/journal.pone.0142806.
39. Liu J, Xie X, Xue M, et al.A pan-cancer analysis of the role of PBRM1 in human tumors. Stem Cells Int. 2022;2022:7676541.doi:10.1155/2022/7676541.
40. Dai J, Cui Y, Liang X, et al. PBRM1 mutation as a predictive biomarker for immunotherapy in multiple cancers. Front Genet. 2023;13:1066347. doi:10.3389/fgene.2022.1066347.
41. Hopson S, Thompson MJ. BAF180: Its roles in DNA repair and consequences in cancer. ACS Chem Biol. 2017;12(10):2482-2490. doi:10.1021/acschembio.7b00541.
42. Huber FM, Greenblatt SM, Davenport AM, et al. Histone-binding of DPF2 mediates its repressive role in myeloid differentiation. Proc Natl Acad Sci USA. 2017;114(23):6016-6021. doi:10.1073/pnas.1700328114.
43. Bakshi R, Hassan MQ, Pratap J, et al. The human SWI/SNF complex associates with RUNX1 to control transcription of hematopoietic target genes. J Cell Physiol. 2010;225(2):569-576. doi:10.1002/jcp.22240.
44. Soshnikova NV, Tatarskiy EV, Tatarskiy VV, et al. PHF10 subunit of PBAF complex mediates transcriptional activation by MYC. Oncogene. 2021;40(42):6071-6080. doi:10.1038/s41388-021-01994-0.
45. Naidu SR, Capitano M, Ropa J, Cooper S, Huang X, Broxmeyer HE. Chromatin remodeling subunit BRM and valine regulate hematopoietic stem/progenitor cell function and self-renewal via intrinsic and extrinsic effects. Leukemia. 2022;36:821-833. doi:10.1038/s41375-021-01426-8.