In Silico Identification of Tacrolimus As A Candidate Anticancer Agent Targeting PBRM1-Associated Pathways

Öz

Cancer continues to be a significant global health burden, and the search for new therapeutic strategies remains an important priority. Computational drug repurposing offers an efficient approach to exploring drug effects across multiple cancer cell line models by identifying novel applications of existing molecules through the integration of molecular and pharmacological data. In this study, we applied an in silico drug-repositioning approach to identify compounds with potential as cancer therapeutics. Using Gene2Drug, a pathway-based screening tool, we focused on agents interacting with the PBRM1 (polybromo-1) gene. Drug Set Enrichment Analysis (DSEA) was used to assist in in silico screening. The anti-tumor activities of candidate drugs were extracted from DepMap via a PRISM viability assay on various cancer cell lines. A total of 655 compounds were evaluated using the Drug Sensitivity AUC (from the CTD2 resource) tool. Among the compounds analyzed, tacrolimus—a calcineurin inhibitor approved for atopic dermatitis and organ transplant rejection—showed a statistically significant association with drug sensitivity (P = 8.29E-9). This finding underscores tacrolimus as a promising candidate for subsequent investigation. While further research is needed, these findings suggest tacrolimus is a potential in silico-identified candidate that could serve as a therapeutic option for various cancer cell line models.

Anahtar Kelimeler

• PBRM1
• targeted treatment
• drug repurposing
• tacrolimus
• in silico screening

PBRM1 ile İlişkili Yolakları Hedefleyen Aday Bir Antikanser Ajan Olarak Takrolimusun İn Silico Tanımlanması

Öz

Kanser, küresel ölçekte önemli bir sağlık sorunu olmaya devam etmektedir ve yeni tedavi stratejilerinin geliştirilmesi hâlâ öncelikli bir araştırma alanıdır. Hesaplamalı ilaç yeniden konumlandırma (computational drug repurposing), mevcut moleküllerin yeni kullanım alanlarını belirlemek için moleküler ve farmakolojik verilerin entegrasyonu yoluyla, birden fazla kanser hücre hattı modeli üzerinde ilaç etkilerinin araştırılmasını sağlayan verimli bir yaklaşımdır. Bu çalışmada, potansiyel kanser tedavi ajanlarını keşfetmek amacıyla in silico bir ilaç yeniden konumlandırma yaklaşımı uygulanmıştır. Gen temelli, yolak odaklı bir tarama aracı olan Gene2Drug kullanılarak, PBRM1 (polybromo-1) geni ile etkileşime giren bileşiklere odaklanılmıştır. Drug Set Enrichment Analysis (DSEA) yöntemi, bu in silico taramayı desteklemek amacıyla kullanılmıştır. Aday ilaçların antitümör aktiviteleri, DepMap veri tabanından elde edilen PRISM canlılık testleri aracılığıyla çeşitli kanser hücre hatlarında değerlendirilmiştir. Toplam 655 bileşik, CTD2 kaynağından elde edilen Drug Sensitivity AUC aracı kullanılarak analiz edilmiştir. Analiz edilen bileşikler arasında, atopik dermatit ve organ nakli reddi tedavisinde onaylanmış bir kalsinörin inhibitörü olan takrolimusun, kanser hücre hatlarında ilaç duyarlılığı ile istatistiksel olarak anlamlı bir ilişki gösterdiği belirlenmiştir (P = 8.29×10⁻⁹). Elde edilen sonuçlar, takrolimusun ileri çalışmalar açısından dikkate alınabilecek bir aday olabileceğini düşündürmektedir. Ek çalışmalara ihtiyaç duyulmakla birlikte, elde edilen sonuçlar takrolimusun farklı kanser hücre hattı modellerinde terapötik bir seçenek olarak değerlendirilebilecek potansiyel bir in silico aday olduğunu düşündürmektedir.

Anahtar Kelimeler

• PBRM1
• hedefe yönelik tedavi
• ilaç yeniden konumlandırma
• takrolimus
• in siliko tarama

Kaynakça

1. 1. Porter EG, Dykhuizen EC. Individual Bromodomains of Polybromo-1 Contribute to Chromatin Association and Tumor Suppression in Clear Cell Renal Carcinoma. J Biol Chem. 2017 Feb 17;292(7):2601-2610.
2. 2. Petell CJ, Burkholder NT, Ruiz PA, Skela J, Foreman JR, Southwell LE, et al. The bromo-adjacent homology domains of PBRM1 associate with histone tails and contribute to PBAF-mediated gene regulation. J Biol Chem. 2023 Aug;299(8):104996.
3. 3. Carril-Ajuria L, Santos M, Roldán-Romero JM, Rodriguez-Antona C, de Velasco G. Prognostic and Predictive Value of PBRM1 in Clear Cell Renal Cell Carcinoma. Cancers (Basel). 2019 Dec 19;12(1):16.
4. 4. Pawłowski R, Mühl SM, Sulser T, Krek W, Moch H, Schraml P. Loss of PBRM1 expression is associated with renal cell carcinoma progression. Int J Cancer. 2013 Jan 15;132(2):E11-7.
5. 5. Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature. 2011 Jan 27;469(7331):539-42.
6. 6. Nargund AM, Pham CG, Dong Y, Wang PI, Osmangeyoglu HU, Xie Y, et al. The SWI/SNF Protein PBRM1 Restrains VHL-Loss-Driven Clear Cell Renal Cell Carcinoma. Cell Rep. 2017 Mar 21;18(12):2893-2906.
7. 7. Wang Z, Peng S, Guo L, Xie H, Wang A, Shang Z, et al. Prognostic and clinicopathological value of PBRM1 expression in renal cell carcinoma. Clin Chim Acta. 2018 Nov;486:9-17.
8. 8. Yang Q, Shen R, Xu H, Shi X, Xu L, Zhang L, et al. Comprehensive analyses of PBRM1 in multiple cancer types and its association with clinical response to immunotherapy and immune infiltrates. Ann Transl Med. 2021 Mar;9(6):465.

9. 9. Jiao Y, Pawlik TM, Anders RA, Selaru FM, Streppel MM, Lucas DJ, et al. Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas. Nat Genet. 2013 Dec;45(12):1470-1473. doi: 10.1038/ng.2813. Epub 2013 Nov 3. PMID: 24185509; PMCID: PMC4013720.
10. 10. Mariano FV, Gondak Rde O, Martins AS, Coletta RD, Paes de Almeida O, Kowalski LP, et al. Genomic copy number alterations of primary and secondary metastasizing pleomorphic adenomas. Histopathology. 2015 Sep;67(3):410-5.
11. 11. Nakazato H, Takeshima H, Kishino T, Kubo E, Hattori N, Nakajima T, et al. Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis. PLoS One. 2016 Jan 26;11(1):e0147372.
12. 12. Xia W, Nagase S, Montia AG, Kalachikov SM, Keniry M, Su T, et al. BAF180 is a critical regulator of p21 induction and a tumor suppressor mutated in breast cancer. Cancer Res. 2008 Mar 15;68(6):1667-74.
13. 13. Dai J, Cui Y, Liang X, Xu J, Li J, Chen Y, et al. PBRM1 mutation as a predictive biomarker for immunotherapy in multiple cancers. Front Genet. 2023 Jan 9;13:1066347.
14. 14. Liu XD, Kong W, Peterson CB, McGrail DJ, Hoang A, Zhang X, et al. PBRM1 loss defines a nonimmunogenic tumor phenotype associated with checkpoint inhibitor resistance in renal carcinoma. Nat Commun. 2020 May 1;11(1):2135.
15. 15. Niknafs N, Balan A, Cherry C, Hummelink K, Monkhorst K, Shao XM, et al. Persistent mutation burden drives sustained anti-tumor immune responses. Nat Med. 2023 Feb;29(2):440-449.
16. 16. Xia Y, Sun M, Huang H, Jin WL. Drug repurposing for cancer therapy. Signal Transduct Target Ther. 2024 Apr 19;9(1):92.
17. 17. Hijazi MA, Gessner A, El-Najjar N. Repurposing of Chronically Used Drugs in Cancer Therapy: A Chance to Grasp. Cancers (Basel). 2023 Jun 15;15(12):3199.
18. 18. Al Khzem AH, Gomaa MS, Alturki MS, Tawfeeq N, Sarafroz M, Alonaizi SM, et al. Drug Repurposing for Cancer Treatment: A Comprehensive Review. Int J Mol Sci. 2024 Nov 19;25(22):12441.
19. 19. Siddiqui S, Deshmukh AJ, Mudaliar P, Nalawade AJ, Iyer D, Aich J. Drug repurposing: re-inventing therapies for cancer without re-entering the development pipeline-a review. J Egypt Natl Canc Inst. 2022 Aug 8;34(1):33.
20. 20. Napolitano F, Carrella D, Mandriani B, Pisonero-Vaquero S, Sirci F, Medina DL, et al. gene2drug: a computational tool for pathway-based rational drug repositioning. Bioinformatics. 2018 May 1;34(9):1498-1505.
21. 21. Lewis KM, Bharadwaj U, Eckols TK, Kolosov M, Kasembeli MM, Fridley C, et al. Small-molecule targeting of signal transducer and activator of transcription (STAT) 3 to treat non-small cell lung cancer. Lung Cancer. 2015 Nov;90(2):182-90.
22. 22. Corsello SM, Nagari RT, Spangler RD, Rossen J, Kocak M, Bryan JG, et al. Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling. Nat Cancer 2020;1:235–48.
23. 23. Arafeh R, Shibue T, Dempster JM, Hahn WC, Vazquez F. The present and future of the Cancer Dependency Map. Nat Rev Cancer. 2025 Jan;25(1):59-73.
24. 24. Hansen FG, Jørgensen MG, Thomsen JB, Sørensen JA. Topical tacrolimus for the amelioration of breast cancer-related lymphedema (TACLE Trial): a study protocol for a randomized, double-blind, placebo-controlled phase II/III trial. Trials. 2025 Apr 8;26(1):127.
25. 25. BindingDB. Tacrolimus (FK506) binding to FKBP1A (FKBP12). BindingDB. Available from: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/MolStructure.jsp?monomerid=50030448 .
26. 26. Tong M, Jiang Y. FK506-Binding Proteins and Their Diverse Functions. Curr Mol Pharmacol. 2015;9(1):48-65.
27. 27. Siamakpour-Reihani S, Caster J, Bandhu Nepal D, Courtwright A, Hilliard E, Usary J, et al. The role of calcineurin/NFAT in SFRP2 induced angiogenesis--a rationale for breast cancer treatment with the calcineurin inhibitor tacrolimus. PLoS One. 2011;6(6):e20412.
28. 28. Shoughy SS. Topical tacrolimus in anterior segment inflammatory disorders. Eye Vis (Lond). 2017 Mar 9;4:7.
29. 29. Bocklud BE, Roberts LT, Roberts DT, Schwartz A, Siddaiah H, Ahmadzadeh S, et al. Topical Medications for Atopic Dermatitis and Effects on Increasing Lymphoma Risks. Cureus. 2023 Nov 20;15(11):e49135.
30. 30. Li Y, Wang Y, Li J, Ling Z, Chen W, Zhang L, et al. Tacrolimus inhibits oral carcinogenesis through cell cycle control. Biomed Pharmacother. 2021 Jul;139:111545.
31. 31. Choi, Y.H. Tacrolimus Induces Apoptosis in Leukemia Jurkat Cells through Inactivation of the Reactive Oxygen Species-dependent Phosphoinositide-3-Kinase/Akt Signaling Pathway. Biotechnol Bioproc E 27, 183–192 (2022).
32. 32. Zhu H, Sun Q, Tan C, Xu M, Dai Z, Wang Z, et al. Tacrolimus promotes hepatocellular carcinoma and enhances CXCR4/SDF‑1α expression in vivo. Mol Med Rep. 2014 Aug;10(2):585-92.
33. 33. Quist-Løkken I, Andersson-Rusch C, Kastnes MH, Kolos JM, Jatzlau J, Hella H, et al. FKBP12 is a major regulator of ALK2 activity in multiple myeloma cells. Cell Commun Signal. 2023 Jan 30;21(1):25.
34. 34. Spiekerkoetter E, Tian X, Cai J, Hopper RK, Sudheendra D, Li CG, et al. FK506 activates BMPR2, rescues endothelial dysfunction, and reverses pulmonary hypertension. J Clin Invest. 2013 Aug;123(8):3600-13.