Project 3 - Drug Mechanism of Action-based targeting of tumor subpopulations

Investigators: Andrea Califano (Project Leader), Cory Abate-Shen, Kenneth Olive, Andrew Kung

In Project 3 we will elucidate the proteome-wide Mechanism of Action (MoA) of clinically relevant compounds via network-based analyses, to target non-oncogene dependencies of molecularly distinct cell states comprising either malignant or immunosuppressive tumor microenvironment (TME) cells coexisting in the same tumor mass. Targeting subpopulations corresponding to distinct cell states is becoming increasingly critical because the heterogeneity and plasticity of both malignant and other TME-related subpopulations have emerged as, perhaps, the most fundamental obstacles to achieving durable responses in cancer patients. To study inter-tumor heterogeneity of drug sensitivity and to develop methodologies to identify high-fidelity, patient-matched models, we will focus on metastatic castration resistant prostate cancer (mCRPC) and on its aggressive neuroendocrine subtype (NEPC) (1, 2). Specifically, we will leverage a novel molecular triangulation methodology (OncoLoop) (3) to first generate drug perturbation profiles and then to validate predicted therapies in preclinical models that recapitulate the drug sensitivity of human tumors. Conversely, to elucidate the molecular dependencies of immunosuppressive TME subpopulations, we will focus on pancreatic ductal adenocarcinoma (PDA) (4, 5, 6), a heterogeneous cancer with a highly immunosuppressive TME. We will first elucidate and target non-oncogene dependencies in six isogenic, yet molecularly distinct malignant subpopulations present in virtually all tumors (4). We will then focus on its TME, which comprises multiple immunosuppressive subpopulations, including three cancer associated fibroblast (CAF) subtypes (6), TREM2+/C1Q+ macrophages (7), and immunosuppressive regulatory T cells (8). We propose that achieving durable response will require targeting distinct malignant compartments, to abrogate viability or reprogram cells to a drug-sensitive state, and/or rescuing immune response by targeting immunosuppressive TME subpopulations. Our goals include:

• Developing novel, fully generalizable methodologies to assess tumor model fidelity in terms of recapitulating drug mechanism of action and drug sensitivity, including for cell lines, organoids, GEMMs, and PDX models. As proof of concept, this will be applied to the elucidation and experimental validation of drugs targeting Master Regulator (MR) proteins representing non-oncogene dependencies of mCRPC and of its aggressive neuroendocrine subtype (NEPC). These methodologies will be developed to be fully generalizable to virtually any other tumor context, including at the single cell level. 
• Extending the OncoTreat (9) and OncoTarget (10) algorithms to elucidate and pharmacologically target Master Regulator dependencies in molecularly distinct, malignant cell subpopulations, at the single cell level. As proof-of-concept, we will focus on six subpopulations contributing to PDA intra-tumor heterogeneity. Drugs will be validated by assessing treatment-induced depletion/reprogramming of target subpopulation(s), first in syngeneic transplants and then in KPC GEMMs. 
• Pharmacological targeting of Master Regulator dependencies in distinct immunosuppressive subpopulations of the TME. As proof-of-concept, we will perform OncoTreat and OncoTarget analysis of subpopulations isolated from the TME of PDA patient/model-derived resections. Predictions aimed at rescuing immune sensitivity and response to immune checkpoint inhibitors will be validated in syngeneic models and KPC GEMM, as monotherapy and in combination with immune checkpoint inhibitors.

References

1. Zou M, Toivanen R, Mitrofanova A, Floch N, Hayati S, Sun Y, Le Magnen C, Chester D, Mostaghel EA, Califano A, Rubin MA, Shen MM, Abate-Shen C. Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer. Cancer Discov. 2017;7(7):736-49. Epub 20170414. doi: 10.1158/2159-8290.CD-16-1174. PubMed PMID: 28411207; PMCID: PMC5501744.

2. Arriaga JM, Panja S, Alshalalfa M, Zhao J, Zou M, Giacobbe A, Madubata CJ, Kim JY, Rodriguez A, Coleman I, Virk RK, Hibshoosh H, Ertunc O, Ozbek B, Fountain J, Jeffrey Karnes R, Luo J, Antonarakis ES, Nelson PS, Feng FY, Rubin MA, De Marzo AM, Rabadan R, Sims PA, Mitrofanova A, Abate-Shen C. A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance. Nat Cancer. 2020;1(11):1082-96. Epub 20201019. doi: 10.1038/s43018-020-00125-0. PubMed PMID: 34085047; PMCID: PMC8171279.

3. Vasciaveo A, Arriaga JM, de Almeida FN, Zou M, Douglass EF, Picech F, Shibata M, Rodriguez-Calero A, de Brot S, Mitrofanova A, Chua CW, Karan C, Realubit R, Pampou S, Kim JY, Afari SN, Mukhammadov T, Zanella L, Corey E, Alvarez MJ, Rubin MA, Shen MM, Califano A, Abate-Shen C. OncoLoop: A Network-Based Precision Cancer Medicine Framework. Cancer Discov. 2023;13(2):386-409. doi: 10.1158/2159-8290.CD-22-0342. PubMed PMID: 36374194; PMCID: PMC9905319.

4. Laise P, Turunen M, Garcia AC, Tomassoni L, Maurer HC, Elyada E, Schmierer B, Worley J, Kesner J, Tan X, Fernandez EC, Wong K, Wasko UN, Tagore S, Wang ALE, Ge S, Iuga AC, Griffin A, Wong W, Manji GA, Alvarez MJ, Notta F, Tuveson DA, Olive KP, Califano A. Developmental and MAPK-responsive transcription factors drive distinct malignant subtypes and genetic dependencies in pancreatic cancer. bioRxiv. 2022:2020.10.27.357269. doi: 10.1101/2020.10.27.357269.

5. Maurer C, Holmstrom SR, He J, Laise P, Su T, Ahmed A, Hibshoosh H, Chabot JA, Oberstein PE, Sepulveda AR, Genkinger JM, Zhang J, Iuga AC, Bansal M, Califano A, Olive KP. Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes. Gut. 2019;68(6):1034-43. Epub 20190118. doi: 10.1136/gutjnl-2018-317706. PubMed PMID: 30658994; PMCID: PMC6509007.

6. Elyada E, Bolisetty M, Laise P, Flynn WF, Courtois ET, Burkhart RA, Teinor JA, Belleau P, Biffi G, Lucito MS, Sivajothi S, Armstrong TD, Engle DD, Yu KH, Hao Y, Wolfgang CL, Park Y, Preall J, Jaffee EM, Califano A, Robson P, Tuveson DA. Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts. Cancer Discov. 2019;9(8):1102-23. Epub 20190613. doi: 10.1158/2159-8290.CD-19-0094. PubMed PMID: 31197017; PMCID: PMC6727976.

7. Obradovic A, Chowdhury N, Haake SM, Ager C, Wang V, Vlahos L, Guo XV, Aggen DH, Rathmell WK, Jonasch E, Johnson JE, Roth M, Beckermann KE, Rini BI, McKiernan J, Califano A, Drake CG. Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages. Cell. 2021;184(11):2988-3005 e16. Epub 20210520. doi: 10.1016/j.cell.2021.04.038. PubMed PMID: 34019793; PMCID: PMC8479759.

8. Hiraoka N, Onozato K, Kosuge T, Hirohashi S. Prevalence of FOXP3+ regulatory T cells increases during the progression of pancreatic ductal adenocarcinoma and its premalignant lesions. Clin Cancer Res. 2006;12(18):5423-34. doi: 10.1158/1078-0432.CCR-06-0369. PubMed PMID: 17000676.

9. Alvarez MJ, Subramaniam PS, Tang LH, Grunn A, Aburi M, Rieckhof G, Komissarova EV, Hagan EA, Bodei L, Clemons PA, Dela Cruz FS, Dhall D, Diolaiti D, Fraker DA, Ghavami A, Kaemmerer D, Karan C, Kidd M, Kim KM, Kim HC, Kunju LP, Langel U, Li Z, Lee J, Li H, LiVolsi V, Pfragner R, Rainey AR, Realubit RB, Remotti H, Regberg J, Roses R, Rustgi A, Sepulveda AR, Serra S, Shi C, Yuan X, Barberis M, Bergamaschi R, Chinnaiyan AM, Detre T, Ezzat S, Frilling A, Hommann M, Jaeger D, Kim MK, Knudsen BS, Kung AL, Leahy E, Metz DC, Milsom JW, Park YS, Reidy-Lagunes D, Schreiber S, Washington K, Wiedenmann B, Modlin I, Califano A. A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors. Nat Genet. 2018;50(7):979-89. Epub 20180618. doi: 10.1038/s41588-018-0138-4. PubMed PMID: 29915428; PMCID: PMC6421579.

10. Coutinho DF, Mundi PS, Marks LJ, Burke C, Ortiz MV, Diolaiti D, Bird L, Vallance KL, Ibanez G, You D, Long M, Rosales N, Grunn A, Ndengu A, Siddiquee A, Gaviria ES, Rainey AR, Fazlollahi L, Hosoi H, Califano A, Kung AL, Dela Cruz FS. Validation of a non-oncogene encoded vulnerability to exportin 1 inhibition in pediatric renal tumors. Med. 2022;3(11):774-91 e7. Epub 20221003. doi: 10.1016/j.medj.2022.09.002. PubMed PMID: 36195086; PMCID: PMC9669237.