Sachet A. Shukla, PhD, MS

Peer-Reviewed Articles

1. Gordon BK, Muhowski EM, Singh J, Ravikrishnan J, Peris-Cuesta A, Diaz Rohena D, Sanchez JR, Thangavadivel S, Benrashid S, He A, Marr AR, Mitchell AD, Urrutia JM, Misra S, Lai TH, Yu L, Walker BR, Perry E, Shukla SA, Grieselhuber NR, Rogers KA, Lapalombella R, Blachly JS, Kittai AS, Bhat SA, Jain N, Wierda WG, Byrd JC, Niesman M, Zhang K, Sampath D, Woyach JA. PKCbeta inhibitor MS-553 displays preclinical efficacy in both treatment-naive and BTK inhibitor-resistant Chronic Lymphocytic Leukemia. Blood Cancer Discov, 2026. e-Pub 2026. PMID: 41190953.
2. Blass, E, Keskin, DB, Tu, CR, Forman, C, Vanasse, AP, Sax, HE, Shim, B, Chea, VA, Kim, N, Carulli, IP, Southard, J, Lyu, H, Lu, W, Rickles-Young, M, Afeyan, AB, Olive, O, Mehndiratta, A, Greenslade, H, Shetty, K, Baginska, J, Gomez Diaz, I, Nau, A, Pfaff, KL, Gans, A, Ranasinghe, S, Buchbinder, E, Sussman, TA, Insco, ML, Yoon, CH, Rodig, SJ, Shukla, SA, Li, S, Aster, JC, Braun, DA, Cibulskis, C, Hacohen, N, Neuberg, D, Giobbie-Hurder, A, Livak, KJ, Fritsch, E, Oliveira, G, Simon, JM, Wu, C, Ott, PA. A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma. Cell 188(19):5125-5141.e27, 2025. e-Pub 2025. PMID: 40645179.
3. Labaki C, Saad E, Madsen KN, Hobeika C, Bi K, Alchoueiry M, Camp S, Hou Y, Bakouny Z, Matar S, El Ahmar N, Nyman J, Zhang L, Priolo C, Rout R, Daou M, Khabibullin D, Salem S, Schindler N, Saliby RM, Meli K, Wells JC, Pimenta E, Takemura K, Park J, Eid M, Semaan K, Fu J, Denize T, El Hajj Chehade R, Machaalani M, Nawfal R, Khatoun WD, eh M, El Masri J, Haddad NR, Xu W, McGregor BA, Hirsch MS, Xie W, Heng DYC, McDermott DF, Signoretti S, Van Allen EM, Shukla SA, Choueiri TK, Henske EP, Braun DA. Tumor-Intrinsic and Microenvironmental Determinants of Impaired Antitumor Immunity in Chromophobe Renal Cell Carcinoma. Journal of Clinical Oncology 43(23):2639-2654, 2025. e-Pub 2025. PMID: 40601888.
4. McCurry D, Ge Z, Lee J, Pasumarthi R, Leng X, Koehnke T, Pasvolsky O, Raparla P, Nguyen V, Maurer K, Li S, Livak KJ, Danson E, Thakkar B, Azizi E, Soiffer RJ, Shukla SA, Majeti R, Ritz J, Wu CJ, Molldrem JJ, Bachireddy P. ASXL1 truncating mutations drive leukemic resistance to T cell attack. bioRxiv, 2025. e-Pub 2025. PMID: 40661385.
5. Hamada, T, Ugai, T, Gurjao, C, Ugai, S, Zhang, X, Haruki, K, Takashima, Y, Akimoto, N, Lau, MC, Matsuda, K, Nakazawa, N, Higashioka, M, Miyahara, S, Kosumi, K, Masugi, Y, Liu, L, Cao, Y, Nevo, D, Wang, M, Nishihara, R, Shukla, SA, Wu, C, Garraway, LA, Meyerhardt, JA, Giovannucci, E, Nowak, JA, Fuchs, C, Chan, AT, Song, M, Giannakis, M, Ogino, S. Smoking habit and long-term colorectal cancer incidence by exome-wide mutational and neoantigen loads. BMJ Oncology 4(1), 2025. e-Pub 2025. PMID: 40519220.
6. Jiang Q, Braun DA, Clauser KR, Ramesh V, Shirole NH, Duke-Cohan JE, Nabilsi N, Kramer NJ, Forman C, Lippincott IE, Klaeger S, Phulphagar KM, Chea V, Kim N, Vanasse AP, Saad E, Parsons T, Carr-Reynolds M, Carulli I, Pinjusic K, Jiang Y, Li R, Syamala S, Rachimi S, Verzani EK, Stevens JD, Lane WJ, Camp SY, Meli K, Pappalardi MB, Herbert ZT, Qiu X, Cejas P, Long HW, Shukla SA, Van Allen EM, Choueiri TK, Churchman LS, Abelin JG, Gurer C, MacBeath G, Childs RW, Carr SA, Keskin DB, Wu CJ, Kaelin WG Jr. HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy. Cell 188(7):1807-1827.e34, 2025. e-Pub 2025. PMID: 40023154.
7. Braun DA, Moranzoni G, Chea V, McGregor BA, Blass E, Tu CR, Vanasse AP, Forman C, Forman J, Afeyan AB, Schindler NR, Liu Y, Li S, Southard J, Chang SL, Hirsch MS, LeBoeuf NR, Olive O, Mehndiratta A, Greenslade H, Shetty K, Klaeger S, Sarkizova S, Pedersen CB, Mossanen M, Carulli I, Tarren A, Duke-Cohan J, Howard AA, Iorgulescu JB, Shim B, Simon JM, Signoretti S, Aster JC, Elagina L, Carr SA, Leshchiner I, Getz G, Gabriel S, Hacohen N, Olsen LR, Oliveira G, Neuberg DS, Livak KJ, Shukla SA, Fritsch EF, Wu CJ, Keskin DB, Ott PA, Choueiri TK. A neoantigen vaccine generates antitumour immunity in renal cell carcinoma. Nature 639(8054):474-482, 2025. e-Pub 2025. PMID: 39910301.
8. Xu W, Birch G, Meliki A, Moritz V, Bharadwaj M, Schindler NR, Labaki C, Saliby RM, Dinh K, Horst JT, Sun M, Kashima S, Hugaboom M, Dighe A, Machaalani M, Lee GM, Hurwitz M, McGregor BA, Hirsch MS, Shukla SA, McDermott DF, Signoretti S, Romee R, Choueiri TK, Braun DA. Progressive natural killer cell dysfunction in advanced-stage clear-cell renal cell carcinoma and association with clinical outcomes. ESMO Open 10(2):104105, 2025. e-Pub 2025. PMID: 39813824.
9. Jammihal T, Saliby RM, Labaki C, Soulati H, Gallegos J, Peris A, McCurry D, Yu C, Shah V, Poduval D, El Zarif T, El Ahmar N, Laimon YN, Eid M, Sheshdeh AB, Krajewski KM, Buttner FA, Schwab M, Heng D, Casellas RC, Rai K, Zacharias Millward NM, Msaouel P, Karam J, Signoretti S, Van Allen E, Choueiri TK, Braun DA, Shukla SA. Immunogenomic determinants of exceptional response to immune checkpoint inhibition in renal cell carcinoma. Nat Cancer 6(2):372-384, 2025. e-Pub 2025. PMID: 39789182.
10. Parry, EM, Lemvigh, C, Deng, S, Dangle, N, Ruthen, NG, Knisbacher, BA, Broséus, J, Hergalant, S, Guièze, R, Li, S, Zhang, W, Johnson, C, Long, JM, Yin, S, Werner, L, Anandappa, AJ, Purroy, N, Gohil, SH, Oliveira, G, Bachireddy, P, Shukla, SA, Huang, T, Khoury, J, Thakral, B, Dickinson, M, Tam, C, Livak, KJ, Getz, G, Neuberg, D, Feugier, P, Kharchenko, PV, Wierda, WG, Olsen, LR, Jain, N, Wu, C. ZNF683 marks a CD8+ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome. Cancer cell 41(10):1803-1816.e8, 2023. e-Pub 2023. PMID: 37738974.
11. Lai TH, Ozer HG, Gasparini P, Nigita G, Distefano R, Yu L, Ravikrishnan J, Yilmaz S, Gallegos J, Shukla S, Puduvalli V, Woyach J, Lapalombella R, Blachly J, Byrd JC, Sampath D. HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia. Blood Adv 7(12):2897-2911, 2023. e-Pub 2023. PMID: 36287107.
12. Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O'Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nat Commun 14(1):346, 2023. e-Pub 2023. PMID: 36681680.
13. Groha S, Alaiwi SA, Xu W, Naranbhai V, Nassar AH, Bakouny Z, El Zarif T, Saliby RM, Wan G, Rajeh A, Adib E, Nuzzo PV, Schmidt AL, Labaki C, Ricciuti B, Alessi JV, Braun DA, Shukla SA, Keenan TE, Van Allen E, Awad MM, Manos M, Rahma O, Zubiri L, Villani AC, Fairfax B, Hammer C, Khan Z, Reynolds K, Semenov Y, Schrag D, Kehl KL, Freedman ML, Choueiri TK, Gusev A. Germline variants associated with toxicity to immune checkpoint blockade. Nat Med 28(12):2584-2591, 2022. e-Pub 2022. PMID: 36526723.
14. Denize T, Hou Y, Pignon JC, Walton E, West DJ, Freeman GJ, Braun DA, Wu CJ, Gupta S, Motzer RJ, Atkins MB, McDermott D, Choueiri TK, Shukla SA, Signoretti S. Transcriptomic Correlates of Tumor Cell PD-L1 Expression and Response to Nivolumab Monotherapy in Metastatic Clear Cell Renal Cell Carcinoma. Clin Cancer Res 28(18):4045-4055, 2022. e-Pub 2022. PMID: 35802667.
15. Barroso-Sousa R, Forman J, Collier K, Weber ZT, Jammihal TR, Kao KZ, Richardson ET, Keenan T, Cohen O, Manos MP, Brennick RC, Ott PA, Hodi FS, Dillon DA, Attaya V, O'Meara T, Lin NU, Van Allen EM, Rodig S, Winer EP, Mittendorf EA, Wu CJ, Wagle N, Stover DG, Shukla SA, Tolaney SM. Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit. JCO Precis Oncol 6:e2100413, 2022. e-Pub 2022. PMID: 35797509.
16. Baldominos P, Barbera-Mourelle A, Barreiro O, Huang Y, Wight A, Cho JW, Zhao X, Estivill G, Adam I, Sanchez X, McCarthy S, Schaller J, Khan Z, Ruzo A, Pastorello R, Richardson ET, Dillon D, Montero-Llopis P, Barroso-Sousa R, Forman J, Shukla SA, Tolaney SM, Mittendorf EA, von Andrian UH, Wucherpfennig KW, Hemberg M, Agudo J. Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche. Cell 185(10):1694-1708.e19, 2022. e-Pub 2022. PMID: 35447074.
17. Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol 40(2):209-217, 2022. e-Pub 2022. PMID: 34663921.
18. Naranbhai V, Viard M, Dean M, Groha S, Braun DA, Labaki C, Shukla SA, Yuki Y, Shah P, Chin K, Wind-Rotolo M, Mu XJ, Robbins PB, Gusev A, Choueiri TK, Gulley JL, Carrington M. HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study. Lancet Oncol 23(1):172-184, 2022. e-Pub 2022. PMID: 34895481.
19. Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, Sanchez-Espiridion B, Janssens S, Taing L, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Sahu A, Jiang P, Yan C, Duose DY, Cerami E, Chen L, Cohen D, Chen Q, Enos R, Huang X, Lee JJ, Liu Y, Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla S, Tang M, Tsuji J, Uduman M, Wang X, Weirather JL, Yu J, Yu J, Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal A, Karlovich C, Gabriel SB, Wistuba II, Liu XS, Wu CJ. Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network. Clin Cancer Res 27(18):5049-5061, 2021. e-Pub 2021. PMID: 33323402.
20. Oliveira G, Stromhaug K, Klaeger S, Kula T, Frederick DT, Le PM, Forman J, Huang T, Li S, Zhang W, Xu Q, Cieri N, Clauser KR, Shukla SA, Neuberg D, Justesen S, MacBeath G, Carr SA, Fritsch EF, Hacohen N, Sade-Feldman M, Livak KJ, Boland GM, Ott PA, Keskin DB, Wu CJ. Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma. Nature 596(7870):119-125, 2021. e-Pub 2021. PMID: 34290406.
21. Adib E, Nassar AH, Akl EW, Abou Alaiwi S, Nuzzo PV, Mouhieddine TH, Sonpavde G, Haddad RI, Mouw KW, Giannakis M, Hodi FS, Shukla SA, Gusev A, Braun DA, Choueiri TK, Kwiatkowski DJ. CDKN2A Alterations and Response to Immunotherapy in Solid Tumors. Clin Cancer Res 27(14):4025-4035, 2021. e-Pub 2021. PMID: 34074656.
22. Weber ZT, Collier KA, Tallman D, Forman J, Shukla S, Asad S, Rhoades J, Freeman S, Parsons HA, Williams NO, Barroso-Sousa R, Stover EH, Mahdi H, Cibulskis C, Lennon NJ, Ha G, Adalsteinsson VA, Tolaney SM, Stover DG. Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer. Genome Med 13(1):89, 2021. e-Pub 2021. PMID: 34016182.
23. Braun DA, Street K, Burke KP, Cookmeyer DL, Denize T, Pedersen CB, Gohil SH, Schindler N, Pomerance L, Hirsch L, Bakouny Z, Hou Y, Forman J, Huang T, Li S, Cui A, Keskin DB, Steinharter J, Bouchard G, Sun M, Pimenta EM, Xu W, Mahoney KM, McGregor BA, Hirsch MS, Chang SL, Livak KJ, McDermott DF, Shukla SA, Olsen LR, Signoretti S, Sharpe AH, Irizarry RA, Choueiri TK, Wu CJ. Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. Cancer Cell 39(5):632-648.e8, 2021. e-Pub 2021. PMID: 33711273.
24. Trinh A, Gil Del Alcazar CR, Shukla SA, Chin K, Chang YH, Thibault G, Eng J, Jovanovic B, Aldaz CM, Park SY, Jeong J, Wu C, Gray J, Polyak K. Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System. Mol Cancer Res 19(4):623-635, 2021. e-Pub 2021. PMID: 33443130.
25. Ficial M, Jegede OA, Sant'Angelo M, Hou Y, Flaifel A, Pignon JC, Braun DA, Wind-Rotolo M, Sticco-Ivins MA, Catalano PJ, Freeman GJ, Sharpe AH, Hodi FS, Motzer RJ, Wu CJ, Atkins MB, McDermott DF, Shukla SA, Choueiri TK, Signoretti S. Expression of T-Cell Exhaustion Molecules and Human Endogenous Retroviruses as Predictive Biomarkers for Response to Nivolumab in Metastatic Clear Cell Renal Cell Carcinoma. Clin Cancer Res 27(5):1371-1380, 2021. e-Pub 2021. PMID: 33219016.
26. Hu Z, Leet DE, Allesøe RL, Oliveira G, Li S, Luoma AM, Liu J, Forman J, Huang T, Iorgulescu JB, Holden R, Sarkizova S, Gohil SH, Redd RA, Sun J, Elagina L, Giobbie-Hurder A, Zhang W, Peter L, Ciantra Z, Rodig S, Olive O, Shetty K, Pyrdol J, Uduman M, Lee PC, Bachireddy P, Buchbinder EI, Yoon CH, Neuberg D, Pentelute BL, Hacohen N, Livak KJ, Shukla SA, Olsen LR, Barouch DH, Wucherpfennig KW, Fritsch EF, Keskin DB, Wu CJ, Ott PA. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma. Nat Med 27(3):515-525, 2021. e-Pub 2021. PMID: 33479501.
27. Bakouny Z, Braun DA, Shukla SA, Pan W, Gao X, Hou Y, Flaifel A, Tang S, Bosma-Moody A, He MX, Vokes N, Nyman J, Xie W, Nassar AH, Abou Alaiwi S, Flippot R, Bouchard G, Steinharter JA, Nuzzo PV, Ficial M, Sant'Angelo M, Forman J, Berchuck JE, Dudani S, Bi K, Park J, Camp S, Sticco-Ivins M, Hirsch L, Baca SC, Wind-Rotolo M, Ross-Macdonald P, Sun M, Lee GM, Chang SL, Wei XX, McGregor BA, Harshman LC, Genovese G, Ellis L, Pomerantz M, Hirsch MS, Freedman ML, Atkins MB, Wu CJ, Ho TH, Linehan WM, McDermott DF, Heng DYC, Viswanathan SR, Signoretti S, Van Allen EM, Choueiri TK. Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma. Nat Commun 12(1):808, 2021. e-Pub 2021. PMID: 33547292.
28. Li Y, Burgman B, McGrail DJ, Sun M, Qi D, Shukla SA, Wu E, Capasso A, Lin SY, Wu CJ, Eckhardt SG, Mills GB, Li B, Sahni N, Yi SS. Integrated Genomic Characterization of the Human Immunome in Cancer. Cancer Res 80(21):4854-4867, 2020. e-Pub 2020. PMID: 32855206.
29. Wells DK, van Buuren MM, Dang KK, Hubbard-Lucey VM, Sheehan KCF, Campbell KM, Lamb A, Ward JP, Sidney J, Blazquez AB, Rech AJ, Zaretsky JM, Comin-Anduix B, Ng AHC, Chour W, Yu TV, Rizvi H, Chen JM, Manning P, Steiner GM, Doan XC, Selection Alliance TN, Merghoub T, Guinney J, Kolom A, Selinsky C, Ribas A, Hellmann MD, Hacohen N, Sette A, Heath JR, Bhardwaj N, Ramsdell F, Schreiber RD, Schumacher TN, Kvistborg P, Defranoux NA. Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction. Cell 183(3):818-834.e13, 2020. e-Pub 2020. PMID: 33038342.
30. Bachireddy P, Ennis C, Nguyen VN, Gohil SH, Clement K, Shukla SA, Forman J, Barkas N, Freeman S, Bavli N, Elagina L, Leshchiner I, Mohammad AW, Mathewson ND, Keskin DB, Rassenti LZ, Kipps TJ, Brown JR, Getz G, Ho VT, Gnirke A, Neuberg D, Soiffer RJ, Ritz J, Alyea EP, Kharchenko PV, Wu CJ. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect. Sci Transl Med 12(561), 2020. e-Pub 2020. PMID: 32938797.
31. Abou Alaiwi S, Nassar AH, Xie W, Bakouny Z, Berchuck JE, Braun DA, Baca SC, Nuzzo PV, Flippot R, Mouhieddine TH, Spurr LF, Li YY, Li T, Flaifel A, Steinharter JA, Margolis CA, Vokes NI, Du H, Shukla SA, Cherniack AD, Sonpavde G, Haddad RI, Awad MM, Giannakis M, Hodi FS, Liu XS, Signoretti S, Kadoch C, Freedman ML, Kwiatkowski DJ, Van Allen EM, Choueiri TK. Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors. Cancer Immunol Res 8(8):1075-1084, 2020. e-Pub 2020. PMID: 32321774.
32. Braun DA, Hou Y, Bakouny Z, Ficial M, Sant' Angelo M, Forman J, Ross-Macdonald P, Berger AC, Jegede OA, Elagina L, Steinharter J, Sun M, Wind-Rotolo M, Pignon JC, Cherniack AD, Lichtenstein L, Neuberg D, Catalano P, Freeman GJ, Sharpe AH, McDermott DF, Van Allen EM, Signoretti S, Wu CJ, Shukla SA, Choueiri TK. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nat Med 26(6):909-918, 2020. e-Pub 2020. PMID: 32472114.
33. Zhang H, Liu L, Zhang J, Chen J, Ye J, Shukla S, Qiao J, Zhan X, Chen H, Wu CJ, Fu YX, Li B. Investigation of Antigen-Specific T-Cell Receptor Clusters in Human Cancers. Clin Cancer Res 26(6):1359-1371, 2020. e-Pub 2020. PMID: 31831563.
34. Braun DA, Ishii Y, Walsh AM, Van Allen EM, Wu CJ, Shukla SA, Choueiri TK. Clinical Validation of PBRM1 Alterations as a Marker of Immune Checkpoint Inhibitor Response in Renal Cell Carcinoma. JAMA Oncol 5(11):1631-1633, 2019. e-Pub 2019. PMID: 31486842.
35. Li H, Bullock K, Gurjao C, Braun D, Shukla SA, Bossé D, Lalani AA, Gopal S, Jin C, Horak C, Wind-Rotolo M, Signoretti S, McDermott DF, Freeman GJ, Van Allen EM, Schreiber SL, Stephen Hodi F, Sellers WR, Garraway LA, Clish CB, Choueiri TK, Giannakis M. Metabolomic adaptations and correlates of survival to immune checkpoint blockade. Nat Commun 10(1):4346, 2019. e-Pub 2019. PMID: 31554815.
36. Li S, Sun J, Allesøe R, Datta K, Bao Y, Oliveira G, Forman J, Jin R, Olsen LR, Keskin DB, Shukla SA, Wu CJ, Livak KJ. RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis. Nat Protoc 14(8):2571-2594, 2019. e-Pub 2019. PMID: 31341290.
37. Pignon JC, Jegede O, Shukla SA, Braun DA, Horak CE, Wind-Rotolo M, Ishii Y, Catalano PJ, Grosha J, Flaifel A, Novak JS, Mahoney KM, Freeman GJ, Sharpe AH, Hodi FS, Motzer RJ, Choueiri TK, Wu CJ, Atkins MB, McDermott DF, Signoretti S. irRECIST for the Evaluation of Candidate Biomarkers of Response to Nivolumab in Metastatic Clear Cell Renal Cell Carcinoma: Analysis of a Phase II Prospective Clinical Trial. Clin Cancer Res 25(7):2174-2184, 2019. e-Pub 2019. PMID: 30670497.
38. Mahoney KM, Shukla SA, Patsoukis N, Chaudhri A, Browne EP, Arazi A, Eisenhaure TM, Pendergraft WF, Hua P, Pham HC, Bu X, Zhu B, Hacohen N, Fritsch EF, Boussiotis VA, Wu CJ, Freeman GJ. A secreted PD-L1 splice variant that covalently dimerizes and mediates immunosuppression. Cancer Immunol Immunother 68(3):421-432, 2019. e-Pub 2019. PMID: 30564891.
39. Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, Oliveira G, Giobbie-Hurder A, Felt K, Gjini E, Shukla SA, Hu Z, Li L, Le PM, Allesøe RL, Richman AR, Kowalczyk MS, Abdelrahman S, Geduldig JE, Charbonneau S, Pelton K, Iorgulescu JB, Elagina L, Zhang W, Olive O, McCluskey C, Olsen LR, Stevens J, Lane WJ, Salazar AM, Daley H, Wen PY, Chiocca EA, Harden M, Lennon NJ, Gabriel S, Getz G, Lander ES, Regev A, Ritz J, Neuberg D, Rodig SJ, Ligon KL, Suvà ML, Wucherpfennig KW, Hacohen N, Fritsch EF, Livak KJ, Ott PA, Wu CJ, Reardon DA. Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial. Nature 565(7738):234-239, 2019. e-Pub 2019. PMID: 30568305.
40. Hu Z, Anandappa AJ, Sun J, Kim J, Leet DE, Bozym DJ, Chen C, Williams L, Shukla SA, Zhang W, Tabbaa D, Steelman S, Olive O, Livak KJ, Kishi H, Muraguchi A, Guleria I, Stevens J, Lane WJ, Burkhardt UE, Fritsch EF, Neuberg D, Ott PA, Keskin DB, Hacohen N, Wu CJ. A cloning and expression system to probe T-cell receptor specificity and assess functional avidity to neoantigens. Blood 132(18):1911-1921, 2018. e-Pub 2018. PMID: 30150207.
41. Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ, Network TR, Weinstein JN, Kwiatkowski DJ, Lerner SP. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell 174(4):1033, 2018. e-Pub 2018. PMID: 30096301.
42. Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJ, Krystofinski P, Leiserson MDM, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U. Genetic Mechanisms of Immune Evasion in Colorectal Cancer. Cancer Discov 8(6):730-749, 2018. e-Pub 2018. PMID: 29510987.
43. Shukla SA, Bachireddy P, Schilling B, Galonska C, Zhan Q, Bango C, Langer R, Lee PC, Gusenleitner D, Keskin DB, Babadi M, Mohammad A, Gnirke A, Clement K, Cartun ZJ, Van Allen EM, Miao D, Huang Y, Snyder A, Merghoub T, Wolchok JD, Garraway LA, Meissner A, Weber JS, Hacohen N, Neuberg D, Potts PR, Murphy GF, Lian CG, Schadendorf D, Hodi FS, Wu CJ. Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell 173(3):624-633.e8, 2018. e-Pub 2018. PMID: 29656892.
44. Ott PA, Hu Z, Keskin DB, Shukla SA, Sun J, Bozym DJ, Zhang W, Luoma A, Giobbie-Hurder A, Peter L, Chen C, Olive O, Carter TA, Li S, Lieb DJ, Eisenhaure T, Gjini E, Stevens J, Lane WJ, Javeri I, Nellaiappan K, Salazar AM, Daley H, Seaman M, Buchbinder EI, Yoon CH, Harden M, Lennon N, Gabriel S, Rodig SJ, Barouch DH, Aster JC, Getz G, Wucherpfennig K, Neuberg D, Ritz J, Lander ES, Fritsch EF, Hacohen N, Wu CJ. Corrigendum: An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 555(7696):402, 2018. e-Pub 2018. PMID: 29542692.
45. Hamada T, Soong TR, Masugi Y, Kosumi K, Nowak JA, da Silva A, Mu XJ, Twombly TS, Koh H, Yang J, Song M, Liu L, Gu M, Shi Y, Nosho K, Morikawa T, Inamura K, Shukla SA, Wu CJ, Garraway LA, Zhang X, Wu K, Meyerhardt JA, Chan AT, Glickman JN, Rodig SJ, Freeman GJ, Fuchs CS, Nishihara R, Giannakis M, Ogino S. TIME (Tumor Immunity in the MicroEnvironment) classification based on tumor CD274 (PD-L1) expression status and tumor-infiltrating lymphocytes in colorectal carcinomas. Oncoimmunology 7(7):e1442999, 2018. e-Pub 2018. PMID: 29900052.
46. Sade-Feldman M, Jiao YJ, Chen JH, Rooney MS, Barzily-Rokni M, Eliane JP, Bjorgaard SL, Hammond MR, Vitzthum H, Blackmon SM, Frederick DT, Hazar-Rethinam M, Nadres BA, Van Seventer EE, Shukla SA, Yizhak K, Ray JP, Rosebrock D, Livitz D, Adalsteinsson V, Getz G, Duncan LM, Li B, Corcoran RB, Lawrence DP, Stemmer-Rachamimov A, Boland GM, Landau DA, Flaherty KT, Sullivan RJ, Hacohen N. Resistance to checkpoint blockade therapy through inactivation of antigen presentation. Nat Commun 8(1):1136, 2017. e-Pub 2017. PMID: 29070816.
47. Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ, Network TR, Weinstein JN, Kwiatkowski DJ, Lerner SP. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell 171(3):540-556.e25, 2017. e-Pub 2017. PMID: 28988769.
48. Wang L, Fan J, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Cin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, Neuberg D, Alessi DR, Zhang CZ, Kharchenko PV, Livak KJ, Wu CJ. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Res 27(8):1300-1311, 2017. e-Pub 2017. PMID: 28679620.
49. Ott PA, Hu Z, Keskin DB, Shukla SA, Sun J, Bozym DJ, Zhang W, Luoma A, Giobbie-Hurder A, Peter L, Chen C, Olive O, Carter TA, Li S, Lieb DJ, Eisenhaure T, Gjini E, Stevens J, Lane WJ, Javeri I, Nellaiappan K, Salazar AM, Daley H, Seaman M, Buchbinder EI, Yoon CH, Harden M, Lennon N, Gabriel S, Rodig SJ, Barouch DH, Aster JC, Getz G, Wucherpfennig K, Neuberg D, Ritz J, Lander ES, Fritsch EF, Hacohen N, Wu CJ. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 547(7662):217-221, 2017. e-Pub 2017. PMID: 28678778.
50. George S, Miao D, Demetri GD, Adeegbe D, Rodig SJ, Shukla S, Lipschitz M, Amin-Mansour A, Raut CP, Carter SL, Hammerman P, Freeman GJ, Wu CJ, Ott PA, Wong KK, Van Allen EM. Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma. Immunity 46(2):197-204, 2017. e-Pub 2017. PMID: 28228279.
51. Shukla SA, Howitt BE, Wu CJ, Konstantinopoulos PA. Predicted neoantigen load in non-hypermutated endometrial cancers: Correlation with outcome and tumor-specific genomic alterations. Gynecol Oncol Rep 19:42-45, 2017. e-Pub 2017. PMID: 28070553.
52. Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell 30(5):750-763, 2016. e-Pub 2016. PMID: 27818134.
53. Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, Bahl S, Cao Y, Amin-Mansour A, Yamauchi M, Sukawa Y, Stewart C, Rosenberg M, Mima K, Inamura K, Nosho K, Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, Ng K, Meyerhardt JA, Van Allen EM, Getz G, Gabriel SB, Lander ES, Wu CJ, Fuchs CS, Ogino S, Garraway LA. Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep 17(4):1206, 2016. e-Pub 2016. PMID: 27760322.
54. Li B, Li T, Pignon JC, Wang B, Wang J, Shukla SA, Dou R, Chen Q, Hodi FS, Choueiri TK, Wu C, Hacohen N, Signoretti S, Liu JS, Liu XS. Landscape of tumor-infiltrating T cell repertoire of human cancers. Nat Genet 48(7):725-32, 2016. e-Pub 2016. PMID: 27240091.
55. Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G, Research Network CGA, Artyomov MN, Schreiber R, Govindan R, Meyerson M. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet 48(6):607-16, 2016. e-Pub 2016. PMID: 27158780.
56. Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, Bahl S, Cao Y, Amin-Mansour A, Yamauchi M, Sukawa Y, Stewart C, Rosenberg M, Mima K, Inamura K, Nosho K, Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, Ng K, Meyerhardt JA, Van Allen EM, Getz G, Gabriel SB, Lander ES, Wu CJ, Fuchs CS, Ogino S, Garraway LA. Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep 15(4):857-865, 2016. e-Pub 2016. PMID: 27149842.
57. McGranahan N, Furness AJ, Rosenthal R, Ramskov S, Lyngaa R, Saini SK, Jamal-Hanjani M, Wilson GA, Birkbak NJ, Hiley CT, Watkins TB, Shafi S, Murugaesu N, Mitter R, Akarca AU, Linares J, Marafioti T, Henry JY, Van Allen EM, Miao D, Schilling B, Schadendorf D, Garraway LA, Makarov V, Rizvi NA, Snyder A, Hellmann MD, Merghoub T, Wolchok JD, Shukla SA, Wu CJ, Peggs KS, Chan TA, Hadrup SR, Quezada SA, Swanton C. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 351(6280):1463-9, 2016. e-Pub 2016. PMID: 26940869.
58. Strickland KC, Howitt BE, Shukla SA, Rodig S, Ritterhouse LL, Liu JF, Garber JE, Chowdhury D, Wu CJ, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. Oncotarget 7(12):13587-98, 2016. e-Pub 2016. PMID: 26871470.
59. Howitt BE, Shukla SA, Konstantinopoulos PA. Neoepitopes and CD3-Positive and CD8-Positive Cells in Polymerase e-Mutated and Microsatellite-Instable Endometrial Cancers--Reply. JAMA Oncol 2(1):141-2, 2016. e-Pub 2016. PMID: 26767553.
60. Howitt BE, Shukla SA, Sholl LM, Ritterhouse LL, Watkins JC, Rodig S, Stover E, Strickland KC, D'Andrea AD, Wu CJ, Matulonis UA, Konstantinopoulos PA. Association of Polymerase e-Mutated and Microsatellite-Instable Endometrial Cancers With Neoantigen Load, Number of Tumor-Infiltrating Lymphocytes, and Expression of PD-1 and PD-L1. JAMA Oncol 1(9):1319-23, 2015. e-Pub 2015. PMID: 26181000.
61. Shukla SA, Rooney MS, Rajasagi M, Tiao G, Dixon PM, Lawrence MS, Stevens J, Lane WJ, Dellagatta JL, Steelman S, Sougnez C, Cibulskis K, Kiezun A, Hacohen N, Brusic V, Wu CJ, Getz G. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol 33(11):1152-8, 2015. e-Pub 2015. PMID: 26372948.
62. Van Allen EM, Miao D, Schilling B, Shukla SA, Blank C, Zimmer L, Sucker A, Hillen U, Foppen MHG, Goldinger SM, Utikal J, Hassel JC, Weide B, Kaehler KC, Loquai C, Mohr P, Gutzmer R, Dummer R, Gabriel S, Wu CJ, Schadendorf D, Garraway LA. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science 350(6257):207-211, 2015. e-Pub 2015. PMID: 26359337.
63. Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160(1-2):48-61, 2015. e-Pub 2015. PMID: 25594174.
64. Moskwa P, Zinn PO, Choi YE, Shukla SA, Fendler W, Chen CC, Lu J, Golub TR, Hjelmeland A, Chowdhury D. A functional screen identifies miRs that induce radioresistance in glioblastomas. Mol Cancer Res 12(12):1767-78, 2014. e-Pub 2014. PMID: 25256711.
65. Crompton BD, Stewart C, Taylor-Weiner A, Alexe G, Kurek KC, Calicchio ML, Kiezun A, Carter SL, Shukla SA, Mehta SS, Thorner AR, de Torres C, Lavarino C, Suñol M, McKenna A, Sivachenko A, Cibulskis K, Lawrence MS, Stojanov P, Rosenberg M, Ambrogio L, Auclair D, Seepo S, Blumenstiel B, DeFelice M, Imaz-Rosshandler I, Schwarz-Cruz Y Celis A, Rivera MN, Rodriguez-Galindo C, Fleming MD, Golub TR, Getz G, Mora J, Stegmaier K. The genomic landscape of pediatric Ewing sarcoma. Cancer Discov 4(11):1326-41, 2014. e-Pub 2014. PMID: 25186949.
66. Wang L, Shalek AK, Lawrence M, Ding R, Gaublomme JT, Pochet N, Stojanov P, Sougnez C, Shukla SA, Stevenson KE, Zhang W, Wong J, Sievers QL, MacDonald BT, Vartanov AR, Goldstein NR, Neuberg D, He X, Lander E, Hacohen N, Regev A, Getz G, Brown JR, Park H, Wu CJ. Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL. Blood 124(7):1089-98, 2014. e-Pub 2014. PMID: 24778153.
67. Rajasagi M, Shukla SA, Fritsch EF, Keskin DB, DeLuca D, Carmona E, Zhang W, Sougnez C, Cibulskis K, Sidney J, Stevenson K, Ritz J, Neuberg D, Brusic V, Gabriel S, Lander ES, Getz G, Hacohen N, Wu CJ. Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia. Blood 124(3):453-62, 2014. e-Pub 2014. PMID: 24891321.
68. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L, Network TR. The somatic genomic landscape of glioblastoma. Cell 155(2):462-77, 2013. e-Pub 2013. PMID: 24120142.
69. Landau DA, Carter SL, Stojanov P, McKenna A, Stevenson K, Lawrence MS, Sougnez C, Stewart C, Sivachenko A, Wang L, Wan Y, Zhang W, Shukla SA, Vartanov A, Fernandes SM, Saksena G, Cibulskis K, Tesar B, Gabriel S, Hacohen N, Meyerson M, Lander ES, Neuberg D, Brown JR, Getz G, Wu CJ. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 152(4):714-26, 2013. e-Pub 2013. PMID: 23415222.
70. Quayle SN, Chheda MG, Shukla SA, Wiedemeyer R, Tamayo P, Dewan RW, Zhuang L, Huang-Hobbs E, Haidar S, Xiao Y, Ligon KL, Hahn WC, Chin L. Integrative functional genomics identifies RINT1 as a novel GBM oncogene. Neuro Oncol 14(11):1325-31, 2012. e-Pub 2012. PMID: 23074196.
71. Research Network CGA. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489(7417):519-25, 2012. e-Pub 2012. PMID: 22960745.
72. Genovese G, Ergun A, Shukla SA, Campos B, Hanna J, Ghosh P, Quayle SN, Rai K, Colla S, Ying H, Wu CJ, Sarkar S, Xiao Y, Zhang J, Zhang H, Kwong L, Dunn K, Wiedemeyer WR, Brennan C, Zheng H, Rimm DL, Collins JJ, Chin L. microRNA regulatory network inference identifies miR-34a as a novel regulator of TGF-β signaling in glioblastoma. Cancer Discov 2(8):736-49, 2012. e-Pub 2012. PMID: 22750848.
73. Atlas Network CG. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407):330-7, 2012. e-Pub 2012. PMID: 22810696.
74. Chen AJ, Paik JH, Zhang H, Shukla SA, Mortensen R, Hu J, Ying H, Hu B, Hurt J, Farny N, Dong C, Xiao Y, Wang YA, Silver PA, Chin L, Vasudevan S, Depinho RA. STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA. Genes Dev 26(13):1459-72, 2012. e-Pub 2012. PMID: 22751500.
75. Research Network CGA. Integrated genomic analyses of ovarian carcinoma. Nature 474(7353):609-15, 2011. e-Pub 2011. PMID: 21720365.
76. Sahin E, Colla S, Liesa M, Moslehi J, Müller FL, Guo M, Cooper M, Kotton D, Fabian AJ, Walkey C, Maser RS, Tonon G, Foerster F, Xiong R, Wang YA, Shukla SA, Jaskelioff M, Martin ES, Heffernan TP, Protopopov A, Ivanova E, Mahoney JE, Kost-Alimova M, Perry SR, Bronson R, Liao R, Mulligan R, Shirihai OS, Chin L, DePinho RA. Telomere dysfunction induces metabolic and mitochondrial compromise. Nature 470(7334):359-65, 2011. e-Pub 2011. PMID: 21307849.

Letters to the Editor

1. Saliby RM, Labaki C, Jammihal TR, Xie W, Sun M, Shah V, Saad E, Kane MH, Kashima S, Sadak K, El Zarif T, Poduval D, Motzer RJ, Powles T, Rini BI, Albiges L, Pal SK, McGregor BA, McKay RR, Signoretti S, Van Allen EM, Shukla SA, Choueiri TK, Braun DA. Impact of renal cell carcinoma molecular subtypes on immunotherapy and targeted therapy outcomes. Cancer Cell 42: 732-735, 2024.