Publications
2022
- HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia
Lai TH, Ozer HG, Gasparini P, Nigita G, Distefano R, Yu L, Ravikrishnan J, Yilmaz S, Gallegos JJ, Shukla SA, Puduvalli VK, Woyach JA, Lapalombella R, Blachly JS, Byrd JC, Sampath D. HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia. Blood Adv. 2022 Oct 26:bloodadvances.2022007998. doi: 10.1182/bloodadvances.2022007998. - Transcriptomic Correlates of Tumor Cell PD-L1 Expression and Response to Nivolumab Monotherapy in Metastatic Clear Cell Renal Cell Carcinoma
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. 2022 Sep 15;28(18):4045-4055. doi: 10.1158/1078-0432.CCR-22-0923. - Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit
Barroso-Sousa R, Forman J, Collier K, Weber ZT, Jammihal TR, Kao KZ, Richardson ET 3rd, 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. 2022 Jul;6:e2100413. doi: 10.1200/PO.21.00413. - Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche
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 et al. Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche. Cell. 2022 May 12;185(10):1694-1708.e19. - HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study
Naranbhai V, Viard M, Dean M, Groha S, Braun DA, Labaki C, Shukla SA et al. HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study. Lancet Oncol. 2022 Jan;23(1):172-184. - Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
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 et al. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol. 2022 Feb;40(2):209-217. - Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma
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 et al. Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma. Nature. 2021 Aug;596(7870):119-125. - CDKN2A Alterations and Response to Immunotherapy in Solid Tumors
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 et al. CDKN2A Alterations and Response to Immunotherapy in Solid Tumors. Clin Cancer Res.2021 Jul 15;27(14):4025-4035. - Progressive immune dysfunction with advancing disease stage in renal cell carcinoma
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. 2021 Mar 9:S1535-6108(21)00115-X. doi: 10.1016/j.ccell.2021.02.013.
2021
- Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma
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. 2021 Feb 5;12(1):808. doi: 10.1038/s41467-021-21068-9. - Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma
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. 2021 Jan 21. doi: 10.1038/s41591-020-01206-4.
2020
- Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System
Trinh A, Gil Del Alcazar CR, Shukla SA, Chin K, Chang YH, Thibault G, Eng J, Jovanović 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. 2020 Dec 18. doi: 10.1158/1541-7786.MCR-20-0949. - Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network
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, Das Sahu A, Jiang P, Yan C, Duose DY, Cerami E, Chen L, Cohen D, Chen QR, Enos RA, Huang X, Lee JJ, Liu Y, Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla SA, Tang M, Tsuji J, Uduman M, Wang X, Weirather JL, Yu J, Yu J, Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal PA, Karlovich C, Gabriel SB, Wistuba II, Liu XS, Wu C. Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC network. Clin Cancer Res. 2020 Dec 15;clincanres.3251.2020. - Expression of T-cell Exhaustion Molecules and Human Endogenous Retroviruses as Predictive Biomarkers for response to Nivolumab in Metastatic Clear Cell Renal Cell Carcinoma
Ficial M, Jegede OA, Sant’Angelo M, Hou Y, Flaifel A, Pignon JC, Braun DA, Wind-Rotolo M, Sticco-Ivins M, 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 Can Res. 2020 Nov 20;clincanres.3084.2020. - Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction
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; Tumor Neoantigen Selection Alliance, 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 2020 Oct 29;183(3):818-834.e13. - Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect
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. 2020 Sep 16;12(561):eabb7661.
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