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1
Beckabir W, Zhou M, Lee JS, Vensko SP, Woodcock MG, Wang HH, Wobker SE, Atassi G, Wilkinson AD, Fowler K, Flick LM, Damrauer JS, Harrison MR, McKinnon KP, Rose TL, Milowsky MI, Serody JS, Kim WY, Vincent BG. Immune features are associated with response to neoadjuvant chemo-immunotherapy for muscle-invasive bladder cancer. Nat Commun 2024;15:4448. [PMID: 38789460 PMCID: PMC11126571 DOI: 10.1038/s41467-024-48480-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/02/2024] [Indexed: 05/26/2024]  Open
2
Grover NS, Hucks G, Riches ML, Ivanova A, Moore DT, Shea TC, Seegars MB, Armistead PM, Kasow KA, Beaven AW, Dittus C, Coghill JM, Jamieson KJ, Vincent BG, Wood WA, Cheng C, Morrison JK, West J, Cavallo T, Dotti G, Serody JS, Savoldo B. Anti-CD30 CAR T cells as consolidation after autologous haematopoietic stem-cell transplantation in patients with high-risk CD30+ lymphoma: a phase 1 study. Lancet Haematol 2024;11:e358-e367. [PMID: 38555923 PMCID: PMC11238265 DOI: 10.1016/s2352-3026(24)00064-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 04/02/2024]
3
Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Liu W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep 2024;43:113063. [PMID: 38578829 DOI: 10.1016/j.celrep.2023.113063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]  Open
4
Di Modugno F, Di Carlo A, Spada S, Palermo B, D'Ambrosio L, D'Andrea D, Morello G, Belmonte B, Sperduti I, Balzano V, Gallo E, Melchionna R, Panetta M, Campo G, De Nicola F, Goeman F, Antoniani B, Carpano S, Frigè G, Warren S, Gallina F, Lambrechts D, Xiong J, Vincent BG, Wheeler N, Bortone DS, Cappuzzo F, Facciolo F, Tripodo C, Visca P, Nisticò P. Tumoral and stromal hMENA isoforms impact tertiary lymphoid structure localization in lung cancer and predict immune checkpoint blockade response in patients with cancer. EBioMedicine 2024;101:105003. [PMID: 38340557 PMCID: PMC10869748 DOI: 10.1016/j.ebiom.2024.105003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]  Open
5
Beckabir W, Wobker SE, Damrauer JS, Midkiff B, De la Cruz G, Makarov V, Flick L, Woodcock MG, Grivas P, Bjurlin MA, Harrison MR, Vincent BG, Rose TL, Gupta S, Kim WY, Milowsky MI. Spatial Relationships in the Tumor Microenvironment Demonstrate Association with Pathologic Response to Neoadjuvant Chemoimmunotherapy in Muscle-invasive Bladder Cancer. Eur Urol 2024;85:242-253. [PMID: 38092611 PMCID: PMC11022933 DOI: 10.1016/j.eururo.2023.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/11/2023] [Accepted: 11/09/2023] [Indexed: 03/09/2024]
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Mason M, Lapuente-Santana Ó, Halkola AS, Wang W, Mall R, Xiao X, Kaufman J, Fu J, Pfeil J, Banerjee J, Chung V, Chang H, Chasalow SD, Lin HY, Chai R, Yu T, Finotello F, Mirtti T, Mäyränpää MI, Bao J, Verschuren EW, Ahmed EI, Ceccarelli M, Miller LD, Monaco G, Hendrickx WRL, Sherif S, Yang L, Tang M, Gu SS, Zhang W, Zhang Y, Zeng Z, Das Sahu A, Liu Y, Yang W, Bedognetti D, Tang J, Eduati F, Laajala TD, Geese WJ, Guinney J, Szustakowski JD, Vincent BG, Carbone DP. A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer. J Transl Med 2024;22:190. [PMID: 38383458 PMCID: PMC10880244 DOI: 10.1186/s12967-023-04705-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/05/2023] [Indexed: 02/23/2024]  Open
7
Yazdani A, Lenz HJ, Pillonetto G, Mendez-Giraldez R, Yazdani A, Sanof H, Hadi R, Samiei E, Venook AP, Ratain MJ, Rashid N, Vincent BG, Qu X, Wen Y, Kosorok M, Symmans WF, Shen JPYC, Lee MS, Kopetz S, Nixon AB, Bertagnolli MM, Perou CM, Innocenti F. Gene signatures derived from transcriptomic-causal networks stratified colorectal cancer patients for effective targeted therapy. RESEARCH SQUARE 2023:rs.3.rs-3673588. [PMID: 38168324 PMCID: PMC10760223 DOI: 10.21203/rs.3.rs-3673588/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
8
Lee JS, Karthikeyan D, Fini M, Vincent BG, Rubinsteyn A. ACE configurator for ELISpot: optimizing combinatorial design of pooled ELISpot assays with an epitope similarity model. Brief Bioinform 2023;25:bbad495. [PMID: 38180831 PMCID: PMC10768796 DOI: 10.1093/bib/bbad495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/16/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024]  Open
9
Sponaugle A, Weideman AMK, Ranek J, Atassi G, Kuruc J, Adimora AA, Archin NM, Gay C, Kuritzkes DR, Margolis DM, Vincent BG, Stanley N, Hudgens MG, Eron JJ, Goonetilleke N. Dominant CD4+ T cell receptors remain stable throughout antiretroviral therapy-mediated immune restoration in people with HIV. Cell Rep Med 2023;4:101268. [PMID: 37949070 PMCID: PMC10694675 DOI: 10.1016/j.xcrm.2023.101268] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/05/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
10
Vincent BG, File DM, McKinnon KP, Moore DT, Frelinger JA, Collins EJ, Ibrahim JG, Bixby L, Reisdorf S, Laurie SJ, Park YA, Anders CK, Collichio FA, Muss HB, Carey LA, van Deventer HW, Dees EC, Serody JS. Efficacy of a Dual-Epitope Dendritic Cell Vaccine as Part of Combined Immunotherapy for HER2-Expressing Breast Tumors. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023:263816. [PMID: 37204246 DOI: 10.4049/jimmunol.2300077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/02/2023] [Indexed: 05/20/2023]
11
Olsen KS, Jadi O, Dexheimer S, Bortone DS, Vensko SP, Bennett S, Tang H, Diiorio M, Saran T, Dingfelder D, Zhu Q, Wang Y, Haiman CA, Pooler L, Sheng X, Webb A, Pasquini MC, McCarthy PL, Spellman SR, Weimer E, Hahn T, Sucheston-Campbell L, Armistead PM, Vincent BG. Shared graft-versus-leukemia minor histocompatibility antigens in DISCOVeRY-BMT. Blood Adv 2023;7:1635-1649. [PMID: 36477467 PMCID: PMC10182302 DOI: 10.1182/bloodadvances.2022008863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/07/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022]  Open
12
Vensko SP, Olsen K, Bortone D, Smith CC, Chai S, Beckabir W, Fini M, Jadi O, Rubinsteyn A, Vincent BG. LENS: Landscape of Effective Neoantigens Software. Bioinformatics 2023;39:btad322. [PMID: 37184881 PMCID: PMC10246587 DOI: 10.1093/bioinformatics/btad322] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/04/2023] [Accepted: 05/12/2023] [Indexed: 05/16/2023]  Open
13
Qi T, Vincent BG, Cao Y. A multispecies framework for modeling adaptive immunity and immunotherapy in cancer. PLoS Comput Biol 2023;19:e1010976. [PMID: 37083574 PMCID: PMC10155959 DOI: 10.1371/journal.pcbi.1010976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 05/03/2023] [Accepted: 02/24/2023] [Indexed: 04/22/2023]  Open
14
Routh ED, Woodcock MG, Beckabir W, Vensko SP, Serody JS, Vincent BG. Evaluation of tumor antigen-specific antibody responses in patients with metastatic triple negative breast cancer treated with cyclophosphamide and pembrolizumab. J Immunother Cancer 2023;11:jitc-2022-005848. [PMID: 36882226 PMCID: PMC10008414 DOI: 10.1136/jitc-2022-005848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2023] [Indexed: 03/09/2023]  Open
15
Jadi O, Tang H, Olsen K, Vensko S, Zhu Q, Wang Y, Haiman CA, Pooler L, Sheng X, Brock G, Webb A, Pasquini M, McCarthy DPL, Spellman S, Hahn TE, Vincent BG, Armistead PM, Sucheston-Campbell L. Associations of Minor Histocompatibility Antigens with Clinical Outcomes Following Allogeneic Hematopoietic Cell Transplantation. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00100-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
16
Damrauer JS, Beckabir W, Klomp J, Zhou M, Plimack ER, Galsky MD, Grivas P, Hahn NM, O'Donnell PH, Iyer G, Quinn DI, Vincent BG, Quale DZ, Wobker SE, Hoadley KA, Kim WY, Milowsky MI. Collaborative study from the Bladder Cancer Advocacy Network for the genomic analysis of metastatic urothelial cancer. Nat Commun 2022;13:6658. [PMID: 36333289 PMCID: PMC9636269 DOI: 10.1038/s41467-022-33980-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/10/2022] [Indexed: 11/06/2022]  Open
17
Li S, Mirlekar B, Johnson BM, Brickey WJ, Wrobel JA, Yang N, Song D, Entwistle S, Tan X, Deng M, Cui Y, Li W, Vincent BG, Gale M, Pylayeva-Gupta Y, Ting JPY. STING-induced regulatory B cells compromise NK function in cancer immunity. Nature 2022;610:373-380. [PMID: 36198789 PMCID: PMC9875944 DOI: 10.1038/s41586-022-05254-3] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/19/2022] [Indexed: 02/08/2023]
18
Routh ED, Van Swearingen AED, Sambade MJ, Vensko S, McClure MB, Woodcock MG, Chai S, Cuaboy LA, Wheless A, Garrett A, Carey LA, Hoyle AP, Parker JS, Vincent BG, Anders CK. Comprehensive Analysis of the Immunogenomics of Triple-Negative Breast Cancer Brain Metastases From LCCC1419. Front Oncol 2022;12:818693. [PMID: 35992833 PMCID: PMC9387304 DOI: 10.3389/fonc.2022.818693] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/30/2022] [Indexed: 11/23/2022]  Open
19
Chai S, Smith CC, Kochar TK, Hunsucker SA, Beck W, Olsen KS, Vensko S, Glish GL, Armistead PM, Prins JF, Vincent BG. NeoSplice: a bioinformatics method for prediction of splice variant neoantigens. BIOINFORMATICS ADVANCES 2022;2:vbac032. [PMID: 35669345 PMCID: PMC9154024 DOI: 10.1093/bioadv/vbac032] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 04/14/2022] [Accepted: 05/04/2022] [Indexed: 01/27/2023]
20
Downs-Canner SM, Meier J, Vincent BG, Serody JS. B Cell Function in the Tumor Microenvironment. Annu Rev Immunol 2022;40:169-193. [PMID: 35044794 DOI: 10.1146/annurev-immunol-101220-015603] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
21
Innocenti F, Yazdani A, Rashid N, Qu X, Ou FS, Van Buren S, Bertagnolli M, Kabbarah O, Blanke CD, Venook AP, Lenz HJ, Vincent BG. Tumor Immunogenomic Features Determine Outcomes in Patients with Metastatic Colorectal Cancer Treated with Standard-of-Care Combinations of Bevacizumab and Cetuximab. Clin Cancer Res 2022;28:1690-1700. [PMID: 35176136 PMCID: PMC9093780 DOI: 10.1158/1078-0432.ccr-21-3202] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/22/2021] [Accepted: 02/11/2022] [Indexed: 12/16/2022]
22
Karasarides M, Cogdill AP, Robbins PB, Bowden M, Burton EM, Butterfield LH, Cesano A, Hammer C, Haymaker CL, Horak CE, McGee HM, Monette A, Rudqvist NP, Spencer CN, Sweis RF, Vincent BG, Wennerberg E, Yuan J, Zappasodi R, Lucey VMH, Wells DK, LaVallee T. Hallmarks of Resistance to Immune-Checkpoint Inhibitors. Cancer Immunol Res 2022;10:372-383. [PMID: 35362046 PMCID: PMC9381103 DOI: 10.1158/2326-6066.cir-20-0586] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/15/2021] [Accepted: 01/24/2022] [Indexed: 01/29/2023]
23
Asad S, Kananen K, Mueller KR, Symmans WF, Wen Y, Perou CM, Blachly JS, Chen J, Vincent BG, Stover DG. Challenges and Gaps in Clinical Trial Genomic Data Management. JCO Clin Cancer Inform 2022;6:e2100193. [PMID: 35404674 PMCID: PMC9012601 DOI: 10.1200/cci.21.00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/17/2022] [Accepted: 02/23/2022] [Indexed: 11/20/2022]  Open
24
Anders CK, Woodcock MG, Van Swearingen AED, Moore DT, Sambade MJ, Laurie S, Robeson A, Kolupaev O, Cuaboy LA, Garrett AL, McKinnon K, Cowens K, Bortone D, Calhoun BC, Wilkinson AD, Carey L, Jolly T, Muss H, Reeder-Hayes K, Kaltman R, Jankowitz R, Gudena V, Olajide O, Perou C, Dees EC, Vincent BG, Serody JS. Evaluating the efficacy of a priming dose of cyclophosphamide prior to pembrolizumab to treat metastatic triple negative breast cancer. J Immunother Cancer 2022;10:jitc-2021-003427. [PMID: 35121644 PMCID: PMC8819787 DOI: 10.1136/jitc-2021-003427] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 12/30/2022]  Open
25
Tsai YS, Woodcock MG, Azam SH, Thorne LB, Kanchi KL, Parker JS, Vincent BG, Pecot CV. Rapid idiosyncratic mechanisms of clinical resistance to KRAS G12C inhibition. J Clin Invest 2022;132:155523. [PMID: 34990404 PMCID: PMC8843735 DOI: 10.1172/jci155523] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022]  Open
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