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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 DOI: 10.1016/s2352-3026(24)00064-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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]
Abstract
BACKGROUND Chimeric antigen receptor (CAR) T cells targeting CD30 are safe and have promising activity when preceded by lymphodepleting chemotherapy. We aimed to determine the safety of anti-CD30 CAR T cells as consolidation after autologous haematopoietic stem-cell transplantation (HSCT) in patients with CD30+ lymphoma at high risk of relapse. METHODS This phase 1 dose-escalation study was performed at two sites in the USA. Patients aged 3 years and older, with classical Hodgkin lymphoma or non-Hodgkin lymphoma with CD30+ disease documented by immunohistochemistry, and a Karnofsky performance score of more than 60% planned for autologous HSCT were eligible if they were considered high risk for relapse as defined by primary refractory disease or relapse within 12 months of initial therapy or extranodal involvement at the start of pre-transplantation salvage therapy. Patients received a single infusion of CAR T cells (2 × 107 CAR T cells per m2, 1 × 108 CAR T cells per m2, or 2 × 108 CAR T cells per m2) as consolidation after trilineage haematopoietic engraftment (defined as absolute neutrophil count ≥500 cells per μL for 3 days, platelet count ≥25 × 109 platelets per L without transfusion for 5 days, and haemoglobin ≥8 g/dL without transfusion for 5 days) following carmustine, etoposide, cytarabine, and melphalan (BEAM) and HSCT. The primary endpoint was the determination of the maximum tolerated dose, which was based on the rate of dose-limiting toxicity in patients who received CAR T-cell infusion. This study is registered with ClinicalTrials.gov (NCT02663297) and enrolment is complete. FINDINGS Between June 7, 2016, and Nov 30, 2020, 21 patients were enrolled and 18 patients (11 with Hodgkin lymphoma, six with T-cell lymphoma, one with grey zone lymphoma) were infused with anti-CD30 CAR T cells at a median of 22 days (range 16-44) after autologous HSCT. There were no dose-limiting toxicities observed, so the highest dose tested, 2 × 108 CAR T cells per m2, was determined to be the maximum tolerated dose. One patient had grade 1 cytokine release syndrome. The most common grade 3-4 adverse events were lymphopenia (two [11%] of 18) and leukopenia (two [11%] of 18). There were no treatment-related deaths. Two patients developed secondary malignancies approximately 2 years and 2·5 years following treatment (one stage 4 non-small cell lung cancer and one testicular cancer), but these were judged unrelated to treatment. At a median follow-up of 48·2 months (IQR 27·5-60·7) post-infusion, the median progression-free survival for all treated patients (n=18) was 32·3 months (95% CI 4·6 months to not estimable) and the median progression-free survival for treated patients with Hodgkin lymphoma (n=11) has not been reached. The median overall survival for all treated patients has not been reached. INTERPRETATION Anti-CD30 CAR T-cell infusion as consolidation after BEAM and autologous HSCT is safe, with low rates of toxicity and encouraging preliminary activity in patients with Hodgkin lymphoma at high risk of relapse, highlighting the need for larger studies to confirm these findings. FUNDING National Heart Lung and Blood Institute, University Cancer Research Fund at the Lineberger Comprehensive Cancer Center.
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Affiliation(s)
- Natalie S Grover
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - George Hucks
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Pediatrics, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Marcie L Riches
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Anastasia Ivanova
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Dominic T Moore
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Thomas C Shea
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Mary Beth Seegars
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Paul M Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Kimberly A Kasow
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Pediatrics, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Anne W Beaven
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Christopher Dittus
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - James M Coghill
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Katarzyna J Jamieson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - William A Wood
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Catherine Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Julia Kaitlin Morrison
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - John West
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Tammy Cavallo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Gianpietro Dotti
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA
| | - Barbara Savoldo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA; Department of Pediatrics, University of North Carolina at Chapel Hill, Chapell Hill, NC, USA.
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
Abstract
BACKGROUND Tertiary Lymphoid Structures (TLS) correlate with positive outcomes in patients with NSCLC and the efficacy of immune checkpoint blockade (ICB) in cancer. The actin regulatory protein hMENA undergoes tissue-specific splicing, producing the epithelial hMENA11a linked to favorable prognosis in early NSCLC, and the mesenchymal hMENAΔv6 found in invasive cancer cells and pro-tumoral cancer-associated fibroblasts (CAFs). This study investigates how hMENA isoforms in tumor cells and CAFs relate to TLS presence, localization and impact on patient outcomes and ICB response. METHODS Methods involved RNA-SEQ on NSCLC cells with depleted hMENA isoforms. A retrospective observational study assessed tissues from surgically treated N0 patients with NSCLC, using immunohistochemistry for tumoral and stromal hMENA isoforms, fibronectin, and TLS presence. ICB-treated patient tumors were analyzed using Nanostring nCounter and GeoMx spatial transcriptomics. Multiparametric flow cytometry characterized B cells and tissue-resident memory T cells (TRM). Survival and ICB response were estimated in the cohort and validated using bioinformatics pipelines in different datasets. FINDINGS Findings indicate that hMENA11a in NSCLC cells upregulates the TLS regulator LTβR, decreases fibronectin, and favors CXCL13 production by TRM. Conversely, hMENAΔv6 in CAFs inhibits LTβR-related NF-kB pathway, reduces CXCL13 secretion, and promotes fibronectin production. These patterns are validated in N0 NSCLC tumors, where hMENA11ahigh expression, CAF hMENAΔv6low, and stromal fibronectinlow are associated with intratumoral TLS, linked to memory B cells and predictive of longer survival. The hMENA isoform pattern, fibronectin, and LTβR expression broadly predict ICB response in tumors where TLS indicates an anti-tumor immune response. INTERPRETATION This study uncovers hMENA alternative splicing as an unexplored contributor to TLS-related Tumor Immune Microenvironment (TIME) and a promising biomarker for clinical outcomes and likely ICB responsiveness in N0 patients with NSCLC. FUNDING This work is supported by AIRC (IG 19822), ACC (RCR-2019-23669120), CAL.HUB.RIA Ministero Salute PNRR-POS T4, "Ricerca Corrente" granted by the Italian Ministry of Health.
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Affiliation(s)
- Francesca Di Modugno
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy.
| | - Anna Di Carlo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Sheila Spada
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Belinda Palermo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Lorenzo D'Ambrosio
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Daniel D'Andrea
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, New Hall Block - Room 171, Clifton Campus - NG11 8NS, Nottingham, United Kingdom
| | - Gaia Morello
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Corso Tukory 211, 90134, Palermo, Italy
| | - Beatrice Belmonte
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Corso Tukory 211, 90134, Palermo, Italy
| | - Isabella Sperduti
- Biostatistics and Scientific Direction, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Vittoria Balzano
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Enzo Gallo
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Roberta Melchionna
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Mariangela Panetta
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Giulia Campo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Francesca De Nicola
- SAFU Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Frauke Goeman
- SAFU Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Barbara Antoniani
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Silvia Carpano
- Second Division of Medical Oncology, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, Milan, Italy
| | - Sarah Warren
- NanoString Technologies Inc., 530 Fairview Ave N, Seattle, WA, 98109, USA
| | - Filippo Gallina
- Thoracic-Surgery Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Diether Lambrechts
- Center for Cancer Biology, Herestraat 49 box 912, VIB, 3000, Leuven, Belgium
| | - Jieyi Xiong
- Center for Cancer Biology, Herestraat 49 box 912, VIB, 3000, Leuven, Belgium
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 5206 Marsico Hall, Chapel Hill, NC, 27599, USA
| | - Nathan Wheeler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 5206 Marsico Hall, Chapel Hill, NC, 27599, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 5206 Marsico Hall, Chapel Hill, NC, 27599, USA
| | - Federico Cappuzzo
- Second Division of Medical Oncology, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Francesco Facciolo
- Thoracic-Surgery Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Corso Tukory 211, 90134, Palermo, Italy
| | - Paolo Visca
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Paola Nisticò
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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]
Abstract
BACKGROUND Platinum-based neoadjuvant chemotherapy (NAC) is standard for patients with muscle-invasive bladder cancer (MIBC). Pathologic response (complete: ypT0N0 and partial: OBJECTIVE Using the NanoString GeoMx platform, we performed proteomic digital spatial profiling (DSP) on transurethral resections of bladder tumors from 18 responders ( DESIGN, SETTING, AND PARTICIPANTS Pretreatment tumor samples were stained by hematoxylin and eosin and immunofluorescence (panCK and CD45) to select four regions of interest (ROIs): tumor enriched (TE), immune enriched (IE), tumor/immune interface (tumor interface = TX and immune interface = IX). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS DSP was performed with 52 protein markers from immune cell profiling, immunotherapy drug target, immune activation status, immune cell typing, and pan-tumor panels. RESULTS AND LIMITATIONS Protein marker expression patterns were analyzed to determine their association with pathologic response, incorporating or agnostic of their ROI designation (TE/IE/TX/IX). Overall, DSP-based marker expression showed high intratumoral heterogeneity; however, response was associated with markers including PD-L1 (ROI agnostic), Ki-67 (ROI agnostic, TE, IE, and TX), HLA-DR (TX), and HER2 (TE). An elastic net model of response with ROI-inclusive markers demonstrated better validation set performance (area under the curve [AUC] = 0.827) than an ROI-agnostic model (AUC = 0.432). A model including DSP, tumor mutational burden, and clinical data performed no better (AUC = 0.821) than the DSP-only model. CONCLUSIONS Despite high intratumoral heterogeneity of DSP-based marker expression, we observed associations between pathologic response and specific DSP-based markers in a spatially dependent context. Further exploration of tumor region-specific biomarkers may help predict response to neoadjuvant chemoimmunotherapy in MIBC. PATIENT SUMMARY In this study, we used the GeoMx platform to perform proteomic digital spatial profiling on transurethral resections of bladder tumors from 18 responders and 18 nonresponders from two studies of neoadjuvant chemotherapy (gemcitabine and cisplatin) plus immune checkpoint inhibitor therapy (LCCC1520 [pembrolizumab] and BLASST-1 [nivolumab]). We found that assessing protein marker expression in the context of tumor architecture improved response prediction.
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Affiliation(s)
- Wolfgang Beckabir
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Sara E Wobker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey S Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bentley Midkiff
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriela De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vladmir Makarov
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Leah Flick
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark G Woodcock
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Petros Grivas
- Department of Medicine, Division of Medical Oncology, University of Washington, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marc A Bjurlin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael R Harrison
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA; Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA; Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Tracy L Rose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shilpa Gupta
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Matthew I Milowsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Oncology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
Abstract
BACKGROUND Predictive biomarkers of immune checkpoint inhibitor (ICI) efficacy are currently lacking for non-small cell lung cancer (NSCLC). Here, we describe the results from the Anti-PD-1 Response Prediction DREAM Challenge, a crowdsourced initiative that enabled the assessment of predictive models by using data from two randomized controlled clinical trials (RCTs) of ICIs in first-line metastatic NSCLC. METHODS Participants developed and trained models using public resources. These were evaluated with data from the CheckMate 026 trial (NCT02041533), according to the model-to-data paradigm to maintain patient confidentiality. The generalizability of the models with the best predictive performance was assessed using data from the CheckMate 227 trial (NCT02477826). Both trials were phase III RCTs with a chemotherapy control arm, which supported the differentiation between predictive and prognostic models. Isolated model containers were evaluated using a bespoke strategy that considered the challenges of handling transcriptome data from clinical trials. RESULTS A total of 59 teams participated, with 417 models submitted. Multiple predictive models, as opposed to a prognostic model, were generated for predicting overall survival, progression-free survival, and progressive disease status with ICIs. Variables within the models submitted by participants included tumor mutational burden (TMB), programmed death ligand 1 (PD-L1) expression, and gene-expression-based signatures. The best-performing models showed improved predictive power over reference variables, including TMB or PD-L1. CONCLUSIONS This DREAM Challenge is the first successful attempt to use protected phase III clinical data for a crowdsourced effort towards generating predictive models for ICI clinical outcomes and could serve as a blueprint for similar efforts in other tumor types and disease states, setting a benchmark for future studies aiming to identify biomarkers predictive of ICI efficacy. TRIAL REGISTRATION CheckMate 026; NCT02041533, registered January 22, 2014. CheckMate 227; NCT02477826, registered June 23, 2015.
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Affiliation(s)
- Mike Mason
- Bristol Myers Squibb, Princeton, NJ, USA
| | - Óscar Lapuente-Santana
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Anni S Halkola
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Wenyu Wang
- Faculty of Medicine, Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Raghvendra Mall
- Qatar Computing Research Institute, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
- Department of Immunology, St. Jude Children's Research Hospital, P.O. Box 38105, Memphis, TN, USA
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
| | - Xu Xiao
- School of Informatics, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jacob Kaufman
- Department of Medicine, Duke University, Durham, NC, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Jingxin Fu
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - Han Chang
- Bristol Myers Squibb, Princeton, NJ, USA
| | | | | | | | | | - Francesca Finotello
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
- Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Tuomas Mirtti
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- iCAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Biomedical Engineering, School of Medicine, Emory University, Atlanta, GA, USA
| | - Mikko I Mäyränpää
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jie Bao
- Faculty of Medicine, Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Eiman I Ahmed
- Human Immunology Department, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", 80125, Naples, Italy
- BIOGEM Institute of Molecular Biology and Genetics, Via Camporeale, Ariano Irpino, Italy
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Gianni Monaco
- BIOGEM Institute of Molecular Biology and Genetics, Via Camporeale, Ariano Irpino, Italy
| | - Wouter R L Hendrickx
- Human Immunology Department, Sidra Medicine, P.O. Box 26999, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 26999, Doha, Qatar
| | - Shimaa Sherif
- Human Immunology Department, Sidra Medicine, P.O. Box 26999, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 26999, Doha, Qatar
| | - Lin Yang
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ming Tang
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Yi Zhang
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zexian Zeng
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yang Liu
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Davide Bedognetti
- Human Immunology Department, Sidra Medicine, P.O. Box 26999, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 26999, Doha, Qatar
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Jing Tang
- Faculty of Medicine, Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Teemu D Laajala
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
- iCAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
- Department of Pharmacology, Anschutz Medical Campus, University of Colorado, Denver, CO, USA
| | | | | | | | - Benjamin G Vincent
- Department of Medicine, Division of Hematology, Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David P Carbone
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
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6
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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. Res Sq 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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Predictive and prognostic gene signatures derived from interconnectivity among genes can tailor clinical care to patients in cancer treatment. We identified gene interconnectivity as the transcriptomic-causal network by integrating germline genotyping and tumor RNA-seq data from 1,165 patients with metastatic colorectal cancer (CRC). The patients were enrolled in a clinical trial with randomized treatment, either cetuximab or bevacizumab in combination with chemotherapy. We linked the network to overall survival (OS) and detected novel biomarkers by controlling for confounding genes. Our data-driven approach discerned sets of genes, each set collectively stratify patients based on OS. Two signatures under the cetuximab treatment were related to wound healing and macrophages. The signature under the bevacizumab treatment was related to cytotoxicity and we replicated its effect on OS using an external cohort. We also showed that the genes influencing OS within the signatures are downregulated in CRC tumor vs. normal tissue using another external cohort. Furthermore, the corresponding proteins encoded by the genes within the signatures interact each other and are functionally related. In conclusion, this study identified a group of genes that collectively stratified patients based on OS and uncovered promising novel prognostic biomarkers for personalized treatment of CRC using transcriptomic causal networks.
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Affiliation(s)
- Akram Yazdani
- University of Texas Health Science center at Houston
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
Abstract
The enzyme-linked immunosorbent spot (ELISpot) assay is a powerful in vitro immunoassay that enables cost-effective quantification of antigen-specific T-cell reactivity. It is used widely in the context of cancer and infectious diseases to validate the immunogenicity of predicted epitopes. While technological advances have kept pace with the demand for increased throughput, efforts to increase scale are bottlenecked by current assay design and deconvolution methods, which have remained largely unchanged. Current methods for designing pooled ELISpot experiments offer limited flexibility of assay parameters, lack support for high-throughput scenarios and do not consider peptide identity during pool assignment. We introduce the ACE Configurator for ELISpot (ACE) to address these gaps. ACE generates optimized peptide-pool assignments from highly customizable user inputs and handles the deconvolution of positive peptides using assay readouts. In this study, we present a novel sequence-aware pooling strategy, powered by a fine-tuned ESM-2 model that groups immunologically similar peptides, reducing the number of false positives and subsequent confirmatory assays compared to existing combinatorial approaches. To validate ACE's performance on real-world datasets, we conducted a comprehensive benchmark study, contextualizing design choices with their impact on prediction quality. Our results demonstrate ACE's capacity to further increase precision of identified immunogenic peptides, directly optimizing experimental efficiency. ACE is freely available as an executable with a graphical user interface and command-line interfaces at https://github.com/pirl-unc/ace.
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Affiliation(s)
- Jin Seok Lee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Dhuvarakesh Karthikeyan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Misha Fini
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
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8
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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]
Abstract
In people with HIV (PWH), the post-antiretroviral therapy (ART) window is critical for immune restoration and HIV reservoir stabilization. We employ deep immune profiling and T cell receptor (TCR) sequencing and examine proliferation to assess how ART impacts T cell homeostasis. In PWH on long-term ART, lymphocyte frequencies and phenotypes are mostly stable. By contrast, broad phenotypic changes in natural killer (NK) cells, γδ T cells, B cells, and CD4+ and CD8+ T cells are observed in the post-ART window. Whereas CD8+ T cells mostly restore, memory CD4+ T subsets and cytolytic NK cells show incomplete restoration 1.4 years post ART. Surprisingly, the hierarchies and frequencies of dominant CD4 TCR clonotypes (0.1%-11% of all CD4+ T cells) remain stable post ART, suggesting that clonal homeostasis can be independent of homeostatic processes regulating CD4+ T cell absolute number, phenotypes, and function. The slow restoration of host immunity post ART also has implications for the design of ART interruption studies.
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Affiliation(s)
- Alexis Sponaugle
- Department of Microbiology & Immunology, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Ann Marie K Weideman
- Department of Biostatistics, UNC Chapel Hill, Chapel Hill, NC, USA; Center for AIDS Research, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Jolene Ranek
- Computational Medicine Program, UNC Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Gatphan Atassi
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill, Chapel Hill, NC, USA
| | - JoAnn Kuruc
- Department of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Adaora A Adimora
- Center for AIDS Research, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, Gillings School of Global Public Health, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Nancie M Archin
- Department of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Cynthia Gay
- Department of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David M Margolis
- Department of Microbiology & Immunology, UNC Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology & Immunology, UNC Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Stanley
- Computational Medicine Program, UNC Chapel Hill, Chapel Hill, NC, USA; Department of Computer Science, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Michael G Hudgens
- Department of Biostatistics, UNC Chapel Hill, Chapel Hill, NC, USA; Center for AIDS Research, School of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Joseph J Eron
- Department of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Nilu Goonetilleke
- Department of Microbiology & Immunology, UNC Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, UNC Chapel Hill, Chapel Hill, NC, USA.
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9
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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. J Immunol 2023:263816. [PMID: 37204246 DOI: 10.4049/jimmunol.2300077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/02/2023] [Indexed: 05/20/2023]
Abstract
Previous work from our group and others has shown that patients with breast cancer can generate a T cell response against specific human epidermal growth factor 2 (HER2) epitopes. In addition, preclinical work has shown that this T cell response can be augmented by Ag-directed mAb therapy. This study evaluated the activity and safety of a combination of dendritic cell (DC) vaccination given with mAb and cytotoxic therapy. We performed a phase I/II study using autologous DCs pulsed with two different HER2 peptides given with trastuzumab and vinorelbine to a study cohort of patients with HER2-overexpressing and a second with HER2 nonoverexpressing metastatic breast cancer. Seventeen patients with HER2-overexpressing and seven with nonoverexpressing disease were treated. Treatment was well tolerated, with one patient removed from therapy because of toxicity and no deaths. Forty-six percent of patients had stable disease after therapy, with 4% achieving a partial response and no complete responses. Immune responses were generated in the majority of patients but did not correlate with clinical response. However, in one patient, who has survived >14 y since treatment in the trial, a robust immune response was demonstrated, with 25% of her T cells specific to one of the peptides in the vaccine at the peak of her response. These data suggest that autologous DC vaccination when given with anti-HER2-directed mAb therapy and vinorelbine is safe and can induce immune responses, including significant T cell clonal expansion, in a subset of patients.
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Affiliation(s)
- Benjamin G Vincent
- Division of Hematology, Department of Medicine, University of North Carolina, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Danielle M File
- Division of Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Karen P McKinnon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Dominic T Moore
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jeffrey A Frelinger
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC
| | - Edward J Collins
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC
| | - Joseph G Ibrahim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Lisa Bixby
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Shannon Reisdorf
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sonia J Laurie
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yara A Park
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC
| | - Carey K Anders
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Frances A Collichio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Hyman B Muss
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Lisa A Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Hendrik W van Deventer
- Division of Hematology, Department of Medicine, University of North Carolina, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - E Claire Dees
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Jonathan S Serody
- Division of Hematology, Department of Medicine, University of North Carolina, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
Abstract
T-cell responses to minor histocompatibility antigens (mHAs) mediate graft-versus-leukemia (GVL) effects and graft-versus-host disease (GVHD) in allogeneic hematopoietic cell transplantation. Therapies that boost T-cell responses improve allogeneic hematopoietic cell transplant (alloHCT) efficacy but are limited by concurrent increases in the incidence and severity of GVHD. mHAs with expression restricted to hematopoietic tissue (GVL mHAs) are attractive targets for driving GVL without causing GVHD. Prior work to identify mHAs has focused on a small set of mHAs or population-level single-nucleotide polymorphism-association studies. We report the discovery of a large set of novel GVL mHAs based on predicted immunogenicity, tissue expression, and degree of sharing among donor-recipient pairs (DRPs) in the DISCOVeRY-BMT data set of 3231 alloHCT DRPs. The total number of predicted mHAs varied by HLA allele, and the total number and number of each class of mHA significantly differed by recipient genomic ancestry group. From the pool of predicted mHAs, we identified the smallest sets of GVL mHAs needed to cover 100% of DRPs with a given HLA allele. We used mass spectrometry to search for high-population frequency mHAs for 3 common HLA alleles. We validated 24 predicted novel GVL mHAs that are found cumulatively within 98.8%, 60.7%, and 78.9% of DRPs within DISCOVeRY-BMT that express HLA-A∗02:01, HLA-B∗35:01, and HLA-C∗07:02, respectively. We confirmed the immunogenicity of an example novel mHA via T-cell coculture with peptide-pulsed dendritic cells. This work demonstrates that the identification of shared mHAs is a feasible and promising technique for expanding mHA-targeting immunotherapeutics.
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Affiliation(s)
- Kelly S. Olsen
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Othmane Jadi
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sarah Dexheimer
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Dante S. Bortone
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Steven P. Vensko
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sarah Bennett
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Hancong Tang
- College of Pharmacy, The Ohio State University, Columbus, OH
| | - Marisa Diiorio
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tanvi Saran
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - David Dingfelder
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Yiwen Wang
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Christopher A. Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Loreall Pooler
- The Center for Genetic Epidemiology, University of South California, Los Angeles, CA
| | - Xin Sheng
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Marcelo C. Pasquini
- Center for International Blood and Marrow Transplant Research and Medical College of Wisconsin, Milwaukee, WI
| | - Philip L. McCarthy
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Stephen R. Spellman
- National Marrow Donor Program, Center for International Blood and Marrow Transplant Research, Minneapolis, MN
| | - Eric Weimer
- Department of Pathology & Laboratory Medicine, UNC School of Medicine, Chapel Hill, NC
| | - Theresa Hahn
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Lara Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH
- College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Paul M. Armistead
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Hematology, Department of Medicine, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Benjamin G. Vincent
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Hematology, Department of Medicine, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
Abstract
MOTIVATION Elimination of cancer cells by T cells is a critical mechanism of anti-tumor immunity and cancer immunotherapy response. T cells recognize cancer cells by engagement of T cell receptors with peptide epitopes presented by major histocompatibility complex molecules on the cancer cell surface. Peptide epitopes can be derived from antigen proteins coded for by multiple genomic sources. Bioinformatics tools used to identify tumor-specific epitopes via analysis of DNA and RNA-sequencing data have largely focused on epitopes derived from somatic variants, though a smaller number have evaluated potential antigens from other genomic sources. RESULTS We report here an open-source workflow utilizing the Nextflow DSL2 workflow manager, Landscape of Effective Neoantigens Software (LENS), which predicts tumor-specific and tumor-associated antigens from single nucleotide variants, insertions and deletions, fusion events, splice variants, cancer-testis antigens, overexpressed self-antigens, viruses, and endogenous retroviruses. The primary advantage of LENS is that it expands the breadth of genomic sources of discoverable tumor antigens using genomics data. Other advantages include modularity, extensibility, ease of use, and harmonization of relative expression level and immunogenicity prediction across multiple genomic sources. We present an analysis of 115 acute myeloid leukemia samples to demonstrate the utility of LENS. We expect LENS will be a valuable platform and resource for T cell epitope discovery bioinformatics, especially in cancers with few somatic variants where tumor-specific epitopes from alternative genomic sources are an elevated priority. AVAILABILITY AND IMPLEMENTATION More information about LENS, including code, workflow documentation, and instructions, can be found at (https://gitlab.com/landscape-of-effective-neoantigens-software).
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Affiliation(s)
- Steven P Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Kelly Olsen
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Dante Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Christof C Smith
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Shengjie Chai
- Uber Technologies, Inc., San Francisco, CA, United States
| | - Wolfgang Beckabir
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Misha Fini
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Othmane Jadi
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Alex Rubinsteyn
- Department of Genetics, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Computational Medicine Program, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Computational Medicine Program, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Division of Hematology, Department of Medicine, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
Abstract
Predator-prey theory is commonly used to describe tumor growth in the presence of selective pressure from the adaptive immune system. These interactions are mediated by the tumor immunopeptidome (what the tumor "shows" the body) and the T-cell receptor (TCR) repertoire (how well the body "sees" cancer cells). The tumor immunopeptidome comprises neoantigens which can be gained and lost throughout tumorigenesis and treatment. Heterogeneity in the immunopeptidome is predictive of poor response to immunotherapy in some tumor types, suggesting that the TCR repertoire is unable to support a fully polyclonal response against every neoantigen. Importantly, while tumor and T-cell populations are known to compete with each other for intratumoral resources, whether between-lineage competition among peripheral T cells influences the TCR repertoire is unknown and difficult to interrogate experimentally. Computational models may offer a way to investigate these phenomena and deepen our understanding of the tumor-immune axis. Here, we construct a predator-prey-like model and calibrate it to preclinical and clinical data to describe tumor growth and immunopeptidome diversification. Simultaneously, we model the expansion of antigen-specific T-cell lineages and their consumption of both lineage-specific antigenic resources and lineage-agnostic, shared resources. This predator-prey-like framework accurately described clinically observed immunopeptidomes; recapitulated response-associated effects of immunotherapy, including immunoediting; and allowed exploration of treatment of tumors with varying growth and mutation rates.
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Affiliation(s)
- Timothy Qi
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Benjamin G. Vincent
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Hematology/Oncology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2023] [Indexed: 03/09/2023] Open
Abstract
The role of B cells in antitumor immunity is becoming increasingly appreciated, as B cell populations have been associated with response to immune checkpoint blockade (ICB) in patients with breast cancer and murine models of breast cancer. Deeper understanding of antibody responses to tumor antigens is needed to clarify the function of B cells in determining response to immunotherapy. We evaluated tumor antigen-specific antibody responses in patients with metastatic triple negative breast cancer treated with pembrolizumab following low-dose cyclophosphamide therapy using computational linear epitope prediction and custom peptide microarrays. We found that a minority of predicted linear epitopes were associated with antibody signal, and signal was associated with both neoepitopes and self-peptides. No association was observed between signal presence and subcellular localization or RNA expression of parent proteins. Patient-specific patterns of antibody signal boostability were observed that were independent of clinical response. Intriguingly, measures of cumulative antibody signal intensity relative to immunotherapy treatment showed that the one complete responder in the trial had the greatest increase in total antibody signal, which supports a potential association between ICB-dependent antibody boosting and clinical response. The antibody boost in the complete responder was largely driven by increased levels of IgG specific to a sequence of N-terminal residues in native Epidermal Growth Factor Receptor Pathway Substrate 8 (EPS8) protein, a known oncogene in several cancer types including breast cancer. Structural protein prediction showed that the targeted epitope of EPS8 was in a region of the protein with mixed linear/helical structure, and that this region was solvent-exposed and not predicted to bind to interacting macromolecules. This study highlights the potential importance of the humoral immune response targeting neoepitopes as well as self epitopes in shaping clinical response to immunotherapy.
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Affiliation(s)
- Eric D Routh
- Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Mark G Woodcock
- Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Division of Medical Oncology, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Wolfgang Beckabir
- Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Steven P Vensko
- Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Department of Microbiology and Immunology, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Division of Hematology, Department of Medicine, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA .,Department of Microbiology and Immunology, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Division of Hematology, Department of Medicine, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Computational Medicine Program, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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14
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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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: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
Abstract
Urothelial Cancer - Genomic Analysis to Improve Patient Outcomes and Research (NCT02643043), UC-GENOME, is a genomic analysis and biospecimen repository study in 218 patients with metastatic urothelial carcinoma. Here we report on the primary outcome of the UC-GENOME-the proportion of subjects who received next generation sequencing (NGS) with treatment options-and present the initial genomic analyses and clinical correlates. 69.3% of subjects had potential treatment options, however only 5.0% received therapy based on NGS. We found an increased frequency of TP53E285K mutations as compared to non-metastatic cohorts and identified features associated with benefit to chemotherapy and immune checkpoint inhibition, including: Ba/Sq and Stroma-rich subtypes, APOBEC mutational signature (SBS13), and inflamed tumor immune phenotype. Finally, we derive a computational model incorporating both genomic and clinical features predictive of immune checkpoint inhibitor response. Future work will utilize the biospecimens alongside these foundational analyses toward a better understanding of urothelial carcinoma biology.
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Affiliation(s)
- Jeffrey S Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Wolfgang Beckabir
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeff Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Mi Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Elizabeth R Plimack
- Department of Hematology and Oncology, Fox Chase Cancer Center, Temple Health, Philadelphia, PA, USA
| | - Matthew D Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Petros Grivas
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Noah M Hahn
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter H O'Donnell
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Gopa Iyer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David I Quinn
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Division of Hematology, University of North Carolina, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, Computational Medicine Program, University of North Carolina, Chapel Hill, USA
| | | | - Sara E Wobker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA.
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
- Division of Oncology, University of North Carolina, Chapel Hill, NC, USA.
| | - Matthew I Milowsky
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.
- Division of Oncology, University of North Carolina, Chapel Hill, NC, USA.
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16
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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: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/19/2022] [Indexed: 02/08/2023]
Abstract
An immunosuppressive tumour microenvironment is a major obstacle in the control of pancreatic and other solid cancers1-3. Agonists of the stimulator of interferon genes (STING) protein trigger inflammatory innate immune responses to potentially overcome tumour immunosuppression4. Although these agonists hold promise as potential cancer therapies5, tumour resistance to STING monotherapy has emerged in clinical trials and the mechanism(s) is unclear5-7. Here we show that the administration of five distinct STING agonists, including cGAMP, results in an expansion of human and mouse interleukin (IL)-35+ regulatory B cells in pancreatic cancer. Mechanistically, cGAMP drives expression of IL-35 by B cells in an IRF3-dependent but type I interferon-independent manner. In several preclinical cancer models, the loss of STING signalling in B cells increases tumour control. Furthermore, anti-IL-35 blockade or genetic ablation of IL-35 in B cells also reduces tumour growth. Unexpectedly, the STING-IL-35 axis in B cells reduces proliferation of natural killer (NK) cells and attenuates the NK-driven anti-tumour response. These findings reveal an intrinsic barrier to systemic STING agonist monotherapy and provide a combinatorial strategy to overcome immunosuppression in tumours.
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Affiliation(s)
- Sirui Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bhalchandra Mirlekar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brandon M Johnson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - W June Brickey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John A Wrobel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Na Yang
- Functional Epigenomics Unit (HNN-2G5), National Institute on Aging, Bethesda, MD, USA
| | - Dingka Song
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xianming Tan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meng Deng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Craniofacial and Surgical Care, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA
| | - Yuliya Pylayeva-Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jenny P-Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Craniofacial and Surgical Care, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
Abstract
Background Triple negative breast cancer (TNBC) is an aggressive variant of breast cancer that lacks the expression of estrogen and progesterone receptors (ER and PR) and HER2. Nearly 50% of patients with advanced TNBC will develop brain metastases (BrM), commonly with progressive extracranial disease. Immunotherapy has shown promise in the treatment of advanced TNBC; however, the immune contexture of BrM remains largely unknown. We conducted a comprehensive analysis of TNBC BrM and matched primary tumors to characterize the genomic and immune landscape of TNBC BrM to inform the development of immunotherapy strategies in this aggressive disease. Methods Whole-exome sequencing (WES) and RNA sequencing were conducted on formalin-fixed, paraffin-embedded samples of BrM and primary tumors of patients with clinical TNBC (n = 25, n = 9 matched pairs) from the LCCC1419 biobank at UNC—Chapel Hill. Matched blood was analyzed by DNA sequencing as a comparison for tumor WES for the identification of somatic variants. A comprehensive genomics assessment, including mutational and copy number alteration analyses, neoantigen prediction, and transcriptomic analysis of the tumor immune microenvironment were performed. Results Primary and BrM tissues were confirmed as TNBC (23/25 primaries, 16/17 BrM) by immunohistochemistry and of the basal intrinsic subtype (13/15 primaries and 16/19 BrM) by PAM50. Compared to primary tumors, BrM demonstrated a higher tumor mutational burden. TP53 was the most frequently mutated gene and was altered in 50% of the samples. Neoantigen prediction showed elevated cancer testis antigen- and endogenous retrovirus-derived MHC class I-binding peptides in both primary tumors and BrM and predicted that single-nucleotide variant (SNV)-derived peptides were significantly higher in BrM. BrM demonstrated a reduced immune gene signature expression, although a signature associated with fibroblast-associated wound healing was elevated in BrM. Metrics of T and B cell receptor diversity were also reduced in BrM. Conclusions BrM harbored higher mutational burden and SNV-derived neoantigen expression along with reduced immune gene signature expression relative to primary TNBC. Immune signatures correlated with improved survival, including T cell signatures. Further research will expand these findings to other breast cancer subtypes in the same biobank. Exploration of immunomodulatory approaches including vaccine applications and immune checkpoint inhibition to enhance anti-tumor immunity in TNBC BrM is warranted.
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Affiliation(s)
- Eric D. Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amanda E. D. Van Swearingen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Maria J. Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marni B. McClure
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- National Cancer Center Research Institute, Tokyo, Japan
| | - Mark G. Woodcock
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shengjie Chai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, United States
| | - Luz A. Cuaboy
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amy Wheless
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amy Garrett
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lisa A. Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alan P. Hoyle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benjamin G. Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Hematology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Carey K. Anders
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Carey K. Anders,
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18
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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. Bioinform Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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]
Abstract
Motivation Splice variant neoantigens are a potential source of tumor-specific antigen (TSA) that are shared between patients in a variety of cancers, including acute myeloid leukemia. Current tools for genomic prediction of splice variant neoantigens demonstrate promise. However, many tools have not been well validated with simulated and/or wet lab approaches, with no studies published that have presented a targeted immunopeptidome mass spectrometry approach designed specifically for identification of predicted splice variant neoantigens. Results In this study, we describe NeoSplice, a novel computational method for splice variant neoantigen prediction based on (i) prediction of tumor-specific k-mers from RNA-seq data, (ii) alignment of differentially expressed k-mers to the splice graph and (iii) inference of the variant transcript with MHC binding prediction. NeoSplice demonstrates high sensitivity and precision (>80% on average across all splice variant classes) through in silico simulated RNA-seq data. Through mass spectrometry analysis of the immunopeptidome of the K562.A2 cell line compared against a synthetic peptide reference of predicted splice variant neoantigens, we validated 4 of 37 predicted antigens corresponding to 3 of 17 unique splice junctions. Lastly, we provide a comparison of NeoSplice against other splice variant prediction tools described in the literature. NeoSplice provides a well-validated platform for prediction of TSA vaccine targets for future cancer antigen vaccine studies to evaluate the clinical efficacy of splice variant neoantigens. Availability and implementation https://github.com/Benjamin-Vincent-Lab/NeoSplice. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Shengjie Chai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Christof C Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Tavleen K Kochar
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Sally A Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Wolfgang Beck
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Kelly S Olsen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Gary L Glish
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Paul M Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jan F Prins
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, 27599, USA,Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA,Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, 27599, USA,Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, 27599, USA,Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, 27599, USA,Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, 27599, USA,To whom correspondence should be addressed.
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19
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Abstract
The tumor microenvironment (TME) is a heterogeneous, complex organization composed of tumor, stroma, and endothelial cells that is characterized by cross talk between tumor and innate and adaptive immune cells. Over the last decade, it has become increasingly clear that the immune cells in the TME play a critical role in controlling or promoting tumor growth. The function of T lymphocytes in this process has been well characterized. On the other hand, the function of B lymphocytes is less clear, although recent data from our group and others have strongly indicated a critical role for B cells in antitumor immunity. There are, however, a multitude of populations of B cells found within the TME, ranging from naive B cells all the way to terminally differentiated plasma cells and memory B cells. Here, we characterize the role of B cells in the TME in both animal models and patients, with an emphasis on dissecting how B cell heterogeneity contributes to the immune response to cancer.
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Affiliation(s)
- Stephanie M Downs-Canner
- Department of Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jeremy Meier
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA;
| | - Benjamin G Vincent
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; .,Bioinformatics and Computational Biology Program, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jonathan S Serody
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; .,Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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20
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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]
Abstract
PURPOSE CALGB/SWOG 80405 was a randomized phase III trial in first-line patients with metastatic colorectal cancer treated with bevacizumab, cetuximab, or both, plus chemotherapy. We tested the effect of tumor immune features on overall survival (OS). EXPERIMENTAL DESIGN Primary tumors (N = 554) were profiled by RNA sequencing. Immune signatures of macrophages, lymphocytes, TGFβ, IFNγ, wound healing, and cytotoxicity were measured. CIBERSORTx scores of naive and memory B cells, plasma cells, CD8+ T cells, resting and activated memory CD4+ T cells, M0 and M2 macrophages, and activated mast cells were measured. RESULTS Increased M2 macrophage score [HR, 6.30; 95% confidence interval (CI), 3.0-12.15] and TGFβ signature expression (HR, 1.35; 95% CI, 1.05-1.77) were associated with shorter OS. Increased scores of plasma cells (HR, 0.55; 95% CI, 0.38-0.87) and activated memory CD4+ T cells (HR, 0.34; 95% CI, 0.16-0.65) were associated with longer OS. Using optimal cutoffs from these four features, patients were categorized as having either 4, 3, 2, or 0-1 beneficial features associated with longer OS, and the median (95% CI) OS decreased from 42.5 (35.8-47.8) to 31.0 (28.8-34.4), 25.2 (20.6-27.9), and 17.7 (13.5-20.4) months respectively (P = 3.48e-11). CONCLUSIONS New immune features can be further evaluated to improve patient response. They provide the rationale for more effective immunotherapy strategies.
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Affiliation(s)
| | - Akram Yazdani
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Naim Rashid
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | - Scott Van Buren
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Alan P. Venook
- University of California at San Francisco, San Francisco, CA
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21
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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: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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]
Abstract
Immune-checkpoint inhibitors (ICI), although revolutionary in improving long-term survival outcomes, are mostly effective in patients with immune-responsive tumors. Most patients with cancer either do not respond to ICIs at all or experience disease progression after an initial period of response. Treatment resistance to ICIs remains a major challenge and defines the biggest unmet medical need in oncology worldwide. In a collaborative workshop, thought leaders from academic, biopharma, and nonprofit sectors convened to outline a resistance framework to support and guide future immune-resistance research. Here, we explore the initial part of our effort by collating seminal discoveries through the lens of known biological processes. We highlight eight biological processes and refer to them as immune resistance nodes. We examine the seminal discoveries that define each immune resistance node and pose critical questions, which, if answered, would greatly expand our notion of immune resistance. Ultimately, the expansion and application of this work calls for the integration of multiomic high-dimensional analyses from patient-level data to produce a map of resistance phenotypes that can be utilized to guide effective drug development and improved patient outcomes.
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Affiliation(s)
- Maria Karasarides
- Worldwide Medical Oncology, Bristol Myers Squibb, Princeton, New Jersey.,Corresponding Authors: Maria Karasarides, Worldwide Medical Oncology, Bristol-Myers Squibb, Boston, MA 021273401. E-mail: ; and Theresa LaVallee, 1 Letterman Drive, Suite D3500, San Francisco, CA 94129. Phone: 628-899-7593; E-mail:
| | - Alexandria P. Cogdill
- Immunai, New York, New York.,Department of Immunology, The University of Texas MD Anderson, Houston, Texas
| | | | - Michaela Bowden
- Translational Medicine, Bristol Myers Squibb, Cambridge, Massachusetts
| | - Elizabeth M. Burton
- Department of Surgical Oncology, The University of Texas MD Anderson, Houston, Texas
| | - Lisa H. Butterfield
- Parker Institute for Cancer Immunotherapy, San Francisco, California.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California
| | | | - Christian Hammer
- Department of Cancer Immunology, Genentech, South San Francisco, California.,Department of Human Genetics, Genentech, South San Francisco, California
| | - Cara L. Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christine E. Horak
- Global Drug Development, Bristol Myers Squibb, Lawrenceville, New Jersey
| | - Heather M. McGee
- Department of Radiation Oncology, City of Hope National Medical Center and Department of Immuno-Oncology, Beckmann Research Institute, City of Hope, Duarte, California
| | - Anne Monette
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
| | | | - Christine N. Spencer
- Department of Informatics, Parker Institute for Cancer Immunotherapy, San Francisco, California.,University of California San Francisco, San Francisco, California
| | - Randy F. Sweis
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois.,Committee on Immunology, University of Chicago, Chicago, Illinois.,Comprehensive Cancer Center, University of Chicago, Chicago, Illinois
| | - Benjamin G. Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | | | - Jianda Yuan
- Translational Oncology, Early Oncology Development Department, Merck Research Laboratories, Rahway, New Jersey
| | - Roberta Zappasodi
- Weill Cornell Medicine, New York, New York.,Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Daniel K. Wells
- Immunai, New York, New York.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Theresa LaVallee
- Parker Institute for Cancer Immunotherapy, San Francisco, California.,Corresponding Authors: Maria Karasarides, Worldwide Medical Oncology, Bristol-Myers Squibb, Boston, MA 021273401. E-mail: ; and Theresa LaVallee, 1 Letterman Drive, Suite D3500, San Francisco, CA 94129. Phone: 628-899-7593; E-mail:
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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
Affiliation(s)
- Sarah Asad
- Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Kathryn Kananen
- Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Kurt R. Mueller
- Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | - Yujia Wen
- Alliance for Clinical Trials in Oncology, Chicago, IL
| | - Charles M. Perou
- Department of Genetics, and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - James Chen
- Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Benjamin G. Vincent
- Department of Genetics, and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
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23
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Triple negative breast cancer (TNBC) is characterized by the presence of immune cells in the tumor microenvironment, however, the response to single-agent immune checkpoint inhibitor (ICI) therapy is modest. Preclinical models have demonstrated that intratumoral regulatory T cells (Tregs) dampen the antitumor response to ICI. We performed a single-arm phase II trial to evaluate the efficacy of a single low dose of cyclophosphamide (Cy) to deplete Tregs administered before initiating pembrolizumab. PATIENTS AND METHODS 40 patients with pretreated metastatic TNBC were enrolled. The primary endpoints were progression-free survival (PFS) and change in peripheral blood Tregs after Cy. Secondary endpoints included overall response rate (ORR), duration of response, overall survival, treatment-related adverse events (AEs), and correlative evaluations. RESULTS Median PFS was 1.8 months, and the ORR was 21%. Tregs were not significantly decreased after Cy prior to ICI (-3.3%, p=0.19), and increased significantly after the first cycle of therapy (+21% between cycles 1 and 2, p=0.005). Immune-related AEs were similar to historical pembrolizumab monotherapy, and were associated with response to therapy (p=0.02). Patients with pretreatment tumors harboring increased expression of B cell metagene signatures and increased circulating B cell receptor repertoire diversity were associated with clinical response and immune-related toxicity (IRT). CONCLUSIONS Among patients with heavily pretreated TNBC, Cy prior to pembrolizumab did not significantly deplete Tregs, and in those with decreased numbers there was rapid recovery following therapy. Increased B cell gene expression in baseline samples was associated with clinical response and IRT.
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Affiliation(s)
| | - Mark G Woodcock
- Division of Medical Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Dominic T Moore
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Maria J Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Sonia Laurie
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Alexander Robeson
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Oleg Kolupaev
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Luz A Cuaboy
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Amy L Garrett
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Karen McKinnon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Division of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Kristen Cowens
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Dante Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Benjamin C Calhoun
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Alec D Wilkinson
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Lisa Carey
- Division of Medical Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Trevor Jolly
- Division of Medical Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Hyman Muss
- Division of Medical Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Katherine Reeder-Hayes
- Division of Medical Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Rebecca Kaltman
- Department of Hematology and Oncology, George Washington Cancer Center, Washington, District of Columbia, USA
| | - Rachel Jankowitz
- Division of Hematology/Oncology, University of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Vinay Gudena
- Division of Hematology/Oncology, Cone Health Cancer Center, Greensboro, North Carolina, USA
| | - Oludamilola Olajide
- Rex Hematology Oncology Associates, Rex Cancer Care, Raleigh, North Carolina, USA
| | - Charles Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - E Claire Dees
- Division of Medical Oncology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Division of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Division of Hematology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA .,Division of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Division of Hematology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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24
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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: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
Abstract
BACKGROUND The KRAS proto-oncogene is among the most frequently mutated genes in cancer, yet for 40 years it remained an elusive therapeutic target. Recently, allosteric inhibitors that covalently bind to KRAS G12C mutations have been approved for use in lung adenocarcinomas. Although responses are observed, they are often short-lived, thus making in-depth characterization of the mechanisms of resistance of paramount importance. METHODS Here, we present a rapid-autopsy case of a patient who had a KRASG12C-mutant lung adenocarcinoma who initially responded to a KRAS G12C inhibitor but then rapidly developed resistance. Using deep-RNA and whole-exome sequencing comparing pretreatment, posttreatment, and matched normal tissues, we uncover numerous mechanisms of resistance to direct KRAS inhibition. RESULTS In addition to decreased KRAS G12C–mutant allele frequency in refractory tumors, we also found reactivation of the MAPK pathway despite no new mutations in KRAS or its downstream mediators. Tumor cell–intrinsic and non–cell autonomous mechanisms included increased complement activation, coagulation, and tumor angiogenesis, and several lines of evidence of immunologic evasion. CONCLUSION Together, our findings reveal numerous mechanisms of resistance to current KRAS G12C inhibitors through enrichment of clonal populations, KRAS-independent downstream signaling, and diverse remodeling of the tumor microenvironment. FUNDING Richard and Fran Duley, Jimmy and Kay Mann, the NIH, and the North Carolina Biotechnology Center.
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Affiliation(s)
- Yihsuan S Tsai
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Mark G Woodcock
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Salma H Azam
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, United States of America
| | - Leigh B Thorne
- Department of Pathology, The University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Krishna L Kanchi
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Joel S Parker
- The University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Chad V Pecot
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, United States of America
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25
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Tschernia NP, Kumar V, Moore DT, Vincent BG, Coombs CC, Van Deventer H, Foster MC, DeZern AE, Luznik L, Riches ML, Serody JS, Gojo I, Zeidner JF. Safety and Efficacy of Pembrolizumab Prior to Allogeneic Stem Cell Transplantation for Acute Myelogenous Leukemia. Transplant Cell Ther 2021; 27:1021.e1-1021.e5. [PMID: 34474164 DOI: 10.1016/j.jtct.2021.08.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/01/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
Programmed death 1 (PD-1) is an integral component of acute myelogenous leukemia (AML) immune evasion, chemotherapy resistance, and disease progression. PD-1 inhibitors are being investigated as treatment for AML in combination with hypomethylating agents and cytotoxic chemotherapy with encouraging findings. Although allogeneic stem cell transplantation (alloSCT) remains the most established curative treatment for patients with relapsed and refractory AML in complete remission, there are limited data on the clinical outcomes and safety of immune checkpoint inhibitors (ICIs) prior to alloSCT in AML. In the present study, we compared clinical outcomes of 9 patients with AML receiving high-dose cytarabine followed by pembrolizumab in a phase II clinical trial (NCT02768792) prior to alloSCT versus a historical control group of 18 AML patients who underwent alloSCT without prior ICI exposure. The nonparametric Jonckheere-Terpstra test was used to test for a difference in the ordered severity categories of acute graft-versus-host disease (GVHD) within 100 days of transplantation. Time-to-event estimates for overall survival and relapse-free survival were calculated using the Kaplan-Meier method and compared using a log-rank test. One-year survival was not significantly different between the treatment groups (67% versus 78%; P = .34). 100-day mortality was 0% in the ICI group versus 17% in the control group, and there was no increase in grade III-IV acute GVHD in patients treated with pembrolizumab prior to alloSCT. No chronic GVHD was seen in patients treated with pembrolizumab prior to alloSCT and who received post-transplantation cyclophosphamide (PTCy) as part of their conditioning regimen. These findings reinforce the safety and feasibility of ICI therapy prior to alloSCT in patients with AML, and suggest that PTCy may abrogate GVHD risk and severity in patients who receive ICI prior to undergoing alloSCT for AML.
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Affiliation(s)
- Nicholas P Tschernia
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Vaibhav Kumar
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Dominic T Moore
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Catherine C Coombs
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Hendrik Van Deventer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Matthew C Foster
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Amy E DeZern
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Leo Luznik
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Marcie L Riches
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Ivana Gojo
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Joshua F Zeidner
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.
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26
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Zeidner JF, Vincent BG, Ivanova A, Moore D, McKinnon KP, Wilkinson AD, Mukhopadhyay R, Mazziotta F, Knaus HA, Foster MC, Coombs CC, Jamieson K, Van Deventer H, Webster JA, Prince GT, DeZern AE, Smith BD, Levis MJ, Montgomery ND, Luznik L, Serody JS, Gojo I. Phase II Trial of Pembrolizumab after High-Dose Cytarabine in Relapsed/Refractory Acute Myeloid Leukemia. Blood Cancer Discov 2021; 2:616-629. [PMID: 34778801 DOI: 10.1158/2643-3230.bcd-21-0070] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/12/2021] [Accepted: 08/25/2021] [Indexed: 12/17/2022] Open
Abstract
Immune suppression, exhaustion, and senescence are frequently seen throughout disease progression in acute myeloid leukemia (AML). We conducted a phase II study of high-dose cytarabine followed by pembrolizumab 200 mg i.v. on day 14 to examine whether PD-1 inhibition improves clinical responses in relapsed/refractory (R/R) AML. Overall responders could receive pembrolizumab maintenance up to 2 years. Among 37 patients enrolled, the overall response rate, composite complete remission (CRc) rate (primary endpoint), and median overall survival (OS) were 46%, 38%, and 11.1 months, respectively. Patients with refractory/early relapse and those receiving treatment as first salvage had encouraging outcomes (median OS, 13.2 and 11.3 months, respectively). Grade ≥3 immune-related adverse events were rare (14%) and self-limiting. Patients who achieved CRc had a higher frequency of progenitor exhausted CD8+ T cells expressing TCF-1 in the bone marrow prior to treatment. A multifaceted correlative approach of genomic, transcriptomic, and immunophenotypic profiling offers insights on molecular correlates of response and resistance to pembrolizumab. Significance Immune-checkpoint blockade with pembrolizumab was tolerable and feasible after high-dose cytarabine in R/R AML, with encouraging clinical activity, particularly in refractory AML and those receiving treatment as first salvage regimen. Further study of pembrolizumab and other immune-checkpoint blockade strategies after cytotoxic chemotherapy is warranted in AML.See related commentary by Wei et al., p. 551. This article is highlighted in the In This Issue feature, p. 549.
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Affiliation(s)
- Joshua F Zeidner
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina.,Division of Hematology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Benjamin G Vincent
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina.,Division of Hematology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,University of North Carolina, Department of Microbiology and Immunology, Chapel Hill, North Carolina.,Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Anastasia Ivanova
- University of North Carolina School of Medicine, Department of Biostatistics, Chapel Hill, North Carolina
| | - Dominic Moore
- University of North Carolina School of Medicine, Department of Biostatistics, Chapel Hill, North Carolina
| | - Karen P McKinnon
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina.,University of North Carolina, Department of Microbiology and Immunology, Chapel Hill, North Carolina
| | - Alec D Wilkinson
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - Rupkatha Mukhopadhyay
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Francesco Mazziotta
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.,University of Siena, Department of Medical Biotechnologies, Siena, Italy
| | - Hanna A Knaus
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Matthew C Foster
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina.,Division of Hematology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Catherine C Coombs
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina.,Division of Hematology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Katarzyna Jamieson
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina.,Division of Hematology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Hendrik Van Deventer
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina.,Division of Hematology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Jonathan A Webster
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.,Department of Oncology, Division of Hematological Malignancies, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Gabrielle T Prince
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.,Department of Oncology, Division of Hematological Malignancies, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Amy E DeZern
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.,Department of Oncology, Division of Hematological Malignancies, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - B Douglas Smith
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.,Department of Oncology, Division of Hematological Malignancies, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Mark J Levis
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.,Department of Oncology, Division of Hematological Malignancies, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Nathan D Montgomery
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina.,Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Leo Luznik
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.,Department of Oncology, Division of Hematological Malignancies, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jonathan S Serody
- University of North Carolina School of Medicine, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina.,Division of Hematology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,University of North Carolina, Department of Microbiology and Immunology, Chapel Hill, North Carolina.,Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ivana Gojo
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.,University of Siena, Department of Medical Biotechnologies, Siena, Italy
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27
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Xu N, Palmer DC, Robeson AC, Shou P, Bommiasamy H, Laurie SJ, Willis C, Dotti G, Vincent BG, Restifo NP, Serody JS. STING agonist promotes CAR T cell trafficking and persistence in breast cancer. J Exp Med 2021; 218:211644. [PMID: 33382402 PMCID: PMC7780733 DOI: 10.1084/jem.20200844] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/22/2020] [Accepted: 11/12/2020] [Indexed: 12/15/2022] Open
Abstract
CAR T therapy targeting solid tumors is restrained by limited infiltration and persistence of those cells in the tumor microenvironment (TME). Here, we developed approaches to enhance the activity of CAR T cells using an orthotopic model of locally advanced breast cancer. CAR T cells generated from Th/Tc17 cells given with the STING agonists DMXAA or cGAMP greatly enhanced tumor control, which was associated with enhanced CAR T cell persistence in the TME. Using single-cell RNA sequencing, we demonstrate that DMXAA promoted CAR T cell trafficking and persistence, supported by the generation of a chemokine milieu that promoted CAR T cell recruitment and modulation of the immunosuppressive TME through alterations in the balance of immune-stimulatory and suppressive myeloid cells. However, sustained tumor regression was accomplished only with the addition of anti-PD-1 and anti-GR-1 mAb to Th/Tc17 CAR T cell therapy given with STING agonists. This study provides new approaches to enhance adoptive T cell therapy in solid tumors.
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Affiliation(s)
- Nuo Xu
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Douglas C Palmer
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Alexander C Robeson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Peishun Shou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Hemamalini Bommiasamy
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sonia J Laurie
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Caryn Willis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Gianpietro Dotti
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Jonathan S Serody
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC
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28
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Truong AS, Zhou M, Krishnan B, Utsumi T, Manocha U, Stewart KG, Beck W, Rose TL, Milowsky MI, He X, Smith CC, Bixby LM, Perou CM, Wobker SE, Bailey ST, Vincent BG, Kim WY. Entinostat induces antitumor immune responses through immune editing of tumor neoantigens. J Clin Invest 2021; 131:e138560. [PMID: 34396985 DOI: 10.1172/jci138560] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/22/2021] [Indexed: 12/31/2022] Open
Abstract
Although immune-checkpoint inhibitors (ICIs) have been a remarkable advancement in bladder cancer treatment, the response rate to single-agent ICIs remains suboptimal. There has been substantial interest in the use of epigenetic agents to enhance ICI efficacy, although precisely how these agents potentiate ICI response has not been fully elucidated. We identified entinostat, a selective HDAC1/3 inhibitor, as a potent antitumor agent in our immune-competent bladder cancer mouse models (BBN963 and BBN966). We demonstrate that entinostat selectively promoted immune editing of tumor neoantigens, effectively remodeling the tumor immune microenvironment, resulting in a robust antitumor response that was cell autonomous, dependent upon antigen presentation, and associated with increased numbers of neoantigen-specific T cells. Finally, combination treatment with anti-PD-1 and entinostat led to complete responses and conferred long-term immunologic memory. Our work defines a tumor cell-autonomous mechanism of action for entinostat and a strong preclinical rationale for the combined use of entinostat and PD-1 blockade in bladder cancer.
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Affiliation(s)
- Andrew S Truong
- Lineberger Comprehensive Cancer Center.,Department of Pharmacology
| | - Mi Zhou
- Lineberger Comprehensive Cancer Center
| | | | | | | | | | | | - Tracy L Rose
- Lineberger Comprehensive Cancer Center.,Department of Medicine
| | | | | | | | | | - Charles M Perou
- Lineberger Comprehensive Cancer Center.,Department of Genetics.,Computational Medicine Program
| | - Sara E Wobker
- Lineberger Comprehensive Cancer Center.,Department of Pathology, and
| | | | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center.,Department of Medicine.,Computational Medicine Program.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill (UNC), Chapel Hill, North Carolina, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center.,Department of Pharmacology.,Department of Medicine.,Department of Genetics
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29
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Smith CC, Olsen KS, Gentry KM, Sambade M, Beck W, Garness J, Entwistle S, Willis C, Vensko S, Woods A, Fini M, Carpenter B, Routh E, Kodysh J, O'Donnell T, Haber C, Heiss K, Stadler V, Garrison E, Sandor AM, Ting JPY, Weiss J, Krajewski K, Grant OC, Woods RJ, Heise M, Vincent BG, Rubinsteyn A. Landscape and selection of vaccine epitopes in SARS-CoV-2. Genome Med 2021; 13:101. [PMID: 34127050 PMCID: PMC8201469 DOI: 10.1186/s13073-021-00910-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 05/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation. The rationale for this design was to drive both humoral and cellular immunity with high specificity while avoiding undesired effects such as antibody-dependent enhancement (ADE). METHODS We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining protein source, concurrent human/murine coverage, and population coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, sequence conservation, source protein abundance, and coverage of high frequency HLA alleles. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for surface accessibility, sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. RESULTS From 58 initial candidates, three B cell epitope regions were identified. From 3730 (MHC-I) and 5045 (MHC-II) candidate ligands, 292 CD8+ and 284 CD4+ T cell epitopes were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we proposed a set of 22 SARS-CoV-2 vaccine peptides for use in subsequent murine studies. We curated a dataset of ~ 1000 observed T cell epitopes from convalescent COVID-19 patients across eight studies, showing 8/15 recurrent epitope regions to overlap with at least one of our candidate peptides. Of the 22 candidate vaccine peptides, 16 (n = 10 T cell epitope optimized; n = 6 B cell epitope optimized) were manually selected to decrease their degree of sequence overlap and then synthesized. The immunogenicity of the synthesized vaccine peptides was validated using ELISpot and ELISA following murine vaccination. Strong T cell responses were observed in 7/10 T cell epitope optimized peptides following vaccination. Humoral responses were deficient, likely due to the unrestricted conformational space inhabited by linear vaccine peptides. CONCLUSIONS Overall, we find our selection process and vaccine formulation to be appropriate for identifying T cell epitopes and eliciting T cell responses against those epitopes. Further studies are needed to optimize prediction and induction of B cell responses, as well as study the protective capacity of predicted T and B cell epitopes.
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Affiliation(s)
- Christof C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kelly S Olsen
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kaylee M Gentry
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Maria Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Wolfgang Beck
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jason Garness
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Caryn Willis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Allison Woods
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Misha Fini
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Brandon Carpenter
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Eric Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Julia Kodysh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Timothy O'Donnell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Adam M Sandor
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jenny P Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
- Institute for Inflammatory Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared Weiss
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Division of Medical Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Mark Heise
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA.
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA.
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
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Min Y, Roche KC, Tian S, Eblan MJ, McKinnon KP, Caster JM, Chai S, Herring LE, Zhang L, Zhang T, DeSimone JM, Tepper JE, Vincent BG, Serody JS, Wang AZ. Author Correction: Antigen-capturing nanoparticles improve the abscopal effect and cancer immunotherapy. Nat Nanotechnol 2021; 16:743-744. [PMID: 33580223 PMCID: PMC9280999 DOI: 10.1038/s41565-021-00864-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Yuanzeng Min
- Laboratory of Nano- and Translational Medicine, Carolina Center for Cancer Nanotechnology Excellence, Carolina Institute of Nanomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Kyle C Roche
- Laboratory of Nano- and Translational Medicine, Carolina Center for Cancer Nanotechnology Excellence, Carolina Institute of Nanomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Shaomin Tian
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Michael J Eblan
- Laboratory of Nano- and Translational Medicine, Carolina Center for Cancer Nanotechnology Excellence, Carolina Institute of Nanomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Karen P McKinnon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Joseph M Caster
- Laboratory of Nano- and Translational Medicine, Carolina Center for Cancer Nanotechnology Excellence, Carolina Institute of Nanomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Shengjie Chai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - Longzhen Zhang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Tian Zhang
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Joseph M DeSimone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695, USA
- Sloan-Kettering Institute for Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, New York, 10021, USA
| | - Joel E Tepper
- Laboratory of Nano- and Translational Medicine, Carolina Center for Cancer Nanotechnology Excellence, Carolina Institute of Nanomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Andrew Z Wang
- Laboratory of Nano- and Translational Medicine, Carolina Center for Cancer Nanotechnology Excellence, Carolina Institute of Nanomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
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Story CM, Wang T, Bhatt VR, Battiwalla M, Badawy SM, Kamoun M, Gragert L, Brown V, Baxter-Lowe LA, Marsh SGE, Gadalla SM, Schetelig J, Mytilineos J, Miklos D, Waller EK, Kuxhausen M, Spellman S, Lee S, Paczesny S, Lansford JL, Vincent BG, Riches ML, Armistead PM. Genetics of HLA Peptide Presentation and Impact on Outcomes in HLA-Matched Allogeneic Hematopoietic Cell Transplantation. Transplant Cell Ther 2021; 27:591-599. [PMID: 33882342 DOI: 10.1016/j.jtct.2021.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 01/06/2023]
Abstract
Minor histocompatibility antigens (mHAs), recipient-derived peptide epitopes presented on the cell surface, are known to mediate graft-versus-host disease (GVHD); however, there are no current methods to associate mHA features with GVHD risk. This deficiency is due in part to the lack of technological means to accurately predict, let alone confirm, the tremendous number of potential mHAs in each individual transplant. Previous studies have shown that different HLA molecules present varying fractions of candidate peptide epitopes; however, the genetic "distance" between HLA-matched donors and recipients is relatively constrained. From these 2 observations, it is possible that the HLA type for a donor-recipient pair (DRP) would provide a surrogate measurement of the number of predicted mHAs, which could be related to GVHD risk. Because different HLA molecules present variable numbers of peptide antigens, a predicted cumulative peptide-binding efficiency can be calculated for individual DRP based on the pair's HLA type. The purpose of this study was to test whether cumulative peptide-binding efficiency is associated with the risk of acute GVHD (aGVHD) or relapse. In this retrospective Center for International Blood and Marrow Transplant Research study, a total of 3242 HLA-matched DRPs were analyzed for predicted cumulative peptide-binding efficiency using their HLA types and were divided into tertiles based on their scores. Univariable and multivariable analyses was performed to test for associations between cumulative peptide-binding efficiency for DRPs, divided into the HLA-matched related donor (MRD) and HLA-matched unrelated donor (MUD) cohorts, and the primary outcomes of aGVHD and relapse. Secondary outcomes investigated included overall survival, disease-free survival, and transplantation-related mortality. Using a computationally generated peptidome as a test dataset, the tested series of HLA class I displayed peptide-binding frequencies ranging from 0.1% to 3.8% of the full peptidome, and HLA class II molecules had peptide-binding frequencies of 12% to 77% across the HLA-DRB1 allotypes. By increasing binding efficiency tertile, the cumulative incidence of aGVHD at 6 months for MUD patients was 41%, 41%, and 45% for HLA class I (P = .336) and 44%, 41%, and 42% for HLA class II (P = .452). The cumulative incidences of relapse at 3 years for MUD transplant recipients were 36%, 38%, and 38% for HLA class I (P = .533) and 37%, 37%, and 38% for HLA class II (P = .896). The findings were similar for MRD transplant recipients. Multivariable analysis did not identify any impact of peptide-binding efficiency on aGVHD or relapse in MUD or MRD transplant recipients. Whereas GVHD is mediated by minor antigen mismatches in the context of HLA-matched allo-HCT, peptide-binding efficiency, which was used as a surrogate measurement for predicted number of binding antigens, did not provide additional clinical information for GVHD risk assessment. The negative result may be due to the limitations of this surrogate marker, or it is possible that GVHD is driven by a subset of immunogenic mHAs. Further research should be directed at direct mHA epitope and immunogenicity prediction.
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Affiliation(s)
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Vijaya Raj Bhatt
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Minoo Battiwalla
- Director of Outcomes Research, Sarah Cannon Blood Cancer Network, Nashville, Tennessee
| | - Sherif M Badawy
- Division of Hematology, Oncology and Stem Cell Transplant, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Malek Kamoun
- Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Valerie Brown
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Penn State Hershey Children's Hospital and College of Medicine, Hershey, Pennsylvania
| | - Lee Ann Baxter-Lowe
- Director of HLA Laboratory, Children's Hospital of Los Angeles, Los Angeles, California
| | - Steven G E Marsh
- Anthony Nolan Research Institute & University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology & Genetics, NIH-NCI Clinical Genetics Branch, Rockville, Maryland
| | - Johannes Schetelig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, and DKMS, Clinical Trials Unit, Dresden, Germany
| | | | - David Miklos
- BMT and Cell Therapy Division, Department of Medicine, Stanford Health Care, Stanford, California
| | - Edmund K Waller
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Michelle Kuxhausen
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Stephanie Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina
| | - Jefferson L Lansford
- Orthopedic Surgery, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Benjamin G Vincent
- BMTCT Program, Division of Hematology, University of North Carolina, Chapel Hill, North Carolina; BMTCT Program, Division of Hematology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Marcie L Riches
- BMTCT Program, Division of Hematology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Paul M Armistead
- Internal Medicine, University of North Carolina, Chapel Hill, North Carolina; BMTCT Program, Division of Hematology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.
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Trembath DG, Davis ES, Rao S, Bradler E, Saada AF, Midkiff BR, Snavely AC, Ewend MG, Collichio FA, Lee CB, Karachaliou GS, Ayvali F, Ollila DW, Krauze MT, Kirkwood JM, Vincent BG, Nikolaishvilli-Feinberg N, Moschos SJ. Brain Tumor Microenvironment and Angiogenesis in Melanoma Brain Metastases. Front Oncol 2021; 10:604213. [PMID: 33552976 PMCID: PMC7860978 DOI: 10.3389/fonc.2020.604213] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND High tumor-infiltrating lymphocytes (TILs) and hemorrhage are important prognostic factors in patients who have undergone craniotomy for melanoma brain metastases (MBM) before 2011 at the University of Pittsburgh Medical Center (UPMC). We have investigated the prognostic or predictive role of these histopathologic factors in a more contemporary craniotomy cohort from the University of North Carolina at Chapel Hill (UNC-CH). We have also sought to understand better how various immune cell subsets, angiogenic factors, and blood vessels may be associated with clinical and radiographic features in MBM. METHODS Brain tumors from the UPMC and UNC-CH patient cohorts were (re)analyzed by standard histopathology, tumor tissue imaging, and gene expression profiling. Variables were associated with overall survival (OS) and radiographic features. RESULTS The patient subgroup with high TILs in craniotomy specimens and subsequent treatment with immune checkpoint inhibitors (ICIs, n=7) trended to have longer OS compared to the subgroup with high TILs and no treatment with ICIs (n=11, p=0.059). Bleeding was significantly associated with tumor volume before craniotomy, high melanoma-specific expression of basic fibroblast growth factor (bFGF), and high density of CD31+αSMA- blood vessels. Brain tumors with high versus low peritumoral edema before craniotomy had low (17%) versus high (41%) incidence of brisk TILs. Melanoma-specific expression of the vascular endothelial growth factor (VEGF) was comparable to VEGF expression by TILs and was not associated with any particular prognostic, radiographic, or histopathologic features. A gene signature associated with gamma delta (gd) T cells was significantly higher in intracranial than same-patient extracranial metastases and primary melanoma. However, gdT cell density in MBM was not prognostic. CONCLUSIONS ICIs may provide greater clinical benefit in patients with brisk TILs in MBM. Intratumoral hemorrhage in brain metastases, a significant clinical problem, is not merely associated with tumor volume but also with underlying biology. bFGF may be an essential pathway to target. VEGF, a factor principally associated with peritumoral edema, is not only produced by melanoma cells but also by TILs. Therefore, suppressing low-grade peritumoral edema using corticosteroids may harm TIL function in 41% of cases. Ongoing clinical trials targeting VEGF in MBM may predict a lack of unfavorable impacts on TIL density and/or intratumoral hemorrhage.
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Affiliation(s)
- Dimitri G. Trembath
- Departments of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Eric S. Davis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shanti Rao
- University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Evan Bradler
- University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Angelica F. Saada
- State University of New York Downstate Medical Center College of Medicine, Brooklyn, NY, United States
| | - Bentley R. Midkiff
- Translational Pathology Laboratory, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Anna C. Snavely
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Matthew G. Ewend
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Neurosurgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frances A. Collichio
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Carrie B. Lee
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Georgia-Sofia Karachaliou
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Fatih Ayvali
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - David W. Ollila
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Michal T. Krauze
- Melanoma and Skin Cancer Program, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - John M. Kirkwood
- Melanoma and Skin Cancer Program, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Benjamin G. Vincent
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nana Nikolaishvilli-Feinberg
- Translational Pathology Laboratory, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stergios J. Moschos
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Vincent BG, Szustakowski JD, Doshi P, Mason M, Guinney J, Carbone DP. Pursuing Better Biomarkers for Immunotherapy Response in Cancer Through a Crowdsourced Data Challenge. JCO Precis Oncol 2021; 5:51-54. [PMID: 34994587 PMCID: PMC9848594 DOI: 10.1200/po.20.00371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Benjamin G. Vincent
- Department of Medicine, Division of
Hematology/Oncology, Department of Microbiology and Immunology, Curriculum in
Bioinformatics and Computational Biology, Computational Medicine Program,
University of North Carolina at Chapel Hill, Chapel Hill, NC,Benjamin G. Vincent, MD, University of North Carolina at Chapel
Hill, 5206 Marsico Hall, Chapel Hill, NC 27599; Twitter: @BenjaminGVincen;
@UNC_Lineberger; @CompMedUNC; e-mail:
| | | | | | | | | | - David P. Carbone
- The Ohio State University Comprehensive
Cancer Center, Columbus, OH
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Bortone DS, Woodcock MG, Parker JS, Vincent BG. Improved T-cell Receptor Diversity Estimates Associate with Survival and Response to Anti-PD-1 Therapy. Cancer Immunol Res 2021; 9:103-112. [PMID: 33177107 DOI: 10.1158/2326-6066.cir-20-0398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/27/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022]
Abstract
T-cell receptor (TCR) repertoire profiling has emerged as a powerful tool for biological discovery and biomarker development in cancer immunology and immunotherapy. A key statistic derived from repertoire profiling data is diversity, which summarizes the frequency distribution of TCRs within a mixed population. Despite the growing use of TCR diversity metrics in clinical trial correlative studies in oncology, their accuracy has not been validated using published ground-truth datasets. Here, we reported the performance characteristics of methods for TCR repertoire profiling from RNA-sequencing data, showed undersampling as a prominent source of bias in diversity estimates, and derived a model via statistical learning that attenuates bias to produce corrected diversity estimates. This modeled diversity improved discrimination in The Cancer Genome Atlas data and associated with survival and treatment response in patients with melanoma treated with anti-PD-1 therapy, where the commonly used diversity normalizations did not. These findings have the potential to increase our understanding of the tumor immune microenvironment and improve the accuracy of predictions of patient responses to immunotherapy.
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Affiliation(s)
- Dante S Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mark G Woodcock
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Division of Hematology/Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, North Carolina
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, North Carolina
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, North Carolina
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
- Division of Hematology/Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, North Carolina
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, North Carolina
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, North Carolina
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
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Beck W, Rose TL, Milowsky MI, Vincent BG, Klomp J, Kim WY. Age is associated with response to immune checkpoint blockade in advanced urothelial carcinoma. Urol Oncol 2020. [DOI: 10.1016/j.urolonc.2020.10.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wood CG, Ferguson JE, Parker JS, Moore DT, Whisenant JG, Maygarden SJ, Wallen EM, Kim WY, Milowsky MI, Beckermann KE, Davis NB, Haake SM, Karam JA, Bortone DS, Vincent BG, Powles T, Rathmell WK. Neoadjuvant pazopanib and molecular analysis of tissue response in renal cell carcinoma. JCI Insight 2020; 5:132852. [PMID: 33208553 PMCID: PMC7710285 DOI: 10.1172/jci.insight.132852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/08/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUNDSurgery remains the frontline therapy for patients with localized clear cell renal cell carcinoma (ccRCC); however, 20%-40% recur. Angiogenesis inhibitors have improved survival in metastatic patients and may result in responses in the neoadjuvant setting. The impact of these agents on the tumor genetic heterogeneity or the immune milieu is largely unknown. This phase II study was designed to evaluate safety, response, and effect on tumor tissue of neoadjuvant pazopanib.METHODSccRCC patients with localized disease received pazopanib (800 mg daily; median 8 weeks), followed by nephrectomy. Five tumors were examined for mutations by whole exome sequencing from samples collected before therapy and at nephrectomy. These samples underwent RNA sequencing; 17 samples were available for posttreatment assessment.RESULTSTwenty-one patients were enrolled. The overall response rate was 8 of 21 (38%). No patients with progressive disease. At 1-year, response-free survival and overall survival was 83% and 89%, respectively. The most frequent grade 3 toxicity was hypertension (33%, 7 of 21). Sequencing revealed strong concordance between pre- and posttreatment samples within individual tumors, suggesting tumors harbor stable core profiles. However, a reduction in private mutations followed treatment, suggesting a selective process favoring enrichment of driver mutations.CONCLUSIONNeoadjuvant pazopanib is safe and active in ccRCC. Future genomic analyses may enable the segregation of driver and passenger mutations. Furthermore, tumor infiltrating immune cells persist during therapy, suggesting that pazopanib can be combined with immune checkpoint inhibitors without dampening the immune response.FUNDINGSupport was provided by Novartis and GlaxoSmithKline as part of an investigator-initiated study.
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Affiliation(s)
| | - James E. Ferguson
- Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Dominic T. Moore
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Jennifer G. Whisenant
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Susan J. Maygarden
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA.,Department of Pathology
| | - Eric M. Wallen
- Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - William Y. Kim
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA.,Department of Medicine, Division of Oncology, and
| | - Mathew I. Milowsky
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA.,Department of Medicine, Division of Oncology, and
| | - Kathryn E. Beckermann
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nancy B. Davis
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Scott M. Haake
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jose A. Karam
- Department of Urology, MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Benjamin G. Vincent
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA.,Department of Medicine, Division of Hematology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - W. Kimryn Rathmell
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA.,Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Norton DL, Ceppe A, Tune MK, McCravy M, Devlin T, Drummond MB, Carson SS, Vincent BG, Hagan RS, Dang H, Doerschuk CM, Mock JR. Bronchoalveolar Tregs are associated with duration of mechanical ventilation in acute respiratory distress syndrome. J Transl Med 2020; 18:427. [PMID: 33176790 PMCID: PMC7656499 DOI: 10.1186/s12967-020-02595-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/29/2020] [Indexed: 02/02/2023] Open
Abstract
Background Foxp3+ regulatory T cells (Tregs) play essential roles in immune homeostasis and repair of damaged lung tissue. We hypothesized that patients whose lung injury resolves quickly, as measured by time to liberation from mechanical ventilation, have a higher percentage of Tregs amongst CD4+ T cells in either airway, bronchoalveolar lavage (BAL) or peripheral blood samples. Methods We prospectively enrolled patients with ARDS requiring mechanical ventilation and collected serial samples, the first within 72 h of ARDS diagnosis (day 0) and the second 48–96 h later (day 3). We analyzed immune cell populations and cytokines in BAL, tracheal aspirates and peripheral blood, as well as cytokines in plasma, obtained at the time of bronchoscopy. The study cohort was divided into fast resolvers (FR; n = 8) and slow resolvers (SR; n = 5), based on the median number of days until first extubation for all participants (n = 13). The primary measure was the percentage of CD4+ T cells that were Tregs. Results The BAL of FR contained more Tregs than SR. This finding did not extend to Tregs in tracheal aspirates or blood. BAL Tregs expressed more of the full-length FOXP3 than a splice variant missing exon 2 compared to Tregs in simultaneously obtained peripheral blood. Conclusion Tregs are present in the bronchoalveolar space during ARDS. A greater percentage of CD4+ cells were Tregs in the BAL of FR than SR. Tregs may play a role in the resolution of ARDS, and enhancing their numbers or functions may be a therapeutic target.
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Affiliation(s)
- Dustin L Norton
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Section of Pulmonary, Critical Care, Allergy and Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Agathe Ceppe
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Miriya K Tune
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew McCravy
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Thomas Devlin
- Department of Respiratory Care, University of North Carolina, Chapel Hill, NC, USA
| | - M Bradley Drummond
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Shannon S Carson
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.,Division of Hematology/Oncology, University of North Carolina, Chapel Hill, NC, USA
| | - Robert S Hagan
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Claire M Doerschuk
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Jason R Mock
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, NC, USA. .,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA. .,Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA. .,Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine, University of North Carolina School of Medicine, Marsico Hall 7203, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA.
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38
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Das M, Zhou X, Liu Y, Das A, Vincent BG, Li J, Liu R, Huang L. Tumor neoantigen heterogeneity impacts bystander immune inhibition of pancreatic cancer growth. Transl Oncol 2020; 13:100856. [PMID: 32862105 PMCID: PMC7475277 DOI: 10.1016/j.tranon.2020.100856] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/19/2020] [Accepted: 08/12/2020] [Indexed: 02/08/2023] Open
Abstract
The immunogenic clonal-fraction threshold in heterogeneous solid-tumor required to induce effective bystander-killing of non-immunogenic subclones is unknown. Pancreatic cancer poses crucial challenges for immune therapeutic interventions due to low mutational-burden and consequent lack of neoantigens. Here, we designed a model to incorporate artificial-neoantigens into genes-of -interest in cancer-cells and to test their potential to actuate bystander-killing. By precisely controlling a neoantigen's abundance in the tumor, we studied the impact of neoantigen frequency on immune-response and immune-escape. Our results showed single, strong, widely-expressed neoantigen could lead to robust antitumor response when over 80% of cancer cells express the neoantigen. Further, immunological assays demonstrated T-cell responses against non-target self-antigen on KRAS-oncoprotein, when we inoculated animals with a high frequency of tumor-cells expressing test-neoantigen. Using nanoparticle-based gene-therapy, we successfully altered tumor-microenvironment by perturbing interleukin-12 and interleukin-10 gene-expression. The subsequent microenvironment-remodeling reduced the neoantigen frequency threshold at which bioluminescent signal intensity for tumor-burden decreased 1.5-log-fold, marking robust tumor-growth inhibition, from 83% to 29%. Our results thus suggest bystander killing is inefficient in immunologically-cold tumors like pancreatic-cancer and requires high neoantigen abundance. However, bystander killing mediated antitumor response can be rescued by adjuvant-immune therapy.
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Affiliation(s)
- Manisit Das
- Division of Pharmacoengineering and Molecular Pharmaceutics, Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xuefei Zhou
- Division of Pharmacoengineering and Molecular Pharmaceutics, Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yun Liu
- Division of Pharmacoengineering and Molecular Pharmaceutics, Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anirban Das
- Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, Department of Medicine, Division of Hematology/Oncology, Curriculum in Bioinformatics and Computational Biology, Computational Medicine Program, University of North Carolina, Chapel Hill, NC 27599-7295, USA
| | - Jingjing Li
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rihe Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Leaf Huang
- Division of Pharmacoengineering and Molecular Pharmaceutics, Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Eddy JA, Thorsson V, Lamb AE, Gibbs DL, Heimann C, Yu JX, Chung V, Chae Y, Dang K, Vincent BG, Shmulevich I, Guinney J. CRI iAtlas: an interactive portal for immuno-oncology research. F1000Res 2020; 9:1028. [PMID: 33214875 PMCID: PMC7658727 DOI: 10.12688/f1000research.25141.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/22/2020] [Indexed: 12/18/2022] Open
Abstract
The Cancer Research Institute (CRI) iAtlas is an interactive web platform for data exploration and discovery in the context of tumors and their interactions with the immune microenvironment. iAtlas allows researchers to study immune response characterizations and patterns for individual tumor types, tumor subtypes, and immune subtypes. iAtlas supports computation and visualization of correlations and statistics among features related to the tumor microenvironment, cell composition, immune expression signatures, tumor mutation burden, cancer driver mutations, adaptive cell clonality, patient survival, expression of key immunomodulators, and tumor infiltrating lymphocyte (TIL) spatial maps. iAtlas was launched to accompany the release of the TCGA PanCancer Atlas and has since been expanded to include new capabilities such as (1) user-defined loading of sample cohorts, (2) a tool for classifying expression data into immune subtypes, and (3) integration of TIL mapping from digital pathology images. We expect that the CRI iAtlas will accelerate discovery and improve patient outcomes by providing researchers access to standardized immunogenomics data to better understand the tumor immune microenvironment and its impact on patient responses to immunotherapy.
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Affiliation(s)
| | | | | | - David L Gibbs
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Jia Xin Yu
- Anna-Maria Kellen Clinical Accelerator, Cancer Research Institute, New York, NY, 10006, USA
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40
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Beckermann KE, Hongo R, Ye X, Young K, Carbonell K, Healey DCC, Siska PJ, Barone S, Roe CE, Smith CC, Vincent BG, Mason FM, Irish JM, Rathmell WK, Rathmell JC. CD28 costimulation drives tumor-infiltrating T cell glycolysis to promote inflammation. JCI Insight 2020; 5:138729. [PMID: 32814710 PMCID: PMC7455120 DOI: 10.1172/jci.insight.138729] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023] Open
Abstract
Metabolic reprogramming dictates the fate and function of stimulated T cells, yet these pathways can be suppressed in T cells in tumor microenvironments. We previously showed that glycolytic and mitochondrial adaptations directly contribute to reducing the effector function of renal cell carcinoma (RCC) CD8+ tumor-infiltrating lymphocytes (TILs). Here we define the role of these metabolic pathways in the activation and effector functions of CD8+ RCC TILs. CD28 costimulation plays a key role in augmenting T cell activation and metabolism, and is antagonized by the inhibitory and checkpoint immunotherapy receptors CTLA4 and PD-1. While RCC CD8+ TILs were activated at a low level when stimulated through the T cell receptor alone, addition of CD28 costimulation greatly enhanced activation, function, and proliferation. CD28 costimulation reprogrammed RCC CD8+ TIL metabolism with increased glycolysis and mitochondrial oxidative metabolism, possibly through upregulation of GLUT3. Mitochondria also fused to a greater degree, with higher membrane potential and overall mass. These phenotypes were dependent on glucose metabolism, as the glycolytic inhibitor 2-deoxyglucose both prevented changes to mitochondria and suppressed RCC CD8+ TIL activation and function. These data show that CD28 costimulation can restore RCC CD8+ TIL metabolism and function through rescue of T cell glycolysis that supports mitochondrial mass and activity.
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Affiliation(s)
| | - Rachel Hongo
- Department of Medicine, Division of Hematology and Oncology, and
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kirsten Young
- Department of Medicine, Division of Hematology and Oncology, and
| | - Katie Carbonell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Diana C Contreras Healey
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Peter J Siska
- Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Sierra Barone
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Caroline E Roe
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Christof C Smith
- Lineberger Comprehensive Cancer Center; Department of Medicine Division of Hematology and Oncology, Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Computational Medicine Program, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center; Department of Medicine Division of Hematology and Oncology, Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Computational Medicine Program, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Frank M Mason
- Department of Medicine, Division of Hematology and Oncology, and
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, and.,Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Crosby EJ, Acharya C, Rabiola C, Muller WJ, Chodosh LA, Broadwater G, Shepherd J, Hollern D, He X, Perou CM, Ashby BK, Vincent BG, Morse MA, Lyerly HK, Hartman ZC. Abstract 904: Stimulation and expansion of oncogene-reactive tumor infiltrating T cells through combined Ad-HER2Δ16 vaccination and anti-PD1 enable anti-tumor responses against established HER2 BC. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite promising advances, overcoming immune suppression and driving productive immune responses in the tumor microenvironment remains a significant challenge. Using a spontaneous breast cancer model, we found that vaccination targeting HER2d16, a highly expressed driver of oncogenicity and HER2-therapeutic resistance, elicited significant anti-tumor responses. In contrast, vaccines targeting a non-driver tumor-specific antigen (GFP) or unique non-driver tumor neoepitopes had no impact on tumor occurrence or progression. While vaccine-induced HER2-specific CD8+ T cells were essential for responses, tumors treated therapeutically with a vaccine alone ultimately progressed. However, long-term tumor control and complete tumor regression was only achieved when vaccine was combined with immune-checkpoint blockade (anti-PD1). Single cell RNAsequencing of tumor-infiltrating T cells (TILs) revealed that while vaccination expanded CD8 T cells within the tumor, only the combination of vaccine with anti-PD1 therapy induced a tumor rejection activation signature that was identified in the expanded T cell clones. We go on to use the single cell data to clone and reexpress the TCRs from expanded TILs from vaccinated mice and show that they are HER2-reactive. This data conclusively demonstrates the efficacy of this vaccination strategy in expanding tumor rejection T cells and supports its further evaluation in an ongoing Phase II trial (NCT03632941). The workflow used to identify and clone expanded, tumor specific T cells has broad potential applications across tumor types and treatment platforms.
Citation Format: Erika J. Crosby, Chaitanya Acharya, Christopher Rabiola, William J. Muller, Lewis A. Chodosh, Gloria Broadwater, Jonathan Shepherd, Daniel Hollern, Xiaping He, Charles M. Perou, Benjamin K. Ashby, Benjamin G. Vincent, Michael A. Morse, Herbert K. Lyerly, Zachary C. Hartman. Stimulation and expansion of oncogene-reactive tumor infiltrating T cells through combined Ad-HER2Δ16 vaccination and anti-PD1 enable anti-tumor responses against established HER2 BC [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 904.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiaping He
- 4University of North Carolina, Chapel Hill, NC
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42
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Abstract
Abstract
Background: Neoantigens are attractive targets for personalized anti-tumor vaccination, given their uniqueness to the tumor and the ability to bypass immune tolerance. Recently, the feasibility of neoantigen vaccine has been demonstrated in patients. However, the response rate of neoantigen vaccines is unsatisfied because of their low immunogenicity, undesired degradation, limited cross-presentation, and acquired resistance. Here, we developed a nanoparticle-based neoantigen vaccine system to overcome these challenges.
Methods: We predicted both MHC Class I and Class II neoantigen peptides for B16-F10 melanoma model using a bioinformatics pipeline. We screened an optimal incorporation strategy to formulate nanovaccines by either directly absorbing neoantigen peptides on PLGA nanoparticle (NP) or conjugating them to PEG-PLGA through a pH-responsive strategy or a redox-responsive strategy. We formulated nanovaccine with redox-responsive neoantigen-polymer conjugates and a STING agonist DMXAA. C57/BL6 mice were inoculated with 50,000 B16-F10 tumor cells on their right flank. Mice were vaccinated subcutaneously on their left flank with different nanovaccines or control arms on day 4, 8 and 12 after tumor inoculation. Mice were given anti-PD1 (200 μg, intraperitoneally) on day 4, 8, 12, 16, 20 after tumor inoculation. Tumor volume and mice survival were recorded. We also evaluated the immune related cytokines in mouse blood on day 15 after treatment.
Results: Four MHC I and three MHC II neoantigen peptides were screened out for B16-F10 melanoma with high IFN-γ immune response. Results indicate that a redox conjugation strategy using PLGA-PEG and SPDP linker were more efficient in tumor inhibition than other incorporation strategies for our neoantigen peptides. By formulating nanovaccine with redox-responsive neoantigen-polymer conjugates and a STING agonist, we demonstrated that our nanovaccine, when combined with αPD1, achieved a 50% survival rate on day 38, compared to 0% of PBS treated group and 20% of non-formulated neoantigen peptides treated group. To confirm the enhanced immunity, we evaluated the immune related cytokines in mouse blood on day 15 after treatment. We found that our neoantigen nanovaccine achieved the highest expression of immune related cytokines among all arms, indicating that our nanovaccine induced higher immune response than non-formulated neoantigen peptides or other NP strategies.
Conclusions: We demonstrate that our nanovaccine achieves increased therapeutic efficacy and higher expression of immune related cytokines than non-formulated neoantigen peptides. Our work develops a novel nanoparticle-based neoantigen vaccine that will improve current personalized cancer immunotherapy.
Citation Format: Yu Mi, Christof C. Smith, Jonathan S. Serody, Benjamin G. Vincent, Andrew Z. Wang, Hyesun Hyun. Neoantigen nanovaccine improves personalized cancer immunotherapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2866.
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Affiliation(s)
- Yu Mi
- UNC Chapel Hill, Chapel Hill, NC
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Keating JE, Chung C, Chai S, Prins JF, Vincent BG, Hunsucker SA, Armistead PM, Glish GL. Alkali Metal Cationization of Tumor-associated Antigen Peptides for Improved Dissociation and Measurement by Differential Ion Mobility-Mass Spectrometry. J Proteome Res 2020; 19:3176-3183. [PMID: 32627559 PMCID: PMC9260395 DOI: 10.1021/acs.jproteome.0c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tandem mass spectrometry (MS/MS) is a highly sensitive and selective method for the detection of tumor-associated peptide antigens. These short, nontryptic sequences may lack basic residues, resulting in the formation of predominantly [peptide + H]+ ions in electrospray. These singly charged ions tend to undergo inefficient dissociation, leading to issues in sequence determination. Addition of alkali metal salts to the electrospray solvent can drive the formation of [peptide + H + metal]2+ ions that have enhanced dissociation characteristics relative to [peptide + H]+ ions. Both previously identified tumor-associated antigens and predicted neoantigen sequences were investigated. The previously reported rearrangement mechanism in MS/MS of sodium-cationized peptides is applied here to demonstrate complete C-terminal sequencing of tumor-associated peptide antigens. Differential ion mobility spectrometry (DIMS) is shown to selectively enrich [peptide + H + metal]2+ species by filtering out singly charged interferences at relatively low field strengths, offsetting the decrease in signal intensity associated with the use of alkali metal cations.
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Affiliation(s)
- James E. Keating
- Department of Chemistry, University of North Carolina at Chapel Hill, NC
| | - Chris Chung
- Department of Chemistry, University of North Carolina at Chapel Hill, NC
| | - Shengjie Chai
- Curriculum in Genetic & Molecular Biology, University of North Carolina at Chapel Hill, NC
| | - Jans F. Prins
- Computer Science, University of North Carolina at Chapel Hill, NC
| | - Benjamin G. Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC
| | - Sally A. Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC
| | - Paul M. Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC
| | - Gary L. Glish
- Department of Chemistry, University of North Carolina at Chapel Hill, NC
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44
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Crosby EJ, Acharya CR, Haddad AF, Rabiola CA, Lei G, Wei JP, Yang XY, Wang T, Liu CX, Wagner KU, Muller WJ, Chodosh LA, Broadwater G, Hyslop T, Shepherd JH, Hollern DP, He X, Perou CM, Chai S, Ashby BK, Vincent BG, Snyder JC, Force J, Morse MA, Lyerly HK, Hartman ZC. Stimulation of Oncogene-Specific Tumor-Infiltrating T Cells through Combined Vaccine and αPD-1 Enable Sustained Antitumor Responses against Established HER2 Breast Cancer. Clin Cancer Res 2020; 26:4670-4681. [PMID: 32732224 DOI: 10.1158/1078-0432.ccr-20-0389] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/17/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022]
Abstract
PURPOSE Despite promising advances in breast cancer immunotherapy, augmenting T-cell infiltration has remained a significant challenge. Although neither individual vaccines nor immune checkpoint blockade (ICB) have had broad success as monotherapies, we hypothesized that targeted vaccination against an oncogenic driver in combination with ICB could direct and enable antitumor immunity in advanced cancers. EXPERIMENTAL DESIGN Our models of HER2+ breast cancer exhibit molecular signatures that are reflective of advanced human HER2+ breast cancer, with a small numbers of neoepitopes and elevated immunosuppressive markers. Using these, we vaccinated against the oncogenic HER2Δ16 isoform, a nondriver tumor-associated gene (GFP), and specific neoepitopes. We further tested the effect of vaccination or anti-PD-1, alone and in combination. RESULTS We found that only vaccination targeting HER2Δ16, a driver of oncogenicity and HER2-therapeutic resistance, could elicit significant antitumor responses, while vaccines targeting a nondriver tumor-specific antigen or tumor neoepitopes did not. Vaccine-induced HER2-specific CD8+ T cells were essential for responses, which were more effective early in tumor development. Long-term tumor control of advanced cancers occurred only when HER2Δ16 vaccination was combined with αPD-1. Single-cell RNA sequencing of tumor-infiltrating T cells revealed that while vaccination expanded CD8 T cells, only the combination of vaccine with αPD-1 induced functional gene expression signatures in those CD8 T cells. Furthermore, we show that expanded clones are HER2-reactive, conclusively demonstrating the efficacy of this vaccination strategy in targeting HER2. CONCLUSIONS Combining oncogenic driver targeted vaccines with selective ICB offers a rational paradigm for precision immunotherapy, which we are clinically evaluating in a phase II trial (NCT03632941).
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Affiliation(s)
- Erika J Crosby
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina
| | - Chaitanya R Acharya
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina
| | - Anthony-Fayez Haddad
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina
| | - Christopher A Rabiola
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina
| | - Gangjun Lei
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina
| | - Jun-Ping Wei
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina
| | - Xiao-Yi Yang
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina
| | - Tao Wang
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina
| | - Cong-Xiao Liu
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina
| | - Kay U Wagner
- Department of Oncology, Wayne State University, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - William J Muller
- Departments of Biochemistry and Medicine, Goodman Cancer Center, McGill University, Montreal, Quebec
| | - Lewis A Chodosh
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gloria Broadwater
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Terry Hyslop
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Jonathan H Shepherd
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Daniel P Hollern
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Xiaping He
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Shengjie Chai
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Medicine, Division of Hematology/Oncology, University of North Carolina, Chapel Hill, North Carolina
| | - Benjamin K Ashby
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Medicine, Division of Hematology/Oncology, University of North Carolina, Chapel Hill, North Carolina
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Medicine, Division of Hematology/Oncology, University of North Carolina, Chapel Hill, North Carolina.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina.,Computational Medicine Program, University of North Carolina, Chapel Hill, North Carolina
| | - Joshua C Snyder
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina.,Department of Cell Biology, Duke University, Durham, North Carolina
| | - Jeremy Force
- Department of Medicine, Duke University, Durham, North Carolina
| | - Michael A Morse
- Department of Medicine, Duke University, Durham, North Carolina
| | - Herbert K Lyerly
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina.,Department of Immunology, Duke University, Durham, North Carolina.,Department of Pathology, Duke University, Durham, North Carolina
| | - Zachary C Hartman
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham North Carolina. .,Department of Pathology, Duke University, Durham, North Carolina
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Smith CC, Entwistle S, Willis C, Vensko S, Beck W, Garness J, Sambade M, Routh E, Olsen K, Kodysh J, O’Donnell T, Haber C, Heiss K, Stadler V, Garrison E, Grant OC, Woods RJ, Heise M, Vincent BG, Rubinsteyn A. Landscape and Selection of Vaccine Epitopes in SARS-CoV-2. bioRxiv 2020:2020.06.04.135004. [PMID: 32577654 PMCID: PMC7302209 DOI: 10.1101/2020.06.04.135004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
There is an urgent need for a vaccine with efficacy against SARS-CoV-2. We hypothesize that peptide vaccines containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation would drive both humoral and cellular immunity with high specificity, potentially avoiding undesired effects such as antibody-dependent enhancement (ADE). Additionally, such vaccines can be rapidly manufactured in a distributed manner. In this study, we combine computational prediction of T cell epitopes, recently published B cell epitope mapping studies, and epitope accessibility to select candidate peptide vaccines for SARS-CoV-2. We begin with an exploration of the space of possible T cell epitopes in SARS-CoV-2 with interrogation of predicted HLA-I and HLA-II ligands, overlap between predicted ligands, protein source, as well as concurrent human/murine coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, viral source protein abundance, sequence conservation, coverage of high frequency HLA alleles and co-localization of CD4+ and CD8+ T cell epitopes. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering to select regions with surface accessibility, high sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. From 58 initial candidates, three B cell epitope regions were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we propose a set of SARS-CoV-2 vaccine peptides for use in subsequent murine studies and clinical trials.
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Affiliation(s)
- Christof C. Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Caryn Willis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Wolfgang Beck
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jason Garness
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Maria Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Eric Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kelly Olsen
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Julia Kodysh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Timothy O’Donnell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | | | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, California
| | - Oliver C. Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Mark Heise
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina
| | - Benjamin G. Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, North Carolina
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, North Carolina
- Division of Hematology/Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, North Carolina
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, North Carolina
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46
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Hollern DP, Xu N, Thennavan A, Glodowski C, Garcia-Recio S, Mott KR, He X, Garay JP, Carey-Ewend K, Marron D, Ford J, Liu S, Vick SC, Martin M, Parker JS, Vincent BG, Serody JS, Perou CM. B Cells and T Follicular Helper Cells Mediate Response to Checkpoint Inhibitors in High Mutation Burden Mouse Models of Breast Cancer. Cell 2020; 179:1191-1206.e21. [PMID: 31730857 DOI: 10.1016/j.cell.2019.10.028] [Citation(s) in RCA: 258] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 09/12/2019] [Accepted: 10/23/2019] [Indexed: 12/28/2022]
Abstract
This study identifies mechanisms mediating responses to immune checkpoint inhibitors using mouse models of triple-negative breast cancer. By creating new mammary tumor models, we find that tumor mutation burden and specific immune cells are associated with response. Further, we developed a rich resource of single-cell RNA-seq and bulk mRNA-seq data of immunotherapy-treated and non-treated tumors from sensitive and resistant murine models. Using this, we uncover that immune checkpoint therapy induces T follicular helper cell activation of B cells to facilitate the anti-tumor response in these models. We also show that B cell activation of T cells and the generation of antibody are key to immunotherapy response and propose a new biomarker for immune checkpoint therapy. In total, this work presents resources of new preclinical models of breast cancer with large mRNA-seq and single-cell RNA-seq datasets annotated for sensitivity to therapy and uncovers new components of response to immune checkpoint inhibitors.
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Affiliation(s)
- Daniel P Hollern
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nuo Xu
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Aatish Thennavan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Oral and Craniofacial Biomedicine Program, School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Cherise Glodowski
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin R Mott
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Xiaping He
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joseph P Garay
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kelly Carey-Ewend
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David Marron
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - John Ford
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Siyao Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah C Vick
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Miguel Martin
- Instituto de Investigación Sanitaria Gregorio Marañon, CIBERONC, Universidad Complutense, Madrid, Spain
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Hematology/Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Hematology/Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
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47
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Weiss J, Sheth S, Deal AM, Grilley Olson JE, Patel S, Hackman TG, Blumberg JM, Galloway TJ, Patel S, Zanation AM, Shen CJ, Hayes DN, Hilliard C, Mehra R, McKinnon KP, Wang HH, Weissler MC, Bauman JR, Chera BS, Vincent BG. Concurrent Definitive Immunoradiotherapy for Patients with Stage III-IV Head and Neck Cancer and Cisplatin Contraindication. Clin Cancer Res 2020; 26:4260-4267. [PMID: 32371539 PMCID: PMC7968114 DOI: 10.1158/1078-0432.ccr-20-0230] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 05/01/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE Although cisplatin plus radiotherapy is a standard treatment of locally advanced head and neck squamous cell carcinoma (LA-HNSCC), cisplatin contraindication is common. Radiation elicits and promotes tumor-directed immune stimulation, which may potentiate anti-PD-1 therapy. We provide the first efficacy report of combined pembrolizumab and definitive radiotherapy in LA-HNSCC. PATIENTS AND METHODS This single-arm, multi-institution, phase II study (NCT02609503) enrolled 29 cisplatin-ineligible patients. Patients received radiotherapy concurrently with three cycles of pembrolizumab 200 mg every 3 weeks followed by three adjuvant cycles. The primary endpoint was a progression-free survival (PFS) of ≥16 months. Correlative studies included peripheral blood flow cytometry and Luminex cytokine profiling. RESULTS Reasons for cisplatin ineligibility included otopathy (69.0%), nephropathy (20.7%), and neuropathy (6.9%). With median follow-up of 21 months, estimated 24-month PFS and overall survival rates were 71% (95% confidence interval, 49%-84%) and 75% (51%-88%). The primary PFS endpoint has exceeded the hypothesis and its median has not been reached. Toxicities were typical of radiotherapy; however, high rates of grade 3/4 lymphopenia (58.6%) were observed. Flow cytometry revealed a relative decline in CD4 T cells and B cells, but not CD8 T cells. Upon treatment, frequencies of transitional B cells and tissue-like memory B cells increased, while resting memory B cells decreased. Patients with progression had greater percentages of baseline naïve B cells and fewer marginal zone B cells. CONCLUSIONS Pembrolizumab and radiotherapy is efficacious in LA-HNSCC and should be evaluated in a randomized trial. The observed changes in B-cell markers deserve further study both as potential biomarkers and as therapeutic targets.
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Affiliation(s)
- Jared Weiss
- Division of Hematology and Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina.
| | - Siddharth Sheth
- Division of Hematology and Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Allision M Deal
- Department of Biostatistics, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Juneko E Grilley Olson
- Division of Hematology and Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Samip Patel
- Department of Otolaryngology/Head and Neck Surgery, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Trevor G Hackman
- Department of Otolaryngology/Head and Neck Surgery, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Jeffrey M Blumberg
- Department of Otolaryngology/Head and Neck Surgery, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Thomas J Galloway
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Shetal Patel
- Division of Hematology and Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Adam M Zanation
- Department of Otolaryngology/Head and Neck Surgery, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Colette J Shen
- Department of Radiation Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - D Neil Hayes
- Division of Hematology and Oncology, University of Tennessee West Institute for Cancer Research, Memphis, Tennessee
| | - Christopher Hilliard
- Division of Hematology and Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Ranee Mehra
- Division of Hematology and Oncology, Marlene and Stewart Greenebaum Comprehensive Cancer Center at the University of Maryland, Baltimore, Maryland
| | - Karen P McKinnon
- Division of Hematology and Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Hsing-Hui Wang
- Division of Hematology and Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Mark Christian Weissler
- Department of Otolaryngology/Head and Neck Surgery, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Jessica R Bauman
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Bhishamjit S Chera
- Department of Radiation Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
| | - Benjamin G Vincent
- Division of Hematology and Oncology, Lineberger Comprehensive Cancer Center at the University of North Carolina, Chapel Hill, North Carolina
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48
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Mirlekar B, Michaud D, Lee SJ, Kren NP, Harris C, Greene K, Goldman EC, Gupta GP, Fields RC, Hawkins WG, DeNardo DG, Rashid NU, Yeh JJ, McRee AJ, Vincent BG, Vignali DAA, Pylayeva-Gupta Y. B cell-Derived IL35 Drives STAT3-Dependent CD8 + T-cell Exclusion in Pancreatic Cancer. Cancer Immunol Res 2020; 8:292-308. [PMID: 32024640 PMCID: PMC7056532 DOI: 10.1158/2326-6066.cir-19-0349] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/13/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is an aggressive malignancy characterized by a paucity of tumor-proximal CD8+ T cells and resistance to immunotherapeutic interventions. Cancer-associated mechanisms that elicit CD8+ T-cell exclusion and resistance to immunotherapy are not well-known. Here, using a Kras- and p53-driven model of PDA, we describe a mechanism of action for the protumorigenic cytokine IL35 through STAT3 activation in CD8+ T cells. Distinct from its action on CD4+ T cells, IL35 signaling in gp130+CD8+ T cells activated the transcription factor STAT3, which antagonized intratumoral infiltration and effector function of CD8+ T cells via suppression of CXCR3, CCR5, and IFNγ expression. Inhibition of STAT3 signaling in tumor-educated CD8+ T cells improved PDA growth control upon adoptive transfer to tumor-bearing mice. We showed that activation of STAT3 in CD8+ T cells was driven by B cell- but not regulatory T cell-specific production of IL35. We also demonstrated that B cell-specific deletion of IL35 facilitated CD8+ T-cell activation independently of effector or regulatory CD4+ T cells and was sufficient to phenocopy therapeutic anti-IL35 blockade in overcoming resistance to anti-PD-1 immunotherapy. Finally, we identified a circulating IL35+ B-cell subset in patients with PDA and demonstrated that the presence of IL35+ cells predicted increased occurrence of phosphorylated (p)Stat3+CXCR3-CD8+ T cells in tumors and inversely correlated with a cytotoxic T-cell signature in patients. Together, these data identified B cell-mediated IL35/gp130/STAT3 signaling as an important direct link to CD8+ T-cell exclusion and immunotherapy resistance in PDA.
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MESH Headings
- Animals
- Apoptosis/immunology
- B-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/immunology
- Carcinoma, Pancreatic Ductal/pathology
- Carcinoma, Pancreatic Ductal/therapy
- Case-Control Studies
- Cell Proliferation/physiology
- Humans
- Immunotherapy, Adoptive/methods
- Interleukins/genetics
- Interleukins/immunology
- Lymphocyte Activation
- Lymphocytes, Tumor-Infiltrating/immunology
- Mice
- Mice, Inbred C57BL
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/immunology
- Pancreatic Neoplasms/pathology
- Pancreatic Neoplasms/therapy
- Receptors, CCR5/genetics
- Receptors, CCR5/immunology
- Receptors, CXCR3/genetics
- Receptors, CXCR3/immunology
- STAT3 Transcription Factor/genetics
- STAT3 Transcription Factor/immunology
- Signal Transduction/immunology
- T-Lymphocytes, Regulatory/immunology
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Bhalchandra Mirlekar
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Daniel Michaud
- Department of Cell Biology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Samuel J Lee
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Nancy P Kren
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Cameron Harris
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Kevin Greene
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Emily C Goldman
- Department of Radiation Oncology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
- Department of Radiation Oncology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Ryan C Fields
- Department of Surgery, Barnes-Jewish Hospital and the Alvin J. Siteman Comprehensive Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - William G Hawkins
- Department of Surgery, Barnes-Jewish Hospital and the Alvin J. Siteman Comprehensive Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - David G DeNardo
- Department of Medicine, Barnes-Jewish Hospital and the Alvin J. Siteman Comprehensive Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Naim U Rashid
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
- Department of Biostatistics, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
- Department of Surgery, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Autumn J McRee
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
- Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
- Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yuliya Pylayeva-Gupta
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.
- Department of Genetics, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
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49
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Li C, Zhu B, Son YM, Wang Z, Jiang L, Xiang M, Ye Z, Beckermann KE, Wu Y, Jenkins JW, Siska PJ, Vincent BG, Prakash Y, Peikert T, Edelson BT, Taneja R, Kaplan MH, Rathmell JC, Dong H, Hitosugi T, Sun J. The Transcription Factor Bhlhe40 Programs Mitochondrial Regulation of Resident CD8 + T Cell Fitness and Functionality. Immunity 2020; 52:201-202. [PMID: 31940270 PMCID: PMC7004238 DOI: 10.1016/j.immuni.2019.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Free ME, Stember KG, Hess JJ, McInnis EA, Lardinois O, Hogan SL, Hu Y, Mendoza C, Le AK, Guseman AJ, Pilkinton MA, Bortone DS, Cowens K, Sidney J, Karosiene E, Peters B, James E, Kwok WW, Vincent BG, Mallal SA, Jennette JC, Ciavatta DJ, Falk RJ. Restricted myeloperoxidase epitopes drive the adaptive immune response in MPO-ANCA vasculitis. J Autoimmun 2020; 106:102306. [PMID: 31383567 PMCID: PMC6930338 DOI: 10.1016/j.jaut.2019.102306] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Treatment of autoimmune diseases has relied on broad immunosuppression. Knowledge of specific interactions between human leukocyte antigen (HLA), the autoantigen, and effector immune cells, provides the foundation for antigen-specific therapies. These studies investigated the role of HLA, specific myeloperoxidase (MPO) epitopes, CD4+ T cells, and ANCA specificity in shaping the immune response in patients with anti-neutrophil cytoplasmic autoantibody (ANCA) vasculitis. METHODS HLA sequence-based typing identified enriched alleles in our patient population (HLA-DPB1*04:01 and HLA-DRB4*01:01), while in silico and in vitro binding studies confirmed binding between HLA and specific MPO epitopes. Class II tetramers with MPO peptides were utilized to detect autoreactive CD4+ T cells. TCR sequencing was performed to determine the clonality of T cell populations. Longitudinal peptide ELISAs assessed the temporal nature of anti-MPO447-461 antibodies. Solvent accessibility combined with chemical modification determined the buried regions of MPO. RESULTS We identified a restricted region of MPO that was recognized by both CD4+ T cells and ANCA. The autoreactive T cell population contained CD4+CD25intermediateCD45RO+ memory T cells and secreted IL-17A. T cell receptor (TCR) sequencing demonstrated that autoreactive CD4+ T cells had significantly less TCR diversity when compared to naïve and memory T cells, indicating clonal expansion. The anti-MPO447-461 autoantibody response was detectable at onset of disease in some patients and correlated with disease activity in others. This region of MPO that is targeted by both T cells and antibodies is not accessible to solvent or chemical modification, indicating these epitopes are buried. CONCLUSIONS These observations reveal interactions between restricted MPO epitopes and the adaptive immune system within ANCA vasculitis that may inform new antigen-specific therapies in autoimmune disease while providing insight into immunopathogenesis.
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Affiliation(s)
- Meghan E Free
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA.
| | - Katherine G Stember
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA; UNC Department of Pathology and Laboratory Medicine, CB #7525, Brinkhous-Bullitt Building, Chapel Hill, NC, 27599, USA
| | - Jacob J Hess
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA
| | - Elizabeth A McInnis
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA
| | - Olivier Lardinois
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA
| | - Susan L Hogan
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA
| | - Yichun Hu
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA
| | - Carmen Mendoza
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA
| | - Andrew K Le
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA
| | - Alex J Guseman
- UNC Department of Chemistry, CB #3290, Chapel Hill, NC, 27599, USA
| | - Mark A Pilkinton
- Vanderbilt Center for Translational Immunology and Infectious Diseases, A2200 MCN, 1161 21st Avenue South, Nashville, TN, 37232, USA
| | - Dante S Bortone
- UNC Lineberger Comprehensive Cancer Center, CB #7295, Chapel Hill, NC, 27599, USA
| | - Kristen Cowens
- UNC Lineberger Comprehensive Cancer Center, CB #7295, Chapel Hill, NC, 27599, USA
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Edita Karosiene
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Eddie James
- Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA, 98101, USA
| | - William W Kwok
- Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA, 98101, USA
| | - Benjamin G Vincent
- UNC Lineberger Comprehensive Cancer Center, CB #7295, Chapel Hill, NC, 27599, USA; UNC Division of Hematology/Oncology, Department of Medicine, Physician's Office Building, 3rd Floor, 170 Manning Drive, CB #7305, Chapel Hill, NC, 27599, USA; UNC Curriculum in Bioinformatics and Computational Biology, CB #7264, Chapel Hill, NC, 27599, USA
| | - Simon A Mallal
- Vanderbilt Center for Translational Immunology and Infectious Diseases, A2200 MCN, 1161 21st Avenue South, Nashville, TN, 37232, USA
| | - J Charles Jennette
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA; UNC Department of Pathology and Laboratory Medicine, CB #7525, Brinkhous-Bullitt Building, Chapel Hill, NC, 27599, USA
| | - Dominic J Ciavatta
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA; UNC Department of Genetics and Molecular Biology, Coker Hall, 120 South Road, CB #3280, Chapel Hill, NC, 27599, USA
| | - Ronald J Falk
- UNC Kidney Center, Department of Medicine, 7024 Burnett-Womack, CB #7155, Chapel Hill, NC, 27599, USA; UNC Department of Pathology and Laboratory Medicine, CB #7525, Brinkhous-Bullitt Building, Chapel Hill, NC, 27599, USA
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