1
|
Carroll TM, Chadwick JA, Owen RP, White MJ, Kaplinsky J, Peneva I, Frangou A, Xie PF, Chang J, Roth A, Amess B, James SA, Rei M, Fuchs HS, McCann KJ, Omiyale AO, Jacobs BA, Lord SR, Norris-Bulpitt S, Dobbie ST, Griffiths L, Ramirez KA, Ricciardi T, Macri MJ, Ryan A, Venhaus RR, Van den Eynde BJ, Karydis I, Schuster-Böckler B, Middleton MR, Lu X. Tumor monocyte content predicts immunochemotherapy outcomes in esophageal adenocarcinoma. Cancer Cell 2023; 41:1222-1241.e7. [PMID: 37433281 DOI: 10.1016/j.ccell.2023.06.006] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 04/07/2023] [Accepted: 06/14/2023] [Indexed: 07/13/2023]
Abstract
For inoperable esophageal adenocarcinoma (EAC), identifying patients likely to benefit from recently approved immunochemotherapy (ICI+CTX) treatments remains a key challenge. We address this using a uniquely designed window-of-opportunity trial (LUD2015-005), in which 35 inoperable EAC patients received first-line immune checkpoint inhibitors for four weeks (ICI-4W), followed by ICI+CTX. Comprehensive biomarker profiling, including generation of a 65,000-cell single-cell RNA-sequencing atlas of esophageal cancer, as well as multi-timepoint transcriptomic profiling of EAC during ICI-4W, reveals a novel T cell inflammation signature (INCITE) whose upregulation correlates with ICI-induced tumor shrinkage. Deconvolution of pre-treatment gastro-esophageal cancer transcriptomes using our single-cell atlas identifies high tumor monocyte content (TMC) as an unexpected ICI+CTX-specific predictor of greater overall survival (OS) in LUD2015-005 patients and of ICI response in prevalent gastric cancer subtypes from independent cohorts. Tumor mutational burden is an additional independent and additive predictor of LUD2015-005 OS. TMC can improve patient selection for emerging ICI+CTX therapies in gastro-esophageal cancer.
Collapse
Affiliation(s)
- Thomas M Carroll
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Joseph A Chadwick
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Richard P Owen
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Michael J White
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Joseph Kaplinsky
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Iliana Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Anna Frangou
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
| | - Phil F Xie
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Jaeho Chang
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Andrew Roth
- Department of Pathology and Molecular Medicine, University of British Columbia, Vancouver, Canada; Department of Computer Science, University of British Columbia, Vancouver, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, Canada
| | - Bob Amess
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Sabrina A James
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Margarida Rei
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Hannah S Fuchs
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Katy J McCann
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ayo O Omiyale
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | | | - Simon R Lord
- Department of Oncology, University of Oxford, Oxford, UK
| | - Stewart Norris-Bulpitt
- Early Phase Clinical Trials Unit, Cancer & Haematology Centre, Churchill Hospital, Oxford, UK
| | - Sam T Dobbie
- Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, UK
| | - Lucinda Griffiths
- Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Benoit J Van den Eynde
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK; Ludwig Institute for Cancer Research, Brussels, Belgium; de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Ioannis Karydis
- Cancer Sciences Unit, University of Southampton and Cancer Care Group, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Mark R Middleton
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK; Early Phase Clinical Trials Unit, Cancer & Haematology Centre, Churchill Hospital, Oxford, UK.
| | - Xin Lu
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.
| |
Collapse
|
2
|
Carroll TM, Chadwick JA, Owen RP, White MJ, Kaplinsky J, Peneva I, Frangou A, Chang J, Xie PF, Roth A, Amess B, Lou H, McCann KJ, Berridge G, Fischer R, Phetsouphanh C, Omiyale AO, Jacobs BA, Ahern D, Lord SR, Norris-Bulpitt S, Dobbie ST, Griffiths L, Ramirez KA, Ricciardi T, Macri MJ, Ryan A, Venhaus RR, Van den Eynde BJ, Karydis I, Kessler BM, Schuster-Böckler B, Middleton MR, Lu X. Abstract 1247: Comprehensive molecular profiling to predict first-line immunochemotherapy outcomes in inoperable esophageal adenocarcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1247] [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
For patients with inoperable esophageal adenocarcinoma (EAC), prognosis on conventional chemotherapy (CTX) remains poor. In 2021, the FDA approved two αPD-1 immune checkpoint inhibitors (ICI) for addition to fluoropyrimidine/platinum-containing CTX in this first-line setting. As ICI+CTX enters the clinic, understanding ICI responses and predicting which patients will benefit from ICI addition are key challenges. To address these challenges, we assessed clinical and molecular profiles from the experimental LUD2015-005 trial (NCT02735239, EudraCT 2015-005298-19). Treatment consisted of an initial four-week ICI-only window with durvalumab (αPD-L1) with or without a single dose of tremelimumab (αCTLA-4), followed by 6 cycles of ICI+CTX (CapOx). 38 inoperable patients received treatment (35 EAC; 3 ESCC); median overall survival (OS) and progression-free survival (PFS) were 13.4 and 9.3 months, respectively. All patients reported at least one treatment emergent adverse event (TEAE), with 29 (76.3%) reporting grade 3 or higher TEAEs. EAC patients with available samples (n = 33) were taken forward for biomarker analysis, using tumor and adjacent normal biopsies collected at pre-treatment (PreTx), after four weeks of ICI-only (ICI-4W), and at the end of ICI+CTX (PostTx).
Transcriptomic comparison of paired PreTx and ICI-4W EAC biopsies (n = 28) revealed ICI-induced upregulation of a novel T-cell inflammation signature (termed INCITE). Stronger INCITE upregulation correlated with greater tumor shrinkage during the ICI-only window, and tumors with minimal INCITE upregulation showed markers of ICI resistance, including Innate PD-1 Resistance (IPRES). Despite correlation with ICI-only responses, INCITE changes were not associated with overall ICI+CTX outcomes.
To find predictive biomarkers of ICI+CTX outcomes, we conducted comprehensive genomic and transcriptomic profiling of PreTx EAC biopsies (n = 33). First, we generated a novel 65,000 cell scRNA-seq dataset and designed a deconvolution workflow to resolve tumor cell composition. Unexpectedly, monocyte composition was strongly linked with greater overall survival (OS) (HR: 0.40 [0.23-0.69]; p = 0.001; FDR = 0.047). Coding tumor mutational burden (TMB) was also associated with improved OS (HR: 0.50 [0.28-0.89]; p = 0.019). Multivariate modelling suggested monocyte composition and TMB were independent and complementary predictors of outcomes. Neither factor was associated with outcomes in a TCGA cohort of EAC patients not treated with ICI, suggesting these biomarkers may be specific to ICI or ICI+CTX.
Our findings suggest monocyte composition and TMB may identify EAC patients likely to benefit from ICI+CTX. INCITE upregulation may also serve as a useful monitor of ICI efficacy. These timely findings further our understanding of ICI response and resistance and may help inform patient selection for ICI+CTX.
Citation Format: Thomas M. Carroll, Joseph A. Chadwick, Richard P. Owen, Michael J. White, Joseph Kaplinsky, Iliana Peneva, Anna Frangou, Jaeho Chang, Phil F. Xie, Andrew Roth, Bob Amess, Hantao Lou, Katy J. McCann, Georgina Berridge, Roman Fischer, Chansavath Phetsouphanh, Ayo O. Omiyale, Brittany-Amber Jacobs, David Ahern, Simon R. Lord, Stewart Norris-Bulpitt, Sam T. Dobbie, Lucinda Griffiths, Kristen Aufiero Ramirez, Toni Ricciardi, Mary J. Macri, Aileen Ryan, Ralph R. Venhaus, Benoit J. Van den Eynde, Ioannis Karydis, Benedikt M. Kessler, Benjamin Schuster-Böckler, Mark R. Middleton, Xin Lu. Comprehensive molecular profiling to predict first-line immunochemotherapy outcomes in inoperable esophageal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1247.
Collapse
Affiliation(s)
- Thomas M. Carroll
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Joseph A. Chadwick
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Richard P. Owen
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Michael J. White
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Joseph Kaplinsky
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Iliana Peneva
- 2Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anna Frangou
- 3Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Jaeho Chang
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Phil F. Xie
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Andrew Roth
- 4Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Bob Amess
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Hantao Lou
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Katy J. McCann
- 5Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Georgina Berridge
- 6Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- 6Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Ayo O. Omiyale
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | | | - David Ahern
- 7Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Simon R. Lord
- 8Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Stewart Norris-Bulpitt
- 9Early Phase Clinical Trials Unit, Cancer & Haematology Centre, Churchill Hospital, Oxford, United Kingdom
| | - Sam T. Dobbie
- 10Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Lucinda Griffiths
- 10Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | | | | | - Ioannis Karydis
- 12Cancer Sciences Unit, University of Southampton and Cancer Care Group, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Benedikt M. Kessler
- 6Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Mark R. Middleton
- 8Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Xin Lu
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
3
|
Chen JL, Dawoodji A, Tarlton A, Gnjatic S, Tajar A, Karydis I, Browning J, Pratap S, Verfaille C, Venhaus RR, Pan L, Altman DG, Cebon JS, Old LL, Nathan P, Ottensmeier C, Middleton M, Cerundolo V. NY-ESO-1 specific antibody and cellular responses in melanoma patients primed with NY-ESO-1 protein in ISCOMATRIX and boosted with recombinant NY-ESO-1 fowlpox virus. Int J Cancer 2015; 136:E590-601. [PMID: 25081390 DOI: 10.1002/ijc.29118] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [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: 05/05/2014] [Revised: 06/19/2014] [Accepted: 07/14/2014] [Indexed: 12/14/2022]
Abstract
Vaccination strategies based on repeated injections of NY-ESO-1 protein formulated in ISCOMATRIX particles (NY-ESO-1 ISCOMATRIX) have shown to elicit combined NY-ESO-1 specific antibody and T cell responses. However, it remains unclear whether heterologous prime-boost strategies based on the combination with NY-ESO-1 ISCOMATRIX with different NY-ESO-1 boosting reagents could be used to increase NY-ESO-1 CD8(+) or CD4(+) T cell responses. To address this question, we carried out a randomized clinical trial in 39 high-risk, resected melanoma patients vaccinated with NY-ESO-1 ISCOMATRIX, and then boosted with repeated injections of either recombinant fowlpox virus encoding full length NY-ESO-1 (rF-NY-ESO-1) (Arm A) or NY-ESO-1 ISCOMATRIX alone (Arm B). We have comprehensively analyzed NY-ESO-1 specific T cells and B cells response in all patients before and after vaccination for a total of seven time points per patient. NY-ESO-1 ISCOMATRIX alone elicited a strong NY-ESO-1 specific CD4(+) T cell and antibody response, which was maintained by both regiments at similar levels. However, CD8(+) T cell responses were significantly boosted in 3 out of 18 patients in Arm A after the first rF-NY-ESO-1 injection and such responses were maintained until the end of the trial, while no patients in Arm B showed similar CD8(+) T cell responses. In addition, our results clearly identified immunodominant regions in the NY-ESO-1 protein: NY-ESO-179-102 and NY-ESO-1115-138 for CD4+ T cells and NY-ESO-185-108 for CD8+ T cells in a large proportion of vaccinated patients. These regions of NY-ESO-1 protein should be considered in future clinical trials as immunodominant epitopes.
Collapse
Affiliation(s)
- Ji-Li Chen
- Radcliffe Department of Medicine, MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Adams S, O'Neill DW, Nonaka D, Hardin E, Chiriboga L, Siu K, Cruz CM, Angiulli A, Angiulli F, Ritter E, Holman RM, Shapiro RL, Berman RS, Berner N, Shao Y, Manches O, Pan L, Venhaus RR, Hoffman EW, Jungbluth A, Gnjatic S, Old L, Pavlick AC, Bhardwaj N. Immunization of malignant melanoma patients with full-length NY-ESO-1 protein using TLR7 agonist imiquimod as vaccine adjuvant. J Immunol 2008; 181:776-84. [PMID: 18566444 DOI: 10.4049/jimmunol.181.1.776] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
T cell-mediated immunity to microbes and to cancer can be enhanced by the activation of dendritic cells (DCs) via TLRs. In this study, we evaluated the safety and feasibility of topical imiquimod, a TLR7 agonist, in a series of vaccinations against the cancer/testis Ag NY-ESO-1 in patients with malignant melanoma. Recombinant, full-length NY-ESO-1 protein was administered intradermally into imiquimod preconditioned sites followed by additional topical applications of imiquimod. The regimen was very well tolerated with only mild and transient local reactions and constitutional symptoms. Secondarily, we examined the systemic immune response induced by the imiquimod/NY-ESO-1 combination, and show that it elicited both humoral and cellular responses in a significant fraction of patients. Skin biopsies were assessed for imiquimod's in situ immunomodulatory effects. Compared with untreated skin, topical imiquimod induced dermal mononuclear cell infiltrates in all patients composed primarily of T cells, monocytes, macrophages, myeloid DCs, NK cells, and, to a lesser extent, plasmacytoid DCs. DC activation was evident. This study demonstrates the feasibility and excellent safety profile of a topically applied TLR7 agonist used as a vaccine adjuvant in cancer patients. Imiquimod's adjuvant effects require further evaluation and likely need optimization of parameters such as formulation, dose, and timing relative to Ag exposure for maximal immunogenicity.
Collapse
Affiliation(s)
- Sylvia Adams
- Department of Medicine, Division of Medical Oncology, New York University Cancer Institute, School of Medicine, New York, NY 10016, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|