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Yarchoan M, Gane EJ, Marron TU, Perales-Linares R, Yan J, Cooch N, Shu DH, Fertig EJ, Kagohara LT, Bartha G, Northcott J, Lyle J, Rochestie S, Peters J, Connor JT, Jaffee EM, Csiki I, Weiner DB, Perales-Puchalt A, Sardesai NY. Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial. Nat Med 2024; 30:1044-1053. [PMID: 38584166 PMCID: PMC11031401 DOI: 10.1038/s41591-024-02894-y] [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: 12/28/2022] [Accepted: 03/01/2024] [Indexed: 04/09/2024]
Abstract
Programmed cell death protein 1 (PD-1) inhibitors have modest efficacy as a monotherapy in hepatocellular carcinoma (HCC). A personalized therapeutic cancer vaccine (PTCV) may enhance responses to PD-1 inhibitors through the induction of tumor-specific immunity. We present results from a single-arm, open-label, phase 1/2 study of a DNA plasmid PTCV (GNOS-PV02) encoding up to 40 neoantigens coadministered with plasmid-encoded interleukin-12 plus pembrolizumab in patients with advanced HCC previously treated with a multityrosine kinase inhibitor. Safety and immunogenicity were assessed as primary endpoints, and treatment efficacy and feasibility were evaluated as secondary endpoints. The most common treatment-related adverse events were injection-site reactions, observed in 15 of 36 (41.6%) patients. No dose-limiting toxicities or treatment-related grade ≥3 events were observed. The objective response rate (modified intention-to-treat) per Response Evaluation Criteria in Solid Tumors 1.1 was 30.6% (11 of 36 patients), with 8.3% (3 of 36) of patients achieving a complete response. Clinical responses were associated with the number of neoantigens encoded in the vaccine. Neoantigen-specific T cell responses were confirmed in 19 of 22 (86.4%) evaluable patients by enzyme-linked immunosorbent spot assays. Multiparametric cellular profiling revealed active, proliferative and cytolytic vaccine-specific CD4+ and CD8+ effector T cells. T cell receptor β-chain (TCRβ) bulk sequencing results demonstrated vaccination-enriched T cell clone expansion and tumor infiltration. Single-cell analysis revealed posttreatment T cell clonal expansion of cytotoxic T cell phenotypes. TCR complementarity-determining region cloning of expanded T cell clones in the tumors following vaccination confirmed reactivity against vaccine-encoded neoantigens. Our results support the PTCV's mechanism of action based on the induction of antitumor T cells and show that a PTCV plus pembrolizumab has clinical activity in advanced HCC. ClinicalTrials.gov identifier: NCT04251117 .
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Affiliation(s)
- Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Edward J Gane
- New Zealand Liver Transplant Unit, University of Auckland, Auckland, New Zealand
| | - Thomas U Marron
- Early Phase Trials Unit, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jian Yan
- Geneos Therapeutics, Philadelphia, PA, USA
| | - Neil Cooch
- Geneos Therapeutics, Philadelphia, PA, USA
| | - Daniel H Shu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Luciane T Kagohara
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | | | | | - Jason T Connor
- ConfluenceStat, Cooper City, FL, USA
- University of Central Florida College of Medicine, Orlando, FL, USA
| | - Elizabeth M Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - David B Weiner
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
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Shu DH, Ho WJ, Kagohara LT, Girgis A, Shin SM, Danilova L, Lee JW, Sidiropoulos DN, Mitchell S, Munjal K, Howe K, Bendinelli KJ, Qi H, Mo G, Montagne J, Leatherman JM, Lopez-Vidal TY, Zhu Q, Huff AL, Yuan X, Hernandez A, Coyne EM, Zaidi N, Zabransky DJ, Engle LL, Ogurtsova A, Baretti M, Laheru D, Durham JN, Wang H, Anders R, Jaffee EM, Fertig EJ, Yarchoan M. Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade. bioRxiv 2023:2023.10.16.562104. [PMID: 37904980 PMCID: PMC10614819 DOI: 10.1101/2023.10.16.562104] [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: 11/02/2023]
Abstract
Neoadjuvant immunotherapy is thought to produce long-term remissions through induction of antitumor immune responses before removal of the primary tumor. Tertiary lymphoid structures (TLS), germinal center-like structures that can arise within tumors, may contribute to the establishment of immunological memory in this setting, but understanding of their role remains limited. Here, we investigated the contribution of TLS to antitumor immunity in hepatocellular carcinoma (HCC) treated with neoadjuvant immunotherapy. We found that neoadjuvant immunotherapy induced the formation of TLS, which were associated with superior pathologic response, improved relapse free survival, and expansion of the intratumoral T and B cell repertoire. While TLS in viable tumor displayed a highly active mature morphology, in areas of tumor regression we identified an involuted TLS morphology, which was characterized by dispersion of the B cell follicle and persistence of a T cell zone enriched for ongoing antigen presentation and T cell-mature dendritic cell interactions. Involuted TLS showed increased expression of T cell memory markers and expansion of CD8+ cytotoxic and tissue resident memory clonotypes. Collectively, these data reveal the circumstances of TLS dissolution and suggest a functional role for late-stage TLS as sites of T cell memory formation after elimination of viable tumor.
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Affiliation(s)
- Daniel H. Shu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Won Jin Ho
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Luciane T. Kagohara
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Alexander Girgis
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah M. Shin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ludmila Danilova
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jae W. Lee
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dimitrios N. Sidiropoulos
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Sarah Mitchell
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kabeer Munjal
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kathryn Howe
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kayla J. Bendinelli
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hanfei Qi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Guanglan Mo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Janelle Montagne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - James M. Leatherman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tamara Y. Lopez-Vidal
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Qingfeng Zhu
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amanda L. Huff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Xuan Yuan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexei Hernandez
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Erin M. Coyne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Neeha Zaidi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Daniel J. Zabransky
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Logan L. Engle
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Aleksandra Ogurtsova
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Marina Baretti
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel Laheru
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Jennifer N. Durham
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hao Wang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Robert Anders
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth M. Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Elana J. Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
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Zimmerman JW, Shu DH, Burkhart RA, Tandurella J, Fertig EJ, Jaffee EM. Abstract 1480: miR-21 as a post-transcriptional regulator of pancreatic ductal adenocarcinoma (PDAC) tumorigenesis. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1480] [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
Introduction: MicroRNAs are short non-coding RNAs that are frequently dysregulated across cancers. Specifically, microRNA-21 (miR-21) is a known oncomir overexpressed in pancreatic adenocarcinoma (PDAC) that regulates multiple gene targets downstream of KRAS, the site of the primary driver mutation in PDAC. Past efforts to target mutant KRAS have been limited by compensatory activation of other growth pathways and treatment-related toxicity. Inhibiting miR-21 expression is a novel therapeutic strategy to target KRAS effector function through post-transcriptional regulation. We previously demonstrated that systemic inhibition of miRNA-21 (miR-21) intercepts tumorigenesis in the transgenic KrasG12D/+;Trp53R172H/+;Pdx-1-Cre (KPC) mice without causing overt toxicity. Our major goal was to verify the translation of the previous findings to human models and examine the mechanistic implications of miR-21 inhibition in PDAC.
Experimental Procedures: Using publicly available data from a cohort of patients with PDAC in The Cancer Genome Atlas (TCGA), we performed differential expression analysis of miR-21 and KRAS-related gene targets as well as gene set enrichment analysis of oncogenic pathways identified by the Molecular Signatures Database (MSigDB). Concurrently, de-novo patient-derived organoid (PDO) models were generated from core biopsies and surgical resection specimens. To evaluate the effects of miR-21 inhibition on KRAS pathway activity in a human model system, we selected 6 PDO cell lines and determined miR-21 gene expression by quantitative PCR at baseline and after knockdown using a lentiviral construct.
Results: Analysis of TCGA PDAC cohort identified heterogeneous endogenous expression of miR-21, which was validated ex vivo in our PDO model system. Gene set enrichment analysis revealed enrichment of gene sets associated with KRAS dependency, MEK, AKT, and MTOR signaling in patients with higher endogenous miR-21 expression. MiR-21 knockdown in PDO cell lines was stable at multiple intervals following lentiviral transduction. Further, expression of PDCD4, a tumor suppressor gene and target of miR-21 downstream of KRAS, was enhanced in PDO lines following miR-21 inhibition.
Conclusions: We previously demonstrated that miR-21 appears to be an early and reliable molecular marker of pancreatic neoplasia and that systemic inhibition in a murine model intercepts PDAC tumorigenesis. We now demonstrate in human models that higher miR-21 expression is associated with enrichment of gene sets downstream of KRAS. Additionally, knocking down miR-21 expression enhances the expression of gene targets with tumor suppressor function, notably PDCD4. This suggests that modulating miR-21 expression subsequently modulates the expression of gene targets with critical cell regulatory functions and provides additional insight into novel therapeutic targets.
Citation Format: Jacquelyn W. Zimmerman, Daniel H. Shu, Richard A. Burkhart, Joseph Tandurella, Elana J. Fertig, Elizabeth M. Jaffee. miR-21 as a post-transcriptional regulator of pancreatic ductal adenocarcinoma (PDAC) tumorigenesis [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 1480.
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Affiliation(s)
| | - Daniel H. Shu
- 1Johns Hopkins Sidney Kimmel Comp. Cancer Center, Baltimore, MD
| | | | | | - Elana J. Fertig
- 1Johns Hopkins Sidney Kimmel Comp. Cancer Center, Baltimore, MD
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Shu DH, Danilova L, Yuan L, Zhu Q, Wang H, Kagohara L, Anders R, Jaffee E, Fertig E, Yarchoan M. Abstract 1323: 12-chemokine gene signature identifies major pathologic response in patients with hepatocellular carcinoma treated with neoadjuvant nivolumab and cabozantinib. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1323] [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
Background: Tertiary lymphoid structures (TLS) are ectopic lymphoid organs that develop at sites of chronic inflammation. In many solid tumors they have been linked with improved survival, but their prognostic value in hepatocellular carcinoma (HCC) remains uncertain. In immunotherapy-naïve patients with HCC, peritumoral and intratumoral TLS have been associated with improved overall survival, but TLS and increased expression of an associated 12-chemokine gene signature in tumor-adjacent liver parenchyma have also been linked to worse outcomes. In patients with HCC receiving immunotherapy, the prognostic value of TLS and the 12-chemokine signature is not known.
Methods: We collected formalin-fixed, paraffin-embedded tumors of 12 patients with locally advanced HCC treated with neoadjuvant nivolumab and cabozantinib followed by surgical resection. We used immunohistochemistry and imaging mass cytometry to determine TLS density and immunophenotype. We obtained bulk RNA sequencing from 9 patients (4 responders and 5 non-responders) and used hierarchical clustering to define subgroups of patients according to expression of a previously validated 12-chemokine gene signature. The prognostic value of the chemokine signature for predicting disease free survival (DFS) was calculated using the Kaplan-Meier method and analyzed by log-rank test. Additional analysis of the spatial heterogeneity of the 12-chemokine signature was performed using spatial transcriptomics.
Results: Increased TLS density was associated with a major pathologic response to treatment (p = 0.006). Hierarchical clustering of expression of the 12-chemokine gene signature identified increased expression in 4 responders and 1 non-responder and decreased expression in 4 non-responders. The association between chemokine expression and pathologic response to treatment was statistically significant by Fisher’s exact test (p = 0.008). Patients with increased expression of the 12-chemokine signature showed a trend toward improved DFS (HR = 0.23, 95% CI 0.03 to 3.05). Spatial transcriptomics showed heterogeneous chemokine expression across the resection specimen which was highest in immune clusters.
Conclusions: Using immunohistochemistry, bulk RNA sequencing, and spatial transcriptomics, we show that TLS and a TLS-associated 12-chemokine gene signature are associated with a favorable response to treatment in patients receiving neoadjuvant nivolumab and cabozantinib for HCC. We found a trend toward improved DFS in patients with increased expression of the 12-chemokine signature, a finding which should be evaluated in a larger cohort. Further research is necessary to determine the functional role of TLS in anti-tumor immunity.
Citation Format: Daniel H. Shu, Ludmila Danilova, Long Yuan, Qingfeng Zhu, Hao Wang, Luciane Kagohara, Robert Anders, Elizabeth Jaffee, Elana Fertig, Mark Yarchoan. 12-chemokine gene signature identifies major pathologic response in patients with hepatocellular carcinoma treated with neoadjuvant nivolumab and cabozantinib [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 1323.
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Affiliation(s)
- Daniel H. Shu
- 1Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Ludmila Danilova
- 1Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Long Yuan
- 2Johns Hopkins University School of Medicine, Baltimore, MD
| | - Qingfeng Zhu
- 2Johns Hopkins University School of Medicine, Baltimore, MD
| | - Hao Wang
- 1Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Luciane Kagohara
- 1Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Robert Anders
- 2Johns Hopkins University School of Medicine, Baltimore, MD
| | - Elizabeth Jaffee
- 1Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Elana Fertig
- 1Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Mark Yarchoan
- 1Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
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