Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy

doi:10.1016/j.ccell.2022.10.001

. 2022 Nov 14;40(11):1374-1391.e7.

doi: 10.1016/j.ccell.2022.10.001. Epub 2022 Oct 27.

Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy

Keyu Li¹, Joseph A Tandurella², Jessica Gai³, Qingfeng Zhu⁴, Su Jin Lim⁵, Dwayne L Thomas 2nd⁶, Tao Xia⁷, Guanglan Mo³, Jacob T Mitchell⁸, Janelle Montagne², Melissa Lyman⁹, Ludmila V Danilova², Jacquelyn W Zimmerman², Benedict Kinny-Köster¹⁰, Tengyi Zhang⁷, Linda Chen¹¹, Alex B Blair¹², Thatcher Heumann¹³, Rose Parkinson¹⁴, Jennifer N Durham¹⁴, Amol K Narang¹⁵, Robert A Anders¹⁶, Christopher L Wolfgang¹⁷, Daniel A Laheru¹², Jin He¹⁷, Arsen Osipov³, Elizabeth D Thompson¹⁸, Hao Wang¹⁹, Elana J Fertig²⁰, Elizabeth M Jaffee²¹, Lei Zheng²²

Affiliations

¹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
² Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
³ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁴ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁵ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁶ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁷ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁸ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁰ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹¹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹² Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹³ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁴ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁵ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁶ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁷ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁸ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
²⁰ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA. Electronic address: ejfertig@jhmi.edu.
²¹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Electronic address: ejaffee@jhmi.edu.
²² Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Electronic address: lzheng6@jhmi.edu.

PMID: 36306792
PMCID: PMC9669212
DOI: 10.1016/j.ccell.2022.10.001

Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy

Keyu Li et al. Cancer Cell. 2022.

. 2022 Nov 14;40(11):1374-1391.e7.

doi: 10.1016/j.ccell.2022.10.001. Epub 2022 Oct 27.

Authors

Affiliations

¹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
² Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
³ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁴ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁵ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁶ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁷ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁸ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁰ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹¹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹² Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹³ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁴ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁵ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁶ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁷ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁸ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
¹⁹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
²⁰ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Quantitative Sciences Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA. Electronic address: ejfertig@jhmi.edu.
²¹ Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Electronic address: ejaffee@jhmi.edu.
²² Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Skip Viragh Pancreatic Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Pancreatic Cancer Precision Medicine Center of Excellence Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Cancer Convergence Institute at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Electronic address: lzheng6@jhmi.edu.

PMID: 36306792
PMCID: PMC9669212
DOI: 10.1016/j.ccell.2022.10.001

Abstract

Successful pancreatic ductal adenocarcinoma (PDAC) immunotherapy necessitates optimization and maintenance of activated effector T cells (Teff). We prospectively collected and applied multi-omic analyses to paired pre- and post-treatment PDAC specimens collected in a platform neoadjuvant study of granulocyte-macrophage colony-stimulating factor-secreting allogeneic PDAC vaccine (GVAX) vaccine ± nivolumab (anti-programmed cell death protein 1 [PD-1]) to uncover sensitivity and resistance mechanisms. We show that GVAX-induced tertiary lymphoid aggregates become immune-regulatory sites in response to GVAX + nivolumab. Higher densities of tumor-associated neutrophils (TANs) following GVAX + nivolumab portend poorer overall survival (OS). Increased T cells expressing CD137 associated with cytotoxic Teff signatures and correlated with increased OS. Bulk and single-cell RNA sequencing found that nivolumab alters CD4⁺ T cell chemotaxis signaling in association with CD11b⁺ neutrophil degranulation, and CD8⁺ T cell expression of CD137 was required for optimal T cell activation. These findings provide insights into PD-1-regulated immune pathways in PDAC that should inform more effective therapeutic combinations that include TAN regulators and T cell activators.

Keywords: CD137; IL-8; RNA sequencing; Th17; anti-PD-1 antibody; immune checkpoint inhibitor; multiplex immunohistochemistry; pancreatic cancer; tumor-associated neutrophils; vaccine therapy.

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Conflict of interest statement

Declaration of interests L.Z. receives grant support from Bristol-Meyer Squibb, Merck, AstraZeneca, iTeos, Amgen, NovaRock, Inxmed, Halozyme, and Abmeta. L.Z. is a paid consultant/Advisory Board member at Biosion, Alphamab, NovaRock, Ambrx, Akrevia/Xilio, QED, Natera, Novagenesis, Snow Lake Capitals, BioArdis, Tempus, Amberstone, Pfizer, Tavotek, and Mingruizhiyao. L.Z. holds shares at Alphamab, Amberstone, and Mingruizhiyao. E.J.F. is on the scientific advisory board of Resistance Bio and is a paid consultant for Merck and Mestag Therapeutics. E.J. receives grant support from Lustgarten Foundation, Bristol-Meyer Squibb, Genentech, and AstroZeneca; is a paid consultant for NextCure, Genocea, DragonFly, Stimit, CSTONE, Achilles, and Candel; is on the advisory board of Parker Institute and Break Through Cancer; is a founder of Abmeta Biotech; and is the Chief Medical Advisor for the Lustgarten Foundation.

Figures

**Figure 1.. Multiplex immunohistochemistry of PDACs before and after immunotherapy**
(A) ROIs were selected within the post-treatment surgical resected tumor areas. CD45 and EpCAM staining were used to identify the lymphoid cells and tumor epithelia, respectively. All scale bars, 200 μm. (B and C) Overlaid images of representative markers assigned with pseudocolors in one representative LA (B) and one representative non-LA tumor area (C) in post-treatment tumors. All scale bars, 100 μm. (D) CD45 and EpCAM staining of one representative ROI from a pre-treatment biopsy tumor area. All scale bars, 200 μm. (E) Overlaid images of one representative ROI of pre-treatment biopsy. All scale bars, 100 μm. (F and G) Summary of the density of all immune cell subtypes analyzed as indicated in the paired pre-treatment versus post-treatment non-LA tumor areas from the same arm A patients (F, n = 6) and arm B patients (G, n = 10). Data shown as the mean ± SD; comparison by paired t test; *p < 0.05, **p < 0.01, ***p < 0.001; all others, not significant. See also Figures S1, S2, Tables S1, S2, S3, and S4.

**Figure 2.. Multiplex IHC of CD8⁺ or CD4⁺ T subtypes and their correlation with OS**
(A and B) Summary of the density of all immune cell subtypes analyzed as indicated in LA (A) and non-LA tumor areas (B) in arm A (n =9) versus arm B (n=10) patients. (C–E) Correlation between OS and CD8⁺ and CD8⁺GZMB⁺ T cells in pre-treatment tumor biopsies (C, pre, n = 6 for GVAX and n = 10 for GVAX + Nivo) and in LA (D) and non-LA tumor areas (E) from post-treatment tumors (see sample numbers in A and B). Three cases with the highest densities of CD8⁺GZMB⁺ T cells and the longest OS are circled. (F) Changes in the density of CD8⁺ or CD8⁺GZMB⁺ T cells between pre-treatment (pre) and matched post-treatment non-LA tumor areas (post) and their correlation with OS. (G) Correlation between OS and CD8⁺CD137⁺ T cells in LA. (H) Correlation between CD8⁺GZMB⁺ T cells and CD8⁺CD137⁺ T cells in LA. Tumors are subgrouped by higher versus lower density of CD8⁺CD137⁺ T cells in LA. (I–R) Correlation between OS and CD4⁺ T cells (I), Th1 (J), Th2 (K), Th1:Th2 ratio (L), Treg (M), and Th17 (N) in LA, Th17 in non-LA tumor area (O), and CD4⁺PD-1⁺ T cells (P), CD8⁺PD-1⁺ T cells (Q), and CD8⁺EOMES⁺ T cells (R) in LA. All data shown as the mean ± SD; all comparisons by t test; *p < 0.05; **p < 0.01; ***p < 0.001; NS, not significant; all others, not significant. See also Figures S3 and S4.

**Figure 3.. Multiplex IHC analysis of TAM and TAN**
(A–G) Correlation between OS and M1-like TAM, M2-like TAM and the ratio of M1- and M2-like TAM in LA (A) and non-LA tumor area (B), PD-L1⁺ M1-like and M2-like TAM in LA (C) and non-LA tumor area (D), TAN (CD66b⁺ Gr) in pre-treatment biopsy (E, pre) and in post-treatment LA (F), and non-LA tumor area (G). (H) Changes in TANs between pre-treatment (pre) and matched post-treatment non-LA tumor areas (post) and their correlation with OS. Sample numbers (A–H) are the same as in Figure 2. (I–K) Correlation between CD8⁺PD-1⁺ T cells and CD4⁺PD-1⁺ T cells, as indicated, and myeloid cell densities in post-treatment tumor areas. Tumors (n = 19) subgrouped by higher versus lower density of M1-like TAM (I), M2-like TAM (J), or CD66b⁺ TAN (K), respectively, in LA. (L and M) Correlation between LAG3⁺ cells (L) and TIM3⁺ cells (M), respectively, and TANs in post-treatment tumor areas. Tumors subgrouped by higher versus lower density of TANs in LA. (N) mIHC images of CD66b and CXCR2, as indicated, and their overlaid image. All scale bars, 100 μm. Pseudocolors assigned by the Halo software. A representative LA shown; one square region enlarged and also shown. Arrow indicates the only CXCR2⁺ cell that was not CD66b⁺ within this region. All data shown as the mean ± SD; all comparisons made by t test; *p < 0.05; **p < 0.01; NS, not significant. See also Figure S5.

**Figure 4.. Spatial relationship between tumor cells and immune cells**
(A) A representative region from six-marker mIHC images integrated by Halo software. Scale bar, 100 μm. (B) Distance measurement schema of a representative region. Positive signals (exemplified by the EpCAM staining signals) and the nearest neighbor cells (exemplified by the nearest CD8⁺ cells) are connected by lines whose lengths are measured as the distances. (C–H) Tumors were subgrouped by higher versus lower density of CD8⁺ T cells (C and F), CD8⁺PD-1⁺ T cells (D and G), and CD8⁺GZMB⁺ T cells (E and H) in LA (C–E) and non-LA tumor areas (F–H). Distances from one cell type to another cell type were compared by t test between subgroups (high versus low density) in two cohorts of tumors treated with GVAX and GVAX + nivolumab, respectively. Tumor cells marked by EpCAM staining and identified by pathologists. mIHC images qualified for distance measurement: n = 7 for GVAX and n = 10 for GVAX + Nivo. All data shown as the mean ± SD; *p < 0.05; **p < 0.01; all others, not significant. See also Figure S6.

**Figure 5.. Transcriptomic profiling of tumor-infiltrating immune cells in PDACs treated with GVAX or GVAX + nivolumab**
(A) Cibersort heatmap of immune cell subtype composition profiling sorted CD19⁺ (n = 10), CD4⁺ (n = 13), CD8⁺ (n = 13), and CD11b⁺ (n = 10) TILs. Treatment arms, OS, and sorted cell types indicated by various colors. (B–D) The proportion of immune cell subtypes profiled by Cibersort was compared between treatment arms by t test. Boxplots display minimum and maximum values (whiskers), interquantile range (box) with median, and outliers. (E–J) TCR and BCR clonality predicted from RNA-seq of sorted CD4⁺ (E and H), CD8⁺ (F and I), and CD19⁺ cells (G and J) were compared between treatment arms (E–G) and between OS > 2 years and OS < 2 years cohorts (H–J) by t test. Data shown as the mean ± SD. Cases with follow-up < 2 years shown separately. See also Figures S7, S8, and Table S5.

**Figure 6.. RNA-seq analysis of differentially expressed genes between different subcohorts from this study cohort of PDACs**
(A–B) Volcano plots showing differentially expressed (DE) genes compared between the OS > 2 years and OS < 2 years cohorts in sorted CD8⁺ (A) and CD4⁺ (B) T cells. (C-F) Volcano plots showing DE genes compared between treatment arms in sorted CD4⁺ T cells (C), CD8⁺ T cells (D), CD11b⁺ cells (E), and CD19⁺ B cells (F). The sample numbers are the same as in Figure 5. Vertical dashed lines indicate Log₂ fold change (FC) at −0.5 and 0.5; horizontal dashed line indicates adjusted p value at 0.05. Genes that met either, both, or neither (NS) of the following two criteria: (1) Log₂ FC > 0.5 or < −0.5 and (2) adjusted p value <0.05 are represented by color-coded dots. Total gene counts are indicated. Genes of interest are annotated. (G–J) Enrichment plots showed upregulation of the REACTOM chemokine receptor bind chemokines pathway in sorted CD4⁺ T cells (G), the GOBP myeloid cells and lymphocyte chemotaxis pathway in sorted CD4⁺ T cells (H), the GOMF extracellular matrix structural constituent pathway in sorted CD8⁺ T cells (I), and the REACTOM neutrophil degranulation pathway in CD11b⁺ cells (J) in the GVAX + Nivo versus GVAX treatment arm. DE by treatment, differentially expressed between treatment arms. See also Tables S6 and S7.

**Figure 7.. Single-cell analysis of CD137 (TNFRSF9)-expressing T cells**
(A) Uniform Manifold Approximation and Projection (UMAP) embedding of color-coded immune cell subtypes from the PDAC atlas. (B) Immune cells from the PDAC atlas were annotated according to high (hi) or low (lo) *TNFRSF9* expression and annotated for different immune cell subtypes. (C) Stacked bar plots of the proportions of CD8⁺, effector CD8⁺, and Treg cells classified as *TNFRSF9*^hi or *TNFRSF9*^lo. (D and E) MsigDB hallmark gene sets significantly enriched in *TNFRSF9*^hi (orange) or *TNFRSF9*^lo (blue) Tregs (D) and effector CD8⁺ cells (E) ordered by normalized enrichment score. (F) Expression of ligands by immune cells that interact with receptors expressed by neutrophils is presented in the heatmap as scaled, log-normalized counts. See also Figure S9.

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References

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1. Alessi M-C, Cenac N, Si-Tahar M, and Riteau B (2017). FPR2: a novel promising target for the treatment of influenza. Front. Microbiol. 8, 1719. - PMC - PubMed
1. Amrollahi P, Rodrigues M, Lyon CJ, Goel A, Han H, and Hu TY (2019). Ultra-sensitive automated profiling of EpCAM expression on tumor-derived extracellular vesicles. Front. Genet. 10, 1273. - PMC - PubMed
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[1] Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine J-C, Geurts P, Aerts J, et al. (2017). SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086. - PMC - PubMed

[2] Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine J-C, Geurts P, Aerts J, et al. (2017). SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086. - PMC - PubMed

[3] Alessi M-C, Cenac N, Si-Tahar M, and Riteau B (2017). FPR2: a novel promising target for the treatment of influenza. Front. Microbiol. 8, 1719. - PMC - PubMed

[4] Alessi M-C, Cenac N, Si-Tahar M, and Riteau B (2017). FPR2: a novel promising target for the treatment of influenza. Front. Microbiol. 8, 1719. - PMC - PubMed

[5] Amrollahi P, Rodrigues M, Lyon CJ, Goel A, Han H, and Hu TY (2019). Ultra-sensitive automated profiling of EpCAM expression on tumor-derived extracellular vesicles. Front. Genet. 10, 1273. - PMC - PubMed

[6] Amrollahi P, Rodrigues M, Lyon CJ, Goel A, Han H, and Hu TY (2019). Ultra-sensitive automated profiling of EpCAM expression on tumor-derived extracellular vesicles. Front. Genet. 10, 1273. - PMC - PubMed

[7] Arroyo Hornero R, Georgiadis C, Hua P, Trzupek D, He L-Z, Qasim W, Todd JA, Ferreira RC, Wood KJ, Issa F, et al. (2020). CD70 expression determines the therapeutic efficacy of expanded human regulatory T cells. Commun. Biol. 3, 375. - PMC - PubMed

[8] Arroyo Hornero R, Georgiadis C, Hua P, Trzupek D, He L-Z, Qasim W, Todd JA, Ferreira RC, Wood KJ, Issa F, et al. (2020). CD70 expression determines the therapeutic efficacy of expanded human regulatory T cells. Commun. Biol. 3, 375. - PMC - PubMed

[9] Avram G, Sánchez-Sendra B, Martín JM, Terrádez L, Ramos D, and Monteagudo C (2013). The density and type of MECA-79-positive high endothelial venules correlate with lymphocytic infiltration and tumour regression in primary cutaneous melanoma. Histopathology 63, 852–861. - PubMed

[10] Avram G, Sánchez-Sendra B, Martín JM, Terrádez L, Ramos D, and Monteagudo C (2013). The density and type of MECA-79-positive high endothelial venules correlate with lymphocytic infiltration and tumour regression in primary cutaneous melanoma. Histopathology 63, 852–861. - PubMed

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Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy

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Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy

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