Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade

Douglas C Palmer; Beau R Webber; Yogin Patel; Matthew J Johnson; Christine M Kariya; Walker S Lahr; Maria R Parkhurst; Jared J Gartner; Todd D Prickett; Frank J Lowery; Rigel J Kishton; Devikala Gurusamy; Zulmarie Franco; Suman K Vodnala; Miechaleen D Diers; Natalie K Wolf; Nicholas J Slipek; David H McKenna; Darin Sumstad; Lydia Viney; Tom Henley; Tilmann Bürckstümmer; Oliver Baker; Ying Hu; Chunhua Yan; Daoud Meerzaman; Kartik Padhan; Winnie Lo; Parisa Malekzadeh; Li Jia; Drew C Deniger; Shashank J Patel; Paul F Robbins; R Scott McIvor; Modassir Choudhry; Steven A Rosenberg; Branden S Moriarity; Nicholas P Restifo

doi:10.1016/j.medj.2022.07.008

Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade

Med. 2022 Oct 14;3(10):682-704.e8. doi: 10.1016/j.medj.2022.07.008. Epub 2022 Aug 24.

Authors

Douglas C Palmer¹, Beau R Webber², Yogin Patel³, Matthew J Johnson⁴, Christine M Kariya³, Walker S Lahr⁴, Maria R Parkhurst³, Jared J Gartner³, Todd D Prickett³, Frank J Lowery³, Rigel J Kishton³, Devikala Gurusamy³, Zulmarie Franco³, Suman K Vodnala³, Miechaleen D Diers⁴, Natalie K Wolf⁴, Nicholas J Slipek⁴, David H McKenna⁵, Darin Sumstad⁶, Lydia Viney⁷, Tom Henley⁷, Tilmann Bürckstümmer⁷, Oliver Baker⁷, Ying Hu⁸, Chunhua Yan⁸, Daoud Meerzaman⁸, Kartik Padhan⁹, Winnie Lo³, Parisa Malekzadeh³, Li Jia³, Drew C Deniger³, Shashank J Patel³, Paul F Robbins³, R Scott McIvor¹⁰, Modassir Choudhry⁷, Steven A Rosenberg¹¹, Branden S Moriarity¹², Nicholas P Restifo¹³

Affiliations

¹ Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA. Electronic address: palmerdc33@gmail.com.
² Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA. Electronic address: webb0178@umn.edu.
³ Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA.
⁴ Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
⁵ Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
⁶ Molecular and Cellular Therapeutics, University of Minnesota, Saint Paul, MN, USA.
⁷ Intima Bioscience, Inc., New York, NY, USA.
⁸ The Center for Biomedical Informatics and Information Technology (CBIIT), National Institutes of Health, Bethesda, MD, USA.
⁹ National Institute of Allergy and Infectious Disease (NIAID), National Institutes of Health, Bethesda, MD, USA.
¹⁰ Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
¹¹ Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA. Electronic address: sar@nih.gov.
¹² Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA. Electronic address: mori0164@umn.edu.
¹³ Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA. Electronic address: restifon@mail.nih.gov.

Abstract

Background: Adoptive transfer of tumor-infiltrating lymphocytes (TIL) fails to consistently elicit tumor rejection. Manipulation of intrinsic factors that inhibit T cell effector function and neoantigen recognition may therefore improve TIL therapy outcomes. We previously identified the cytokine-induced SH2 protein (CISH) as a key regulator of T cell functional avidity in mice. Here, we investigate the mechanistic role of CISH in regulating human T cell effector function in solid tumors and demonstrate that CRISPR/Cas9 disruption of CISH enhances TIL neoantigen recognition and response to checkpoint blockade.

Methods: Single-cell gene expression profiling was used to identify a negative correlation between high CISH expression and TIL activation in patient-derived TIL. A GMP-compliant CRISPR/Cas9 gene editing process was developed to assess the impact of CISH disruption on the molecular and functional phenotype of human peripheral blood T cells and TIL. Tumor-specific T cells with disrupted Cish function were adoptively transferred into tumor-bearing mice and evaluated for efficacy with or without checkpoint blockade.

Findings: CISH expression was associated with T cell dysfunction. CISH deletion using CRISPR/Cas9 resulted in hyper-activation and improved functional avidity against tumor-derived neoantigens without perturbing T cell maturation. Cish knockout resulted in increased susceptibility to checkpoint blockade in vivo.

Conclusions: CISH negatively regulates human T cell effector function, and its genetic disruption offers a novel avenue to improve the therapeutic efficacy of adoptive TIL therapy.

Funding: This study was funded by Intima Bioscience, U.S. and in part through the Intramural program CCR at the National Cancer Institute.

Keywords: CISH; CRISPR; PD-1; T cell therapy; TIL; cancer; checkpoint; immunotherapy; neoantigen; preclinical research; scRNAseq.

Publication types

Research Support, N.I.H., Intramural
Research Support, N.I.H., Extramural

MeSH terms

Adoptive Transfer
Animals
Cytokines / metabolism
Humans
Immunotherapy, Adoptive / methods
Lymphocytes, Tumor-Infiltrating*
Mice
T-Lymphocytes*

Substances

Cytokines

Abstract

Publication types

MeSH terms

Substances

Grants and funding