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; Micki 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

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, Micki D Diers, Natalie K. Wolf, Nicholas J Slipek, David H. McKenna, Darin Sumstad, Lydia VineyTom 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

Research output: Contribution to journal › Article › peer-review

24 Scopus citations

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.

Original language	English (US)
Pages (from-to)	682-704.e8
Journal	Med
Volume	3
Issue number	10
DOIs	https://doi.org/10.1016/j.medj.2022.07.008
State	Published - Oct 14 2022

Bibliographical note

Funding Information:
This study was funded by Intima Bioscience, U.S. and in part through the Intramural program CCR at the National Cancer Institute. Support from CCR Single Cell Analysis Facility was funded by FNLCR Contract HSN261200800001E. Sequencing was performed with the CCR Genomics Core. This work used the computational resources of the NIH HPC Biowulf cluster. (http://hpc.nih.gov) Next-generation sequencing and bioinformatic analysis of CRISPR off-target activity was conducted at the University of Minnesota Genomics Center (UMGC). D.C.P. B.R.W. S.A.R. B.S.M. and N.P.R. were involved in study design and had complete access to the data. M.C. S.A.R. B.S.M. P.F.R. and R.S.M. contributed to study concepts. B.R.W. D.S. D.H.M. N.J.S. and M.D.D. were responsible for manufacturing and validating therapeutic cells. D.C.P. B.R.W. Y.P. C.M.K. F.J.L. R.J.K. D.G. Z.F. S.K.V. K.P. P.M. D.C.D. S.J.P. D.S. N.J.S. M.D.D. M.J.J. W.S.L. N.K.W. L.V. T.H. T.B. and O.B. were involved in data acquisition. J.J.G. and T.D.P. were involved in quality control of data and algorithms. Y.H. C.Y. D.M. and L.J. were involved in data analysis and interpretation. D.C.P. B.R.W. Y.H. and L.J. contributed to statistical analysis. D.C.P. and B.R.W. wrote the manuscript. All authors approved the article for submission and publication. M.C. is a co-founder of Intima Bioscience. B.R.W. S.A.R. and B.S.M. have received sponsored research support from Intima Bioscience. D.C.P. B.R.W. M.C. S.A.R. B.S.M. and N.P.R. have patents filed based on the findings described here.

Funding Information:
This study was funded by Intima Bioscience, U.S. and in part through the Intramural program CCR at the National Cancer Institute . Support from CCR Single Cell Analysis Facility was funded by FNLCR Contract HSN261200800001E . Sequencing was performed with the CCR Genomics Core. This work used the computational resources of the NIH HPC Biowulf cluster. ( http://hpc.nih.gov ) Next-generation sequencing and bioinformatic analysis of CRISPR off-target activity was conducted at the University of Minnesota Genomics Center (UMGC).

Publisher Copyright:
© 2022 The Author(s)

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.medj.2022.07.008

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Palmer, D. C., Webber, B. R., Patel, Y., Johnson, M. J., Kariya, C. M., Lahr, W. S., Parkhurst, M. R., Gartner, J. J., Prickett, T. D., Lowery, F. J., Kishton, R. J., Gurusamy, D., Franco, Z., Vodnala, S. K., Diers, M. D., Wolf, N. K., Slipek, N. J., McKenna, D. H., Sumstad, D., ... Restifo, N. P. (2022). Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade. Med, 3(10), 682-704.e8. https://doi.org/10.1016/j.medj.2022.07.008

Palmer, DC, Webber, BR, Patel, Y, Johnson, MJ, Kariya, CM, Lahr, WS, Parkhurst, MR, Gartner, JJ, Prickett, TD, Lowery, FJ, Kishton, RJ, Gurusamy, D, Franco, Z, Vodnala, SK, Diers, MD, Wolf, NK, Slipek, NJ , McKenna, DH, Sumstad, D, Viney, L, Henley, T, Bürckstümmer, T, Baker, O, Hu, Y, Yan, C, Meerzaman, D, Padhan, K, Lo, W, Malekzadeh, P, Jia, L, Deniger, DC, Patel, SJ, Robbins, PF, McIvor, RS, Choudhry, M, Rosenberg, SA, Moriarity, BS & Restifo, NP 2022, 'Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade', Med, vol. 3, no. 10, pp. 682-704.e8. https://doi.org/10.1016/j.medj.2022.07.008

@article{77f8d3329d2c4ad4a3738e665962c20c,

title = "Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade",

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",

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

note = "Funding Information: This study was funded by Intima Bioscience, U.S. and in part through the Intramural program CCR at the National Cancer Institute. Support from CCR Single Cell Analysis Facility was funded by FNLCR Contract HSN261200800001E. Sequencing was performed with the CCR Genomics Core. This work used the computational resources of the NIH HPC Biowulf cluster. (http://hpc.nih.gov) Next-generation sequencing and bioinformatic analysis of CRISPR off-target activity was conducted at the University of Minnesota Genomics Center (UMGC). D.C.P. B.R.W. S.A.R. B.S.M. and N.P.R. were involved in study design and had complete access to the data. M.C. S.A.R. B.S.M. P.F.R. and R.S.M. contributed to study concepts. B.R.W. D.S. D.H.M. N.J.S. and M.D.D. were responsible for manufacturing and validating therapeutic cells. D.C.P. B.R.W. Y.P. C.M.K. F.J.L. R.J.K. D.G. Z.F. S.K.V. K.P. P.M. D.C.D. S.J.P. D.S. N.J.S. M.D.D. M.J.J. W.S.L. N.K.W. L.V. T.H. T.B. and O.B. were involved in data acquisition. J.J.G. and T.D.P. were involved in quality control of data and algorithms. Y.H. C.Y. D.M. and L.J. were involved in data analysis and interpretation. D.C.P. B.R.W. Y.H. and L.J. contributed to statistical analysis. D.C.P. and B.R.W. wrote the manuscript. All authors approved the article for submission and publication. M.C. is a co-founder of Intima Bioscience. B.R.W. S.A.R. and B.S.M. have received sponsored research support from Intima Bioscience. D.C.P. B.R.W. M.C. S.A.R. B.S.M. and N.P.R. have patents filed based on the findings described here. Funding Information: This study was funded by Intima Bioscience, U.S. and in part through the Intramural program CCR at the National Cancer Institute . Support from CCR Single Cell Analysis Facility was funded by FNLCR Contract HSN261200800001E . Sequencing was performed with the CCR Genomics Core. This work used the computational resources of the NIH HPC Biowulf cluster. ( http://hpc.nih.gov ) Next-generation sequencing and bioinformatic analysis of CRISPR off-target activity was conducted at the University of Minnesota Genomics Center (UMGC). Publisher Copyright: {\textcopyright} 2022 The Author(s)",

year = "2022",

month = oct,

day = "14",

doi = "10.1016/j.medj.2022.07.008",

language = "English (US)",

volume = "3",

pages = "682--704.e8",

journal = "Med",

issn = "2666-6359",

publisher = "Cell Press",

number = "10",

}

TY - JOUR

T1 - Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade

AU - Palmer, Douglas C.

AU - Webber, Beau R.

AU - Patel, Yogin

AU - Johnson, Matthew J.

AU - Kariya, Christine M.

AU - Lahr, Walker S

AU - Parkhurst, Maria R.

AU - Gartner, Jared J.

AU - Prickett, Todd D.

AU - Lowery, Frank J.

AU - Kishton, Rigel J.

AU - Gurusamy, Devikala

AU - Franco, Zulmarie

AU - Vodnala, Suman K.

AU - Diers, Micki D

AU - Wolf, Natalie K.

AU - Slipek, Nicholas J

AU - McKenna, David H.

AU - Sumstad, Darin

AU - Viney, Lydia

AU - Henley, Tom

AU - Bürckstümmer, Tilmann

AU - Baker, Oliver

AU - Hu, Ying

AU - Yan, Chunhua

AU - Meerzaman, Daoud

AU - Padhan, Kartik

AU - Lo, Winnie

AU - Malekzadeh, Parisa

AU - Jia, Li

AU - Deniger, Drew C.

AU - Patel, Shashank J.

AU - Robbins, Paul F.

AU - McIvor, R. Scott

AU - Choudhry, Modassir

AU - Rosenberg, Steven A.

AU - Moriarity, Branden S.

AU - Restifo, Nicholas P.

N1 - Funding Information: This study was funded by Intima Bioscience, U.S. and in part through the Intramural program CCR at the National Cancer Institute. Support from CCR Single Cell Analysis Facility was funded by FNLCR Contract HSN261200800001E. Sequencing was performed with the CCR Genomics Core. This work used the computational resources of the NIH HPC Biowulf cluster. (http://hpc.nih.gov) Next-generation sequencing and bioinformatic analysis of CRISPR off-target activity was conducted at the University of Minnesota Genomics Center (UMGC). D.C.P. B.R.W. S.A.R. B.S.M. and N.P.R. were involved in study design and had complete access to the data. M.C. S.A.R. B.S.M. P.F.R. and R.S.M. contributed to study concepts. B.R.W. D.S. D.H.M. N.J.S. and M.D.D. were responsible for manufacturing and validating therapeutic cells. D.C.P. B.R.W. Y.P. C.M.K. F.J.L. R.J.K. D.G. Z.F. S.K.V. K.P. P.M. D.C.D. S.J.P. D.S. N.J.S. M.D.D. M.J.J. W.S.L. N.K.W. L.V. T.H. T.B. and O.B. were involved in data acquisition. J.J.G. and T.D.P. were involved in quality control of data and algorithms. Y.H. C.Y. D.M. and L.J. were involved in data analysis and interpretation. D.C.P. B.R.W. Y.H. and L.J. contributed to statistical analysis. D.C.P. and B.R.W. wrote the manuscript. All authors approved the article for submission and publication. M.C. is a co-founder of Intima Bioscience. B.R.W. S.A.R. and B.S.M. have received sponsored research support from Intima Bioscience. D.C.P. B.R.W. M.C. S.A.R. B.S.M. and N.P.R. have patents filed based on the findings described here. Funding Information: This study was funded by Intima Bioscience, U.S. and in part through the Intramural program CCR at the National Cancer Institute . Support from CCR Single Cell Analysis Facility was funded by FNLCR Contract HSN261200800001E . Sequencing was performed with the CCR Genomics Core. This work used the computational resources of the NIH HPC Biowulf cluster. ( http://hpc.nih.gov ) Next-generation sequencing and bioinformatic analysis of CRISPR off-target activity was conducted at the University of Minnesota Genomics Center (UMGC). Publisher Copyright: © 2022 The Author(s)

PY - 2022/10/14

Y1 - 2022/10/14

N2 - 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.

AB - 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.

KW - CISH

KW - CRISPR

KW - PD-1

KW - T cell therapy

KW - TIL

KW - cancer

KW - checkpoint

KW - immunotherapy

KW - neoantigen

KW - preclinical research

KW - scRNAseq

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UR - http://www.scopus.com/inward/citedby.url?scp=85139991372&partnerID=8YFLogxK

U2 - 10.1016/j.medj.2022.07.008

DO - 10.1016/j.medj.2022.07.008

M3 - Article

C2 - 36007524

AN - SCOPUS:85139991372

SN - 2666-6359

VL - 3

SP - 682-704.e8

JO - Med

JF - Med

IS - 10

ER -

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

Abstract

Bibliographical note

Keywords

UN SDGs

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