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1
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Cohen Shvefel S, Pai JA, Cao Y, Pal LR, Levy R, Yao W, Cheng K, Zemanek M, Bartok O, Weller C, Yin Y, Du PP, Yakubovich E, Orr I, Ben-Dor S, Oren R, Fellus-Alyagor L, Golani O, Goliand I, Ranmar D, Savchenko I, Ketrarou N, Schäffer AA, Ruppin E, Satpathy AT, Samuels Y. Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion. bioRxiv 2023:2023.11.29.569032. [PMID: 38077050 PMCID: PMC10705560 DOI: 10.1101/2023.11.29.569032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Decreased intra-tumor heterogeneity (ITH) correlates with increased patient survival and immunotherapy response. However, even highly homogenous tumors may display variability in their aggressiveness, and how immunologic-factors impinge on their aggressiveness remains understudied. Here we studied the mechanisms responsible for the immune-escape of murine tumors with low ITH. We compared the temporal growth of homogeneous, genetically-similar single-cell clones that are rejected vs. those that are not-rejected after transplantation in-vivo using single-cell RNA sequencing and immunophenotyping. Non-rejected clones showed high infiltration of tumor-associated-macrophages (TAMs), lower T-cell infiltration, and increased T-cell exhaustion compared to rejected clones. Comparative analysis of rejection-associated gene expression programs, combined with in-vivo CRISPR knockout screens of candidate mediators, identified Mif (macrophage migration inhibitory factor) as a regulator of immune rejection. Mif knockout led to smaller tumors and reversed non-rejection-associated immune composition, particularly, leading to the reduction of immunosuppressive macrophage infiltration. Finally, we validated these results in melanoma patient data.
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Affiliation(s)
- Sapir Cohen Shvefel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joy A Pai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yingying Cao
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Lipika R Pal
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ronen Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Winnie Yao
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- MSD R&D (China) Co., Ltd
| | - Marie Zemanek
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Osnat Bartok
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Weller
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Peter P Du
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Elizabeta Yakubovich
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Orr
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Liat Fellus-Alyagor
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Goliand
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Dean Ranmar
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Savchenko
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Nadav Ketrarou
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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2
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Taylor KR, Barron T, Hui A, Spitzer A, Yalçin B, Ivec AE, Geraghty AC, Hartmann GG, Arzt M, Gillespie SM, Kim YS, Maleki Jahan S, Zhang H, Shamardani K, Su M, Ni L, Du PP, Woo PJ, Silva-Torres A, Venkatesh HS, Mancusi R, Ponnuswami A, Mulinyawe S, Keough MB, Chau I, Aziz-Bose R, Tirosh I, Suvà ML, Monje M. Glioma synapses recruit mechanisms of adaptive plasticity. Nature 2023; 623:366-374. [PMID: 37914930 PMCID: PMC10632140 DOI: 10.1038/s41586-023-06678-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 11/01/2021] [Accepted: 09/26/2023] [Indexed: 11/03/2023]
Abstract
The role of the nervous system in the regulation of cancer is increasingly appreciated. In gliomas, neuronal activity drives tumour progression through paracrine signalling factors such as neuroligin-3 and brain-derived neurotrophic factor1-3 (BDNF), and also through electrophysiologically functional neuron-to-glioma synapses mediated by AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors4,5. The consequent glioma cell membrane depolarization drives tumour proliferation4,6. In the healthy brain, activity-regulated secretion of BDNF promotes adaptive plasticity of synaptic connectivity7,8 and strength9-15. Here we show that malignant synapses exhibit similar plasticity regulated by BDNF. Signalling through the receptor tropomyosin-related kinase B16 (TrkB) to CAMKII, BDNF promotes AMPA receptor trafficking to the glioma cell membrane, resulting in increased amplitude of glutamate-evoked currents in the malignant cells. Linking plasticity of glioma synaptic strength to tumour growth, graded optogenetic control of glioma membrane potential demonstrates that greater depolarizing current amplitude promotes increased glioma proliferation. This potentiation of malignant synaptic strength shares mechanistic features with synaptic plasticity17-22 that contributes to memory and learning in the healthy brain23-26. BDNF-TrkB signalling also regulates the number of neuron-to-glioma synapses. Abrogation of activity-regulated BDNF secretion from the brain microenvironment or loss of glioma TrkB expression robustly inhibits tumour progression. Blocking TrkB genetically or pharmacologically abrogates these effects of BDNF on glioma synapses and substantially prolongs survival in xenograft models of paediatric glioblastoma and diffuse intrinsic pontine glioma. Together, these findings indicate that BDNF-TrkB signalling promotes malignant synaptic plasticity and augments tumour progression.
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Affiliation(s)
- Kathryn R Taylor
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Tara Barron
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Alexa Hui
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Avishay Spitzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Belgin Yalçin
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Alexis E Ivec
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Anna C Geraghty
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Griffin G Hartmann
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Marlene Arzt
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Shawn M Gillespie
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Yoon Seok Kim
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Samin Maleki Jahan
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Helena Zhang
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kiarash Shamardani
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Minhui Su
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Lijun Ni
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Peter P Du
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Pamelyn J Woo
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Arianna Silva-Torres
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Humsa S Venkatesh
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Rebecca Mancusi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Anitha Ponnuswami
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Sara Mulinyawe
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Michael B Keough
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Isabelle Chau
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Razina Aziz-Bose
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Neurosurgery, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford California, Stanford, CA, USA.
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3
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Durrant MG, Fanton A, Tycko J, Hinks M, Chandrasekaran SS, Perry NT, Schaepe J, Du PP, Lotfy P, Bassik MC, Bintu L, Bhatt AS, Hsu PD. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat Biotechnol 2023; 41:488-499. [PMID: 36217031 PMCID: PMC10083194 DOI: 10.1038/s41587-022-01494-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [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: 11/09/2021] [Accepted: 09/01/2022] [Indexed: 11/09/2022]
Abstract
Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold and enabling the prediction of their insertion site specificities. We tested their recombination activity in human cells, classifying them as landing pad, genome-targeting or multi-targeting LSRs. Overall, we achieved up to seven-fold higher recombination than Bxb1 and genome integration efficiencies of 40-75% with cargo sizes over 7 kb. We also demonstrate virus-free, direct integration of plasmid or amplicon libraries for improved functional genomics applications. This systematic discovery of recombinases directly from microbial sequencing data provides a resource of over 60 LSRs experimentally characterized in human cells for large-payload genome insertion without exposed DNA double-stranded breaks.
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Affiliation(s)
- Matthew G Durrant
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michaela Hinks
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sita S Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Nicholas T Perry
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Julia Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Peter P Du
- Department of Genetics, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Peter Lotfy
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA.
| | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
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4
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Sun Y, Revach OY, Anderson S, Kessler EA, Wolfe CH, Jenney A, Mills CE, Robitschek EJ, Davis TGR, Kim S, Fu A, Ma X, Gwee J, Tiwari P, Du PP, Sindurakar P, Tian J, Mehta A, Schneider AM, Yizhak K, Sade-Feldman M, LaSalle T, Sharova T, Xie H, Liu S, Michaud WA, Saad-Beretta R, Yates KB, Iracheta-Vellve A, Spetz JKE, Qin X, Sarosiek KA, Zhang G, Kim JW, Su MY, Cicerchia AM, Rasmussen MQ, Klempner SJ, Juric D, Pai SI, Miller DM, Giobbie-Hurder A, Chen JH, Pelka K, Frederick DT, Stinson S, Ivanova E, Aref AR, Paweletz CP, Barbie DA, Sen DR, Fisher DE, Corcoran RB, Hacohen N, Sorger PK, Flaherty KT, Boland GM, Manguso RT, Jenkins RW. Targeting TBK1 to overcome resistance to cancer immunotherapy. Nature 2023; 615:158-167. [PMID: 36634707 PMCID: PMC10171827 DOI: 10.1038/s41586-023-05704-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [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: 07/16/2021] [Accepted: 01/04/2023] [Indexed: 01/14/2023]
Abstract
Despite the success of PD-1 blockade in melanoma and other cancers, effective treatment strategies to overcome resistance to cancer immunotherapy are lacking1,2. Here we identify the innate immune kinase TANK-binding kinase 1 (TBK1)3 as a candidate immune-evasion gene in a pooled genetic screen4. Using a suite of genetic and pharmacological tools across multiple experimental model systems, we confirm a role for TBK1 as an immune-evasion gene. Targeting TBK1 enhances responses to PD-1 blockade by decreasing the cytotoxicity threshold to effector cytokines (TNF and IFNγ). TBK1 inhibition in combination with PD-1 blockade also demonstrated efficacy using patient-derived tumour models, with concordant findings in matched patient-derived organotypic tumour spheroids and matched patient-derived organoids. Tumour cells lacking TBK1 are primed to undergo RIPK- and caspase-dependent cell death in response to TNF and IFNγ in a JAK-STAT-dependent manner. Taken together, our results demonstrate that targeting TBK1 is an effective strategy to overcome resistance to cancer immunotherapy.
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Affiliation(s)
- Yi Sun
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Or-Yam Revach
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Seth Anderson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Clara H Wolfe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne Jenney
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | | | | | - Sarah Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amina Fu
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiang Ma
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jia Gwee
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Payal Tiwari
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter P Du
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Princy Sindurakar
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jun Tian
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Arnav Mehta
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexis M Schneider
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Keren Yizhak
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Institute of Technology, Technion, Haifa, Israel
| | - Moshe Sade-Feldman
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thomas LaSalle
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tatyana Sharova
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Hongyan Xie
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Shuming Liu
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - William A Michaud
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Rodrigo Saad-Beretta
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kathleen B Yates
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Johan K E Spetz
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA, USA
- John B. Little Center for Radiation Sciences, Harvard School of Public Health, Boston, MA, USA
| | - Xingping Qin
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA, USA
- John B. Little Center for Radiation Sciences, Harvard School of Public Health, Boston, MA, USA
| | - Kristopher A Sarosiek
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA, USA
- John B. Little Center for Radiation Sciences, Harvard School of Public Health, Boston, MA, USA
| | - Gao Zhang
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Preston Robert Tisch Brain Tumor Center, Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Jong Wook Kim
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
- Center for Novel Therapeutics, UC San Diego, La Jolla, CA, USA
- Department of Medicine, UC San Diego, La Jolla, CA, USA
| | - Mack Y Su
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Angelina M Cicerchia
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin Q Rasmussen
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel J Klempner
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara I Pai
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - David M Miller
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Anita Giobbie-Hurder
- Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan H Chen
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Karin Pelka
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dennie T Frederick
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Elena Ivanova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amir R Aref
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Xsphera Biosciences, Boston, MA, USA
| | - Cloud P Paweletz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Debattama R Sen
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Genevieve M Boland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Robert T Manguso
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Russell W Jenkins
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA.
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5
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Dubrot J, Du PP, Lane-Reticker SK, Kessler EA, Muscato AJ, Mehta A, Freeman SS, Allen PM, Olander KE, Ockerman KM, Wolfe CH, Wiesmann F, Knudsen NH, Tsao HW, Iracheta-Vellve A, Schneider EM, Rivera-Rosario AN, Kohnle IC, Pope HW, Ayer A, Mishra G, Zimmer MD, Kim SY, Mahapatra A, Ebrahimi-Nik H, Frederick DT, Boland GM, Haining WN, Root DE, Doench JG, Hacohen N, Yates KB, Manguso RT. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer. Nat Immunol 2022; 23:1495-1506. [PMID: 36151395 DOI: 10.1038/s41590-022-01315-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/15/2022] [Indexed: 02/04/2023]
Abstract
The immune system can eliminate tumors, but checkpoints enable immune escape. Here, we identify immune evasion mechanisms using genome-scale in vivo CRISPR screens across cancer models treated with immune checkpoint blockade (ICB). We identify immune evasion genes and important immune inhibitory checkpoints conserved across cancers, including the non-classical major histocompatibility complex class I (MHC class I) molecule Qa-1b/HLA-E. Surprisingly, loss of tumor interferon-γ (IFNγ) signaling sensitizes many models to immunity. The immune inhibitory effects of tumor IFN sensing are mediated through two mechanisms. First, tumor upregulation of classical MHC class I inhibits natural killer cells. Second, IFN-induced expression of Qa-1b inhibits CD8+ T cells via the NKG2A/CD94 receptor, which is induced by ICB. Finally, we show that strong IFN signatures are associated with poor response to ICB in individuals with renal cell carcinoma or melanoma. This study reveals that IFN-mediated upregulation of classical and non-classical MHC class I inhibitory checkpoints can facilitate immune escape.
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Affiliation(s)
- Juan Dubrot
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Peter P Du
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Samuel S Freeman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Peter M Allen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Clara H Wolfe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nelson H Knudsen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | | | - Ian C Kohnle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hans W Pope
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Austin Ayer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gargi Mishra
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Sarah Y Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Dennie T Frederick
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - W Nicholas Haining
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- ArsenalBio, South San Francisco, CA, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathleen B Yates
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Robert T Manguso
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
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Zhang SQY, Du PP, Shu X, Wu HX, Mu YZ, Wu XN, Zhang Y. [The effect of pregnant rats exposed to radio frequency electromagnetic field on the hippocampal morphology and nerve growth factor of offspring rats]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2022; 40:656-660. [PMID: 36229209 DOI: 10.3760/cma.j.cn121094-20210607-00281] [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] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Objective: To explore the effects of exposure of pregnant rats to radio frequency electromagnetic field on the ultrastructure of hippocampus and the levels of obesity related protein (FTO) and nerve growth factor (NGF) in offspring rats. Methods: In September 2019, 36 healthy 7-week-old Wistar rats were selected, including 24 female rats (150-200 g) and 12 male rats (200-250 g) . The male and female mice were mated in the cage at 2: 1 ratio at 18: 00 every night. The smear results showed that the sperm was positive and the mating was successful. The day was regarded as the 0 day of pregnancy. Pregnant rats were randomly divided into 3 experimental groups and 3 control groups, with 4 rats in each group. The experimental group was exposed to 1 800 MHz, Wi-Fi and 1 800 MHz+Wi-Fi respectively, and the three control groups were exposed to virtual exposure. 12 hours a day for 21 days in three batches. After the end of exposure, the offspring of each group were raised for 7 weeks. The ultrastructural changes of the hippocampus were observed by transmission electron microscopy, the FTO level in the hippocampus was determined by Western blot, and the NGF level in the brain tissue was determined by ELISA. Results: Transmission electron microscopy showed that the nuclei of hippocampal tissue of female and male rats in the 1800 MHz group were slightly contracted, the cytoplasm was slightly edema, and the nuclei of male rats were obviously irregular. In the offspring of male and female rats in the Wi-Fi group, the nucleus of hippocampal tissue contracted seriously, the cell membrane was irregular, and the cytoplasm appeared obvious edema. In the 1800 MHz+Wi-Fi group, the nuclei of hippocampal tissue of both male and female offspring rats were severely contracted, the nuclear membrane was irregular, and the cytoplasm was severely edema. there was no significant difference in FTO level among the groups (P>0.05) . Compared with other groups, NGF content in hippocampus of offspring rats in the 1800 MHz+Wi-Fi group was significantly higher (P<0.05) . Conclusion: Exposure to radio frequency electromagnetic fields will damage the morphological structure of hippocampal tissue of offspring and stimulate the increase of NGF expression in the hippocampus.
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Affiliation(s)
- S Q Y Zhang
- School of Public Health, Kunming Medical University, Kunming 650500, China Kunming Panlong District People's Hospital (Medical Department) , Kunming 650500, China
| | - P P Du
- Community Health Service Center of Changle Square, Beilin District, Xi'an 710000
| | - X Shu
- School of Public Health, Kunming Medical University, Kunming 650500, China
| | - H X Wu
- School of Public Health, Kunming Medical University, Kunming 650500, China
| | - Y Z Mu
- School of Public Health, Kunming Medical University, Kunming 650500, China
| | - X N Wu
- Graduate School, Kunming Medical University, Kunming 650500, China
| | - Y Zhang
- Biomedical Engineering Institute, Kunming Medical University, Kunming 650500, China
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Dubrot J, Du PP, Lane-Reticker SK, Kessler EA, Muscato AJ, Mehta A, Freeman SS, Allen PM, Olander KE, Ockerman KM, Wolfe CH, Wiesmann F, Knudsen NH, Tsao HW, Iracheta-Vellve A, Schneider EM, Rivera-Rosario AN, Kohnle IC, Pope HW, Ayer A, Mishra G, Zimmer MD, Kim SY, Mahapatra A, Ebrahimi-Nik H, Frederick DT, Boland GM, Haining WN, Root DE, Doench JG, Hacohen N, Yates KB, Manguso RT. Abstract 3610: In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3610] [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
The immune system can eliminate tumors, but checkpoints enable tumors to escape immune destruction. Here, we report the systematic identification of immune evasion mechanisms using genome-scale in vivo CRISPR screens in eight murine cancer models treated with immune checkpoint blockade (ICB). We identify and validate previously unreported immune evasion genes and identify key immune inhibitory checkpoints that have a conserved role across several cancer models, such as the non-classical MHC-I molecule Qa-1b/HLA-E, which scores as the top overall sensitizing hit across all screens. Surprisingly, we find that loss of IFNγ signaling by tumor cells sensitizes 6 of 8 cancer models to ICB. While IFN-mediated inflammation has been associated with response to ICB, there have also been reports of ICB-resistance driven by IFN sensing. However, several divergent mechanisms have been proposed to explain the inhibitory effect of tumor IFN sensing, leading to uncertainty about how this key immune signaling pathway is regulating anti-tumor immunity in different contexts. Using in vivo screening data, transcriptional profiling, and genetic interaction studies, we reveal that the immune-inhibitory effects of tumor IFN sensing are the direct result of tumor upregulation of classical and non-classical MHC-I genes. The interferon-MHC-I axis can inhibit anti-tumor immunity through two mechanisms: first, upregulation of classical MHC-I inhibits the cytotoxicity of natural killer cells, which are activated by ICB. Second, IFN-mediated upregulation of Qa-1b directly inhibits cytotoxicity by effector CD8+ T cells via the NKG2A/CD94 receptor, which is induced on CD8+ T cells by ICB. Finally, we show that high interferon-stimulated gene expression in patients is associated with decreased survival in RCC and poor response to ICB in melanoma. Our study establishes a unifying mechanism to explain the inhibitory role of tumor IFN sensing, revealing that IFN-mediated upregulation of classical and non-classical MHC-I inhibitory checkpoints can facilitate immune escape.
Citation Format: Juan Dubrot, Peter P. Du, Sarah Kate Lane-Reticker, Emily A. Kessler, Audrey J. Muscato, Arnav Mehta, Samuel S. Freeman, Peter M. Allen, Kira E. Olander, Kyle M. Ockerman, Clara H. Wolfe, Fabius Wiesmann, Nelson H. Knudsen, Hsiao-Wei Tsao, Arvin Iracheta-Vellve, Emily M. Schneider, Andrea N. Rivera-Rosario, Ian C. Kohnle, Hans W. Pope, Austin Ayer, Gargi Mishra, Margaret D. Zimmer, Sarah Y. Kim, Animesh Mahapatra, Hakimeh Ebrahimi-Nik, Dennie T. Frederick, Genevieve M. Boland, W. Nicholas Haining, David E. Root, John G. Doench, Nir Hacohen, Kathleen B. Yates, Robert T. Manguso. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer [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 3610.
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Du PP, Liu K, Bassik MC, Hess GT. Pathogenic or benign? Nat Biotechnol 2022; 40:834-836. [PMID: 35578021 DOI: 10.1038/s41587-022-01333-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Peter P Du
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Gaelen T Hess
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA. .,Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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Dubrot J, Lane-Reticker SK, Kessler EA, Ayer A, Mishra G, Wolfe CH, Zimmer MD, Du PP, Mahapatra A, Ockerman KM, Davis TGR, Kohnle IC, Pope HW, Allen PM, Olander KE, Iracheta-Vellve A, Doench JG, Haining WN, Yates KB, Manguso RT. In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma. Immunity 2021; 54:571-585.e6. [PMID: 33497609 DOI: 10.1016/j.immuni.2021.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/20/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023]
Abstract
CRISPR-Cas9 genome engineering has increased the pace of discovery for immunology and cancer biology, revealing potential therapeutic targets and providing insight into mechanisms underlying resistance to immunotherapy. However, endogenous immune recognition of Cas9 has limited the applicability of CRISPR technologies in vivo. Here, we characterized immune responses against Cas9 and other expressed CRISPR vector components that cause antigen-specific tumor rejection in several mouse cancer models. To avoid unwanted immune recognition, we designed a lentiviral vector system that allowed selective CRISPR antigen removal (SCAR) from tumor cells. The SCAR system reversed immune-mediated rejection of CRISPR-modified tumor cells in vivo and enabled high-throughput genetic screens in previously intractable models. A pooled in vivo screen using SCAR in a CRISPR-antigen-sensitive renal cell carcinoma revealed resistance pathways associated with autophagy and major histocompatibility complex class I (MHC class I) expression. Thus, SCAR presents a resource that enables CRISPR-based studies of tumor-immune interactions and prevents unwanted immune recognition of genetically engineered cells, with implications for clinical applications.
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Affiliation(s)
- Juan Dubrot
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Emily A Kessler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Austin Ayer
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gargi Mishra
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Clara H Wolfe
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Margaret D Zimmer
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter P Du
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Animesh Mahapatra
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle M Ockerman
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas G R Davis
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian C Kohnle
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hans W Pope
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter M Allen
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kira E Olander
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arvin Iracheta-Vellve
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - W Nicholas Haining
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Division of Pediatric Hematology and Oncology, Children's Hospital, Boston, MA, USA; Merck Research Laboratories, Boston, MA, USA
| | - Kathleen B Yates
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Robert T Manguso
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
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