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Herzfeldt AK, Gamez MP, Martin E, Boryn LM, Baskaran P, Huber HJ, Schuler M, Park JE, Swee LK. Complementary CRISPR screen highlights the contrasting role of membrane-bound and soluble ICAM-1 in regulating antigen-specific tumor cell killing by cytotoxic T cells. eLife 2023; 12:e84314. [PMID: 37732732 PMCID: PMC10586807 DOI: 10.7554/elife.84314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 09/20/2023] [Indexed: 09/22/2023] Open
Abstract
Cytotoxic CD8 +T lymphocytes (CTLs) are key players of adaptive anti-tumor immunity based on their ability to specifically recognize and destroy tumor cells. Many cancer immunotherapies rely on unleashing CTL function. However, tumors can evade killing through strategies which are not yet fully elucidated. To provide deeper insight into tumor evasion mechanisms in an antigen-dependent manner, we established a human co-culture system composed of tumor and primary immune cells. Using this system, we systematically investigated intrinsic regulators of tumor resistance by conducting a complementary CRISPR screen approach. By harnessing CRISPR activation (CRISPRa) and CRISPR knockout (KO) technology in parallel, we investigated gene gain-of-function as well as loss-of-function across genes with annotated function in a colon carcinoma cell line. CRISPRa and CRISPR KO screens uncovered 187 and 704 hits, respectively, with 60 gene hits overlapping between both. These data confirmed the role of interferon-γ (IFN-γ), tumor necrosis factor α (TNF-α) and autophagy pathways and uncovered novel genes implicated in tumor resistance to killing. Notably, we discovered that ILKAP encoding the integrin-linked kinase-associated serine/threonine phosphatase 2 C, a gene previously unknown to play a role in antigen specific CTL-mediated killing, mediate tumor resistance independently from regulating antigen presentation, IFN-γ or TNF-α responsiveness. Moreover, our work describes the contrasting role of soluble and membrane-bound ICAM-1 in regulating tumor cell killing. The deficiency of membrane-bound ICAM-1 (mICAM-1) or the overexpression of soluble ICAM-1 (sICAM-1) induced resistance to CTL killing, whereas PD-L1 overexpression had no impact. These results highlight the essential role of ICAM-1 at the immunological synapse between tumor and CTL and the antagonist function of sICAM-1.
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Affiliation(s)
- Ann-Kathrin Herzfeldt
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Marta Puig Gamez
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Eva Martin
- Department of Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | | | - Praveen Baskaran
- Department of Global Computational Biology and Digital Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - Heinrich J Huber
- Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - Michael Schuler
- Department of Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - John E Park
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Lee Kim Swee
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
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Benaoudia S, Martin A, Puig Gamez M, Gay G, Lagrange B, Cornut M, Krasnykov K, Claude J, Bourgeois CF, Hughes S, Gillet B, Allatif O, Corbin A, Ricci R, Henry T. A genome-wide screen identifies IRF2 as a key regulator of caspase-4 in human cells. EMBO Rep 2019; 20:e48235. [PMID: 31353801 PMCID: PMC6727027 DOI: 10.15252/embr.201948235] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [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: 04/05/2019] [Revised: 07/01/2019] [Accepted: 07/10/2019] [Indexed: 12/12/2022] Open
Abstract
Caspase-4, the cytosolic LPS sensor, and gasdermin D, its downstream effector, constitute the non-canonical inflammasome, which drives inflammatory responses during Gram-negative bacterial infections. It remains unclear whether other proteins regulate cytosolic LPS sensing, particularly in human cells. Here, we conduct a genome-wide CRISPR/Cas9 screen in a human monocyte cell line to identify genes controlling cytosolic LPS-mediated pyroptosis. We find that the transcription factor, IRF2, is required for pyroptosis following cytosolic LPS delivery and functions by directly regulating caspase-4 levels in human monocytes and iPSC-derived monocytes. CASP4, GSDMD, and IRF2 are the only genes identified with high significance in this screen highlighting the simplicity of the non-canonical inflammasome. Upon IFN-γ priming, IRF1 induction compensates IRF2 deficiency, leading to robust caspase-4 expression. Deficiency in IRF2 results in dampened inflammasome responses upon infection with Gram-negative bacteria. This study emphasizes the central role of IRF family members as specific regulators of the non-canonical inflammasome.
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Affiliation(s)
- Sacha Benaoudia
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonUniv LyonLyonFrance
| | - Amandine Martin
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonUniv LyonLyonFrance
| | - Marta Puig Gamez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)Centre National de la Recherche Scientifique, UMR 7104Institut National de la Santé et de la Recherche Médicale U964Université de StrasbourgIllkirchFrance
- Laboratoire de Biochimie et de Biologie MoléculaireNouvel Hôpital CivilStrasbourgFrance
- Université de StrasbourgStrasbourgFrance
- INGESTEM National iPSC InfrastructureVillejuifFrance
| | - Gabrielle Gay
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonUniv LyonLyonFrance
| | - Brice Lagrange
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonUniv LyonLyonFrance
| | - Maxence Cornut
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonUniv LyonLyonFrance
| | - Kyrylo Krasnykov
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonUniv LyonLyonFrance
| | - Jean‐Baptiste Claude
- LBMC, Laboratoire de Biologie et Modélisation de la celluleUniversité Claude Bernard Lyon 1INSERM U1210, CNRS, UMR5239École Normale Supérieure de LyonUniv LyonLyonFrance
| | - Cyril F Bourgeois
- LBMC, Laboratoire de Biologie et Modélisation de la celluleUniversité Claude Bernard Lyon 1INSERM U1210, CNRS, UMR5239École Normale Supérieure de LyonUniv LyonLyonFrance
| | - Sandrine Hughes
- Sequencing PlatformInstitut de Génomique Fonctionnelle de Lyon (IGFL)Université Claude Bernard Lyon 1, CNRS, UMR5242École Normale Supérieure de LyonUniv LyonLyonFrance
| | - Benjamin Gillet
- Sequencing PlatformInstitut de Génomique Fonctionnelle de Lyon (IGFL)Université Claude Bernard Lyon 1, CNRS, UMR5242École Normale Supérieure de LyonUniv LyonLyonFrance
| | - Omran Allatif
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonUniv LyonLyonFrance
- BIBS, Bioinformatic and Biostatic ServicesCIRILyonFrance
| | - Antoine Corbin
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonUniv LyonLyonFrance
- BIBS, Bioinformatic and Biostatic ServicesCIRILyonFrance
| | - Romeo Ricci
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)Centre National de la Recherche Scientifique, UMR 7104Institut National de la Santé et de la Recherche Médicale U964Université de StrasbourgIllkirchFrance
- Laboratoire de Biochimie et de Biologie MoléculaireNouvel Hôpital CivilStrasbourgFrance
- Université de StrasbourgStrasbourgFrance
- INGESTEM National iPSC InfrastructureVillejuifFrance
| | - Thomas Henry
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonUniv LyonLyonFrance
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