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Chen B, Deng Y, Ren X, Zhao J, Jiang C. CRISPR/Cas9 screening: unraveling cancer immunotherapy's 'Rosetta Stone'. Trends Mol Med 2024; 30:736-749. [PMID: 38763850 DOI: 10.1016/j.molmed.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/10/2024] [Accepted: 04/19/2024] [Indexed: 05/21/2024]
Abstract
Clustered regularly interspaced palindromic repeats (CRISPR)-based technology, a powerful toolset for the unbiased functional genomic screening of biological processes, has facilitated several scientific breakthroughs in the biomedical field. Cancer immunotherapy has advanced the treatment of numerous malignancies that previously had restricted treatment options or unfavorable outcomes. In the realm of cancer immunotherapy, the application of CRISPR/CRISPR-associated protein 9 (Cas9)-based genetic perturbation screening has enabled the identification of genes, biomarkers, and signaling pathways that govern various cancer immunoreactivities, as well as the development of effective immunotherapeutic targets. In this review, we summarize the advances in CRISPR/Cas9-based screening for cancer immunotherapy and outline the immunotherapeutic targets identified via CRISPR screening based on cancer-type classification.
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Affiliation(s)
- Baoxiang Chen
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Hubei Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3G 0B1, Canada
| | - Yanrong Deng
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Hubei Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xianghai Ren
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Hubei Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
| | - Jianhong Zhao
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Hubei Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
| | - Congqing Jiang
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Hubei Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
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2
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Witalisz-Siepracka A, Denk CM, Zdársky B, Hofmann L, Edtmayer S, Harm T, Weiss S, Heindl K, Hessenberger M, Summer S, Dutta S, Casanova E, Obermair GJ, Győrffy B, Putz EM, Sill H, Stoiber D. STAT3 in acute myeloid leukemia facilitates natural killer cell-mediated surveillance. Front Immunol 2024; 15:1374068. [PMID: 39034990 PMCID: PMC11257888 DOI: 10.3389/fimmu.2024.1374068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024] Open
Abstract
Acute myeloid leukemia (AML) is a heterogenous disease characterized by the clonal expansion of myeloid progenitor cells. Despite recent advancements in the treatment of AML, relapse still remains a significant challenge, necessitating the development of innovative therapies to eliminate minimal residual disease. One promising approach to address these unmet clinical needs is natural killer (NK) cell immunotherapy. To implement such treatments effectively, it is vital to comprehend how AML cells escape the NK-cell surveillance. Signal transducer and activator of transcription 3 (STAT3), a component of the Janus kinase (JAK)-STAT signaling pathway, is well-known for its role in driving immune evasion in various cancer types. Nevertheless, the specific function of STAT3 in AML cell escape from NK cells has not been deeply investigated. In this study, we unravel a novel role of STAT3 in sensitizing AML cells to NK-cell surveillance. We demonstrate that STAT3-deficient AML cell lines are inefficiently eliminated by NK cells. Mechanistically, AML cells lacking STAT3 fail to form an immune synapse as efficiently as their wild-type counterparts due to significantly reduced surface expression of intercellular adhesion molecule 1 (ICAM-1). The impaired killing of STAT3-deficient cells can be rescued by ICAM-1 overexpression proving its central role in the observed phenotype. Importantly, analysis of our AML patient cohort revealed a positive correlation between ICAM1 and STAT3 expression suggesting a predominant role of STAT3 in ICAM-1 regulation in this disease. In line, high ICAM1 expression correlates with better survival of AML patients underscoring the translational relevance of our findings. Taken together, our data unveil a novel role of STAT3 in preventing AML cells from escaping NK-cell surveillance and highlight the STAT3/ICAM-1 axis as a potential biomarker for NK-cell therapies in AML.
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Affiliation(s)
- Agnieszka Witalisz-Siepracka
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Clio-Melina Denk
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Bernhard Zdársky
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Lorenz Hofmann
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Sophie Edtmayer
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Theresa Harm
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Stefanie Weiss
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Kerstin Heindl
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Manuel Hessenberger
- Division Physiology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Sabrina Summer
- Department for Biomedical Research, University for Continuing Education Krems, Krems, Austria
| | | | - Emilio Casanova
- Institute of Pharmacology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC), Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Gerald J. Obermair
- Division Physiology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
- Cancer Biomarker Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Eva Maria Putz
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Heinz Sill
- Division of Hematology, Medical University of Graz, Graz, Austria
| | - Dagmar Stoiber
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria
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3
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Grothusen GP, Chang R, Cao Z, Zhou N, Mittal M, Datta A, Wulfridge P, Beer T, Wang B, Zheng N, Tang HY, Sarma K, Greenberg RA, Shi J, Busino L. DCAF15 control of cohesin dynamics sustains acute myeloid leukemia. Nat Commun 2024; 15:5604. [PMID: 38961054 PMCID: PMC11222469 DOI: 10.1038/s41467-024-49882-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/21/2024] [Indexed: 07/05/2024] Open
Abstract
The CRL4-DCAF15 E3 ubiquitin ligase complex is targeted by the aryl-sulfonamide molecular glues, leading to neo-substrate recruitment, ubiquitination, and proteasomal degradation. However, the physiological function of DCAF15 remains unknown. Using a domain-focused genetic screening approach, we reveal DCAF15 as an acute myeloid leukemia (AML)-biased dependency. Loss of DCAF15 results in suppression of AML through compromised replication fork integrity and consequent accumulation of DNA damage. Accordingly, DCAF15 loss sensitizes AML to replication stress-inducing therapeutics. Mechanistically, we discover that DCAF15 directly interacts with the SMC1A protein of the cohesin complex and destabilizes the cohesin regulatory factors PDS5A and CDCA5. Loss of PDS5A and CDCA5 removal precludes cohesin acetylation on chromatin, resulting in uncontrolled chromatin loop extrusion, defective DNA replication, and apoptosis. Collectively, our findings uncover an endogenous, cell autonomous function of DCAF15 in sustaining AML proliferation through post-translational control of cohesin dynamics.
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Affiliation(s)
- Grant P Grothusen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Renxu Chang
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhendong Cao
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nan Zhou
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Monika Mittal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arindam Datta
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phillip Wulfridge
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Thomas Beer
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Baiyun Wang
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Kavitha Sarma
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luca Busino
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Hofman T, Ng SW, Garcés-Lázaro I, Heigwer F, Boutros M, Cerwenka A. IFNγ mediates the resistance of tumor cells to distinct NK cell subsets. J Immunother Cancer 2024; 12:e009410. [PMID: 38955423 PMCID: PMC11218003 DOI: 10.1136/jitc-2024-009410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Immune checkpoint blockade targeting the adaptive immune system has revolutionized the treatment of cancer. Despite impressive clinical benefits observed, patient subgroups remain non-responsive underscoring the necessity for combinational therapies harnessing additional immune cells. Natural killer (NK) cells are emerging tools for cancer therapy. However, only subpopulations of NK cells that are differentially controlled by inhibitory receptors exert reactivity against particular cancer types. How to leverage the complete anti-tumor potential of all NK cell subsets without favoring the emergence of NK cell-resistant tumor cells remains unresolved. METHODS We performed a genome-wide CRISPR/Cas9 knockout resistance screen in melanoma cells in co-cultures with human primary NK cells. We comprehensively evaluated factors regulating tumor resistance and susceptibility by focusing on NK cell subsets in an allogenic setting. Moreover, we tested therapeutic blocking antibodies currently used in clinical trials. RESULTS Melanoma cells deficient in antigen-presenting or the IFNγ-signaling pathways were depleted in remaining NK cell-co-cultured melanoma cells and displayed enhanced sensitivity to NK cells. Treatment with IFNγ induced potent resistance of melanoma cells to resting, IL-2-cultured and ADCC-activated NK cells that depended on B2M required for the expression of both classical and non-classical MHC-I. IFNγ-induced expression of HLA-E mediated the resistance of melanoma cells to the NKG2A+ KIR- and partially to the NKG2A+ KIR+ NK cell subset. The expression of classical MHC-I by itself was sufficient for the inhibition of the NKG2A- KIR+, but not the NKG2A+ KIR+ NK cell subset. Treatment of NK cells with monalizumab, an NKG2A blocking mAb, enhanced the reactivity of a corresponding subset of NK cells. The combination of monalizumab with lirilumab, blocking KIR2 receptors, together with DX9, blocking KIR3DL1, was required to restore cytotoxicity of all NK cell subsets against IFNγ-induced resistant tumor cells in melanoma and tumors of different origins. CONCLUSION Our data reveal that in the context of NK cells, IFNγ induces the resistance of tumor cells by the upregulation of classical and non-classical MHC-I. Moreover, we reveal insights into NK cell subset reactivity and propose a therapeutic strategy involving combinational monalizumab/lirilumab/DX9 treatment to fully restore the antitumor response across NK cell subsets.
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Affiliation(s)
- Tomáš Hofman
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Siu Wang Ng
- Signalling and Functional Genomics, German Cancer Research Centre, Heidelberg, Germany
| | - Irene Garcés-Lázaro
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Florian Heigwer
- Signalling and Functional Genomics, German Cancer Research Centre, Heidelberg, Germany
- Department of Life Sciences and Engineering, University of Applied Sciences Bingen, Bingen am Rhein, Germany
| | - Michael Boutros
- Signalling and Functional Genomics, German Cancer Research Centre, Heidelberg, Germany
| | - Adelheid Cerwenka
- Department of Immunobiochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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5
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Vacchini A, Chancellor A, Yang Q, Colombo R, Spagnuolo J, Berloffa G, Joss D, Øyås O, Lecchi C, De Simone G, Beshirova A, Nosi V, Loureiro JP, Morabito A, De Gregorio C, Pfeffer M, Schaefer V, Prota G, Zippelius A, Stelling J, Häussinger D, Brunelli L, Villalta P, Lepore M, Davoli E, Balbo S, Mori L, De Libero G. Nucleobase adducts bind MR1 and stimulate MR1-restricted T cells. Sci Immunol 2024; 9:eadn0126. [PMID: 38728413 DOI: 10.1126/sciimmunol.adn0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024]
Abstract
MR1T cells are a recently found class of T cells that recognize antigens presented by the major histocompatibility complex-I-related molecule MR1 in the absence of microbial infection. The nature of the self-antigens that stimulate MR1T cells remains unclear, hampering our understanding of their physiological role and therapeutic potential. By combining genetic, pharmacological, and biochemical approaches, we found that carbonyl stress and changes in nucleobase metabolism in target cells promote MR1T cell activation. Stimulatory compounds formed by carbonyl adducts of nucleobases were detected within MR1 molecules produced by tumor cells, and their abundance and antigenicity were enhanced by drugs that induce carbonyl accumulation. Our data reveal carbonyl-nucleobase adducts as MR1T cell antigens. Recognizing cells under carbonyl stress allows MR1T cells to monitor cellular metabolic changes with physiological and therapeutic implications.
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Affiliation(s)
- Alessandro Vacchini
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Andrew Chancellor
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Qinmei Yang
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Rodrigo Colombo
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Julian Spagnuolo
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Giuliano Berloffa
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, Basel 4056, Switzerland
| | - Ove Øyås
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel 4058, Switzerland
| | - Chiara Lecchi
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Giulia De Simone
- Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano 20156, Italy
| | - Aisha Beshirova
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Vladimir Nosi
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - José Pedro Loureiro
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Aurelia Morabito
- Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano 20156, Italy
| | - Corinne De Gregorio
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Michael Pfeffer
- Department of Chemistry, University of Basel, Basel 4056, Switzerland
| | - Verena Schaefer
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Gennaro Prota
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Alfred Zippelius
- Cancer Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel 4058, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, Basel 4056, Switzerland
| | - Laura Brunelli
- Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano 20156, Italy
| | - Peter Villalta
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Marco Lepore
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Enrico Davoli
- Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano 20156, Italy
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lucia Mori
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
| | - Gennaro De Libero
- Experimental Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel 4031, Switzerland
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6
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Martin KE, Hammer Q, Perica K, Sadelain M, Malmberg KJ. Engineering immune-evasive allogeneic cellular immunotherapies. Nat Rev Immunol 2024:10.1038/s41577-024-01022-8. [PMID: 38658708 DOI: 10.1038/s41577-024-01022-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2024] [Indexed: 04/26/2024]
Abstract
Allogeneic cellular immunotherapies hold a great promise for cancer treatment owing to their potential cost-effectiveness, scalability and on-demand availability. However, immune rejection of adoptively transferred allogeneic T and natural killer (NK) cells is a substantial obstacle to achieving clinical responses that are comparable to responses obtained with current autologous chimeric antigen receptor T cell therapies. In this Perspective, we discuss strategies to confer cell-intrinsic, immune-evasive properties to allogeneic T cells and NK cells in order to prevent or delay their immune rejection, thereby widening the therapeutic window. We discuss how common viral and cancer immune escape mechanisms can serve as a blueprint for improving the persistence of off-the-shelf allogeneic cell therapies. The prospects of harnessing genome editing and synthetic biology to design cell-based precision immunotherapies extend beyond programming target specificities and require careful consideration of innate and adaptive responses in the recipient that may curtail the biodistribution, in vivo expansion and persistence of cellular therapeutics.
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Affiliation(s)
- Karen E Martin
- Precision Immunotherapy Alliance, The University of Oslo, Oslo, Norway
- Department of Cancer Immunology, Institute for Cancer Research Oslo, Oslo University Hospital, Oslo, Norway
| | - Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Karlo Perica
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karl-Johan Malmberg
- Precision Immunotherapy Alliance, The University of Oslo, Oslo, Norway.
- Department of Cancer Immunology, Institute for Cancer Research Oslo, Oslo University Hospital, Oslo, Norway.
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
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7
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Kristenson L, Badami C, Ljungberg A, Islamagic E, Tian Y, Xie G, Hussein BA, Pesce S, Tang KW, Thorén FB. Deletion of the TMEM30A gene enables leukemic cell evasion of NK cell cytotoxicity. Proc Natl Acad Sci U S A 2024; 121:e2316447121. [PMID: 38557174 PMCID: PMC11009675 DOI: 10.1073/pnas.2316447121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
Natural killer (NK) cell immunotherapy has gained attention as a promising strategy for treatment of various malignancies. In this study, we used a genome-wide CRISPR screen to identify genes that provide protection or susceptibility to NK cell cytotoxicity. The screen confirmed the role of several genes in NK cell regulation, such as genes involved in interferon-γ signaling and antigen presentation, as well as genes encoding the NK cell receptor ligands B7-H6 and CD58. Notably, the gene TMEM30A, encoding CDC50A-beta-subunit of the flippase shuttling phospholipids in the plasma membrane, emerged as crucial for NK cell killing. Accordingly, a broad range of TMEM30A knock-out (KO) leukemia and lymphoma cells displayed increased surface levels of phosphatidylserine (PtdSer). TMEM30A KO cells triggered less NK cell degranulation, cytokine production and displayed lower susceptibility to NK cell cytotoxicity. Blockade of PtdSer or the inhibitory receptor TIM-3, restored the NK cell ability to eliminate TMEM30A-mutated cells. The key role of the TIM-3 - PtdSer interaction for NK cell regulation was further substantiated by disruption of the receptor gene in primary NK cells, which significantly reduced the impact of elevated PtdSer in TMEM30A KO leukemic cells. Our study underscores the potential significance of agents targeting the interaction between PtdSer and TIM-3 in the realm of cancer immunotherapy.
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Affiliation(s)
- Linnea Kristenson
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
| | - Chiara Badami
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
| | - Angelica Ljungberg
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
| | - Erna Islamagic
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
| | - Yarong Tian
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 46, Sweden
| | - Guojiang Xie
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 46, Sweden
| | - Brwa Ali Hussein
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
| | - Silvia Pesce
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Dipartimento di Medicina Sperimentale, Università di Genova, Genoa16132, Italy
| | - Ka-Wei Tang
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 46, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg413 46, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg413 90, Sweden
| | - Fredrik B. Thorén
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
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8
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Singh S, Fang J, Jin H, Van de Velde LA, Wu Q, Cortes A, Morton CL, Woolard MA, Quarni W, Steele JA, Connelly JP, He L, Thorne R, Turner G, Confer T, Johnson M, Caufield WV, Freeman BB, Lockey T, Pruett-Miller SM, Wang R, Davidoff AM, Thomas PG, Yang J. RBM39 degrader invigorates natural killer cells to eradicate neuroblastoma despite cancer cell plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586157. [PMID: 38585889 PMCID: PMC10996557 DOI: 10.1101/2024.03.21.586157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The cellular plasticity of neuroblastoma is defined by a mixture of two major cell states, adrenergic (ADRN) and mesenchymal (MES), which may contribute to therapy resistance. However, how neuroblastoma cells switch cellular states during therapy remains largely unknown and how to eradicate neuroblastoma regardless of their cell states is a clinical challenge. To better understand the lineage switch of neuroblastoma in chemoresistance, we comprehensively defined the transcriptomic and epigenetic map of ADRN and MES types of neuroblastomas using human and murine models treated with indisulam, a selective RBM39 degrader. We showed that cancer cells not only undergo a bidirectional switch between ADRN and MES states, but also acquire additional cellular states, reminiscent of the developmental pliancy of neural crest cells. The lineage alterations are coupled with epigenetic reprogramming and dependency switch of lineage-specific transcription factors, epigenetic modifiers and targetable kinases. Through targeting RNA splicing, indisulam induces an inflammatory tumor microenvironment and enhances anticancer activity of natural killer cells. The combination of indisulam with anti-GD2 immunotherapy results in a durable, complete response in high-risk transgenic neuroblastoma models, providing an innovative, rational therapeutic approach to eradicate tumor cells regardless of their potential to switch cell states.
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9
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Choy L, Norris S, Wu X, Kolumam G, Firestone A, Settleman J, Stokoe D. Inhibition of Aurora Kinase Induces Endogenous Retroelements to Induce a Type I/III IFN Response via RIG-I. CANCER RESEARCH COMMUNICATIONS 2024; 4:540-555. [PMID: 38358346 PMCID: PMC10896070 DOI: 10.1158/2767-9764.crc-23-0432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/20/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Type I IFN signaling is a crucial component of antiviral immunity that has been linked to promoting the efficacy of some chemotherapeutic drugs. We developed a reporter system in HCT116 cells that detects activation of the endogenous IFI27 locus, an IFN target gene. We screened a library of annotated compounds in these cells and discovered Aurora kinase inhibitors (AURKi) as strong hits. Type I IFN signaling was found to be the most enriched gene signature after AURKi treatment in HCT116, and this signature was also strongly enriched in other colorectal cancer cell lines. The ability of AURKi to activate IFN in HCT116 was dependent on MAVS and RIG-I, but independent of STING, whose signaling is deficient in these cells. MAVS dependence was recapitulated in other colorectal cancer lines with STING pathway deficiency, whereas in cells with intact STING signaling, the STING pathway was required for IFN induction by AURKi. AURKis were found to induce expression of endogenous retroviruses (ERV). These ERVs were distinct from those induced by the DNA methyltransferase inhibitors (DNMTi), which can induce IFN signaling via ERV induction, suggesting a novel mechanism of action. The antitumor effect of alisertib in mice was accompanied by an induction of IFN expression in HCT116 or CT26 tumors. CT26 tumor growth inhibition by alisertib was absent in NSG mice versus wildtype (WT) mice, and tumors from WT mice with alisertib treatment showed increased in CD8+ T-cell infiltration, suggesting that antitumor efficacy of AURKi depends, at least in part, on an intact immune response. SIGNIFICANCE Some cancers deactivate STING signaling to avoid consequences of DNA damage from aberrant cell division. The surprising activation of MAVS/RIG-I signaling by AURKi might represent a vulnerability in STING signaling deficient cancers.
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Affiliation(s)
- Lisa Choy
- Calico Life Sciences LLC, South San Francisco, California
| | - Stephen Norris
- Calico Life Sciences LLC, South San Francisco, California
| | - Xiumin Wu
- Calico Life Sciences LLC, South San Francisco, California
| | - Ganesh Kolumam
- Calico Life Sciences LLC, South San Francisco, California
| | - Ari Firestone
- Calico Life Sciences LLC, South San Francisco, California
| | | | - David Stokoe
- Calico Life Sciences LLC, South San Francisco, California
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10
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Lee SY, Park SY, Park HJ. Immuno-Enhancing Effects of Galium aparine L. in Cyclophosphamide-Induced Immunosuppressed Animal Models. Nutrients 2024; 16:597. [PMID: 38474724 DOI: 10.3390/nu16050597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
This study investigates the immunomodulatory potential of Galium aparine L. (GAE) in immunodeficient animals. In this study, animals were categorized into five groups: the normal group, CYP group (cyclophosphamide intraperitoneal injection), GA5 group (cyclophosphamide + 5 μg GAE), GA50 group (cyclophosphamide + 50 μg GAE), and GA500 group (cyclophosphamide + 500 μg GAE). The CYP group exhibited significantly reduced spleen weights compared to the normal group, while the groups obtaining GAE displayed a dose-dependent increase in spleen weight. Furthermore, the GAE demonstrated dose-dependent enhancement of splenocyte proliferating activity, with significant increases observed in both LPS and ConA-induced assays. NK cell activity significantly increased in the GA50 and GA500 groups compared to the CYP group. Cytokine analysis revealed a significant increase in IL-6, TNF-α, and IFN-γ levels in ConA-induced splenocytes treated with GAE. Gene expression analysis identified 2434 DEG genes in the extract groups. Notable genes, such as Entpd1, Pgf, Thdb, Syt7, Sqor, and Rsc1al, displayed substantial differences in individual gene expression levels, suggesting their potential as target genes for immune enhancement. In conclusion, Galium aparine L. extract exhibits immunomodulatory properties. The observed gene expression changes further support the potential of Galium aparine L. extract as a natural agent for immune augmentation.
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Affiliation(s)
- Seo-Yeon Lee
- Department Foodservice Management and Nutrition, Sangmyung University, Seoul 03016, Republic of Korea
| | - Seo-Yeon Park
- Department Foodservice Management and Nutrition, Sangmyung University, Seoul 03016, Republic of Korea
| | - Hee-Jung Park
- Department Foodservice Management and Nutrition, Sangmyung University, Seoul 03016, Republic of Korea
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11
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Liu J, Xing L, Li J, Wen K, Liu N, Liu Y, Wu G, Wang S, Ogiya D, Song TY, Kurata K, Penailillo J, Morelli E, Wang T, Hong X, Gulla A, Tai YT, Munshi N, Richardson P, Carrasco R, Hideshima T, Anderson KC. Epigenetic regulation of CD38/CD48 by KDM6A mediates NK cell response in multiple myeloma. Nat Commun 2024; 15:1367. [PMID: 38355622 PMCID: PMC10866908 DOI: 10.1038/s41467-024-45561-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Anti-CD38 monoclonal antibodies like Daratumumab (Dara) are effective in multiple myeloma (MM); however, drug resistance ultimately occurs and the mechanisms behind this are poorly understood. Here, we identify, via two in vitro genome-wide CRISPR screens probing Daratumumab resistance, KDM6A as an important regulator of sensitivity to Daratumumab-mediated antibody-dependent cellular cytotoxicity (ADCC). Loss of KDM6A leads to increased levels of H3K27me3 on the promoter of CD38, resulting in a marked downregulation in CD38 expression, which may cause resistance to Daratumumab-mediated ADCC. Re-introducing CD38 does not reverse Daratumumab-mediated ADCC fully, which suggests that additional KDM6A targets, including CD48 which is also downregulated upon KDM6A loss, contribute to Daratumumab-mediated ADCC. Inhibition of H3K27me3 with an EZH2 inhibitor resulted in CD38 and CD48 upregulation and restored sensitivity to Daratumumab. These findings suggest KDM6A loss as a mechanism of Daratumumab resistance and lay down the proof of principle for the therapeutic application of EZH2 inhibitors, one of which is already FDA-approved, in improving MM responsiveness to Daratumumab.
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Affiliation(s)
- Jiye Liu
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Lijie Xing
- Department of Hematology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Jiang Li
- Clinical Big Data Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Kenneth Wen
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ning Liu
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Marine Bio-Pharmacology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Yuntong Liu
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gongwei Wu
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Su Wang
- Vertex pharmaceuticals, Boston, MA, 02210, USA
| | - Daisuke Ogiya
- Department of Hematology and Oncology, School of Medicine, Tokai University, Isehara, 259-1193, Japan
| | - Tian-Yu Song
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Keiji Kurata
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Johany Penailillo
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Eugenio Morelli
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tingjian Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Annamaria Gulla
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO), 10060, Italy
| | - Yu-Tzu Tai
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Nikhil Munshi
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Paul Richardson
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ruben Carrasco
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Teru Hideshima
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kenneth C Anderson
- Jerome Lipper Multiple Myeloma Center, Lebow Institute for Myeloma Therapeutics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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12
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Dufva O, Gandolfi S, Huuhtanen J, Dashevsky O, Duàn H, Saeed K, Klievink J, Nygren P, Bouhlal J, Lahtela J, Näätänen A, Ghimire BR, Hannunen T, Ellonen P, Lähteenmäki H, Rumm P, Theodoropoulos J, Laajala E, Härkönen J, Pölönen P, Heinäniemi M, Hollmén M, Yamano S, Shirasaki R, Barbie DA, Roth JA, Romee R, Sheffer M, Lähdesmäki H, Lee DA, De Matos Simoes R, Kankainen M, Mitsiades CS, Mustjoki S. Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers. Immunity 2023; 56:2816-2835.e13. [PMID: 38091953 DOI: 10.1016/j.immuni.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/19/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Cancer cells can evade natural killer (NK) cell activity, thereby limiting anti-tumor immunity. To reveal genetic determinants of susceptibility to NK cell activity, we examined interacting NK cells and blood cancer cells using single-cell and genome-scale functional genomics screens. Interaction of NK and cancer cells induced distinct activation and type I interferon (IFN) states in both cell types depending on the cancer cell lineage and molecular phenotype, ranging from more sensitive myeloid to less sensitive B-lymphoid cancers. CRISPR screens in cancer cells uncovered genes regulating sensitivity and resistance to NK cell-mediated killing, including adhesion-related glycoproteins, protein fucosylation genes, and transcriptional regulators, in addition to confirming the importance of antigen presentation and death receptor signaling pathways. CRISPR screens with a single-cell transcriptomic readout provided insight into underlying mechanisms, including regulation of IFN-γ signaling in cancer cells and NK cell activation states. Our findings highlight the diversity of mechanisms influencing NK cell susceptibility across different cancers and provide a resource for NK cell-based therapies.
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Affiliation(s)
- Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Sara Gandolfi
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hanna Duàn
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Khalid Saeed
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Petra Nygren
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jonas Bouhlal
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Anna Näätänen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Bishwa R Ghimire
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Tiina Hannunen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Hanna Lähteenmäki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Pauliina Rumm
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Essi Laajala
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jouni Härkönen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Petri Pölönen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Merja Heinäniemi
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Maija Hollmén
- Medicity Research Laboratory, University of Turku, 20014 Turku, Finland
| | - Shizuka Yamano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Dean A Lee
- Hematology/Oncology/BMT, Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Ricardo De Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Matti Kankainen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusima (HUS), 00290 Helsinki, Finland
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland.
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13
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Sudholz H, Delconte RB, Huntington ND. Interleukin-15 cytokine checkpoints in natural killer cell anti-tumor immunity. Curr Opin Immunol 2023; 84:102364. [PMID: 37451129 DOI: 10.1016/j.coi.2023.102364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Over recent years, the use of immune checkpoint inhibitors (ICI) has progressed to first and second-line treatments in several cancer types, transforming patient outcomes. While these treatments target T cell checkpoints, such as PD-1, LAG3 and CTLA-4, their efficacy can be compromised through adaptive resistance whereby tumors acquire mutations in genes regulating neoantigen presentation by MHC-I [93]. ICI-responsive tumor types such as advanced metastatic melanoma typically have a high mutational burden and immune infiltration; however, most patients still do not benefit from ICI monotherapy for a number of reasons [94]. This highlights the need for novel immunotherapy strategies that evoke the immune control of tumor cells with low neoantigen/MHC-I expression, overcome immune suppressive tumor microenvironments and promote tumor inflammation. In this regard, targeting natural killer (NK) cells may offer a solution to some of these bottlenecks.
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Affiliation(s)
- Harrison Sudholz
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rebecca B Delconte
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York 10065, USA
| | - Nicholas D Huntington
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; oNKo-Innate Pty Ltd, Moonee Ponds, Victoria 3039, Australia.
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14
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Tharp KM, Park S, Timblin GA, Richards AL, Berg JA, Twells NM, Riley NM, Peltan EL, Shon DJ, Stevenson E, Tsui K, Palomba F, Lefebvre AEYT, Soens RW, Ayad NM, Hoeve-Scott JT, Healy K, Digman M, Dillin A, Bertozzi CR, Swaney DL, Mahal LK, Cantor JR, Paszek MJ, Weaver VM. The microenvironment dictates glycocalyx construction and immune surveillance. RESEARCH SQUARE 2023:rs.3.rs-3164966. [PMID: 37645943 PMCID: PMC10462183 DOI: 10.21203/rs.3.rs-3164966/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Efforts to identify anti-cancer therapeutics and understand tumor-immune interactions are built with in vitro models that do not match the microenvironmental characteristics of human tissues. Using in vitro models which mimic the physical properties of healthy or cancerous tissues and a physiologically relevant culture medium, we demonstrate that the chemical and physical properties of the microenvironment regulate the composition and topology of the glycocalyx. Remarkably, we find that cancer and age-related changes in the physical properties of the microenvironment are sufficient to adjust immune surveillance via the topology of the glycocalyx, a previously unknown phenomenon observable only with a physiologically relevant culture medium.
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Affiliation(s)
- Kevin M. Tharp
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Sangwoo Park
- Field of Biophysics, Cornell University, Ithaca, NY 14850, USA
| | - Greg A. Timblin
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alicia L. Richards
- Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jordan A. Berg
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Nicholas M. Twells
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Nicholas M. Riley
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Egan L. Peltan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA USA 94305
- Sarafan ChEM-H, Stanford University, Stanford, CA USA 94305
| | - D. Judy Shon
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Erica Stevenson
- Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kimberly Tsui
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94597, USA
| | - Francesco Palomba
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, CA 92697, USA
| | | | - Ross W. Soens
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nadia M.E. Ayad
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Johanna ten Hoeve-Scott
- UCLA Metabolomics Center, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Kevin Healy
- Department of Chemical and Systems Biology, Sarafan ChEM-H and Howard Hughes Medical Institute, Stanford University, Stanford, CA USA 94305
| | - Michelle Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, CA 92697, USA
| | - Andrew Dillin
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94597, USA
| | - Carolyn R. Bertozzi
- Department of Chemical and Systems Biology, Sarafan ChEM-H and Howard Hughes Medical Institute, Stanford University, Stanford, CA USA 94305
| | - Danielle L. Swaney
- Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Lara K. Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Jason R. Cantor
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry and Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew J. Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, Department of Radiation Oncology, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, CA 94143, USA
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15
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Coomar S, Mota P, Penson A, Schwaller J, Abdel-Wahab O, Gillingham D. Overlaid Transcriptional and Proteome Analyses Identify Mitotic Kinesins as Important Targets of Arylsulfonamide-Mediated RBM39 Degradation. Mol Cancer Res 2023; 21:768-778. [PMID: 37255411 PMCID: PMC10395616 DOI: 10.1158/1541-7786.mcr-22-0541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/16/2023] [Accepted: 05/09/2023] [Indexed: 05/14/2023]
Abstract
Certain arylsulfonamides (ArSulf) induce an interaction between the E3 ligase substrate adaptor DCAF15 and the critical splicing factor RBM39, ultimately causing its degradation. However, degradation of a splicing factor introduces complex pleiotropic effects that are difficult to untangle, since, aside from direct protein degradation, downstream transcriptional effects also influence the proteome. By overlaying transcriptional data and proteome datasets, we distinguish transcriptional from direct degradation effects, pinpointing those proteins most impacted by splicing changes. Using our workflow, we identify and validate the upregulation of the arginine-and-serine rich protein (RSRP1) and the downregulation of the key kinesin motor proteins KIF20A and KIF20B due to altered splicing in the absence of RBM39. We further show that kinesin downregulation is connected to the multinucleation phenotype observed upon RBM39 depletion by ArSulfs. Our approach should be helpful in the assessment of potential cancer drug candidates which target splicing factors. IMPLICATIONS Our approach provides a workflow for identifying and studying the most strongly modulated proteins when splicing is altered. The work also uncovers a splicing-based approach toward pharmacologic targeting of mitotic kinesins.
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Affiliation(s)
- Seemon Coomar
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Pedro Mota
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Alexander Penson
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jürg Schwaller
- Department of Biomedicine, University Children's Hospital (UKBB), University of Basel, Basel, Switzerland
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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16
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Kaulfuss M, Mietz J, Fabri A, Vom Berg J, Münz C, Chijioke O. The NK cell checkpoint NKG2A maintains expansion capacity of human NK cells. Sci Rep 2023; 13:10555. [PMID: 37386090 PMCID: PMC10310841 DOI: 10.1038/s41598-023-37779-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023] Open
Abstract
Human natural killer (NK) cells are cytotoxic effector cells that are increasingly harnessed in cancer immunotherapy. NKG2A/CD94 is an inhibitory receptor on NK cells that has established regulatory functions in the direct interaction with target cells when engaged with its ligand, the non-classical HLA class I molecule HLA-E. Here, we confirmed NKG2A as a checkpoint molecule in primary human NK cells and identified a novel role for NKG2A in maintaining NK cell expansion capacity by dampening both proliferative activity and excessive activation-induced cell death. Maintenance of NK cell expansion capacity might contribute to the preferential accumulation of human NKG2A+ NK cells after hematopoietic cell transplantation and enrichment of functionally impaired NK cells in human cancers. Functional silencing of NKG2A for cancer immunotherapy is highly attractive but will need to consider that this might also lead to a reduced survival by driving activation-induced cell death in targeted NK cells.
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Affiliation(s)
- Meike Kaulfuss
- Cellular Immunotherapy, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Juliane Mietz
- Cellular Immunotherapy, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Astrid Fabri
- Cellular Immunotherapy, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
- Institute of Immunity & Transplantation, University College London Division of Infection & Immunity, London, UK
| | - Johannes Vom Berg
- Institute of Laboratory Animal Science, University of Zürich, Schlieren, Switzerland
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Obinna Chijioke
- Cellular Immunotherapy, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland.
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
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17
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Alturki NA. Review of the Immune Checkpoint Inhibitors in the Context of Cancer Treatment. J Clin Med 2023; 12:4301. [PMID: 37445336 DOI: 10.3390/jcm12134301] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Checkpoint proteins are an integral part of the immune system and are used by the tumor cells to evade immune response, which helps them grow uncontrollably. By blocking these proteins, immune checkpoint inhibitors can restore the capability of the immune system to attack cancer cells and stop their growth. These findings are backed by adequate clinical trial data and presently, several FDA-approved immune checkpoint inhibitors exist in the market for treating various types of cancers, including melanoma, hepatocellular, endometrial, lung, kidney and others. Their mode of action is inhibition by targeting the checkpoint proteins CTLA-4, PD-1, PD-L1, etc. They can be used alone as well as in amalgamation with other cancer treatments, like surgery, radiation or chemotherapy. Since these drugs target only specific immune system proteins, their side effects are reduced in comparison with the traditional chemotherapy drugs, but may still cause a few affects like fatigue, skin rashes, and fever. In rare cases, these inhibitors are known to have caused more serious side effects, such as cardiotoxicity, and inflammation in the intestines or lungs. Herein, we provide an overview of these inhibitors and their role as biomarkers, immune-related adverse outcomes and clinical studies in the treatment of various cancers, as well as present some future perspectives.
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Affiliation(s)
- Norah A Alturki
- Clinical Laboratory Science Department, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
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18
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Vredevoogd DW, Peeper DS. Heterogeneity in functional genetic screens: friend or foe? Front Immunol 2023; 14:1162706. [PMID: 37398651 PMCID: PMC10312307 DOI: 10.3389/fimmu.2023.1162706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Functional genetic screens to uncover tumor-intrinsic nodes of immune resistance have uncovered numerous mechanisms by which tumors evade our immune system. However, due to technical limitations, tumor heterogeneity is imperfectly captured with many of these analyses. Here, we provide an overview of the nature and sources of heterogeneity that are relevant for tumor-immune interactions. We argue that this heterogeneity may actually contribute to the discovery of novel mechanisms of immune evasion, given a sufficiently large and heterogeneous set of input data. Taking advantage of tumor cell heterogeneity, we provide proof-of-concept analyses of mechanisms of TNF resistance. Thus, consideration of tumor heterogeneity is imperative to increase our understanding of immune resistance mechanisms.
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19
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Lu H, Lou H, Wengert G, Paudel R, Patel N, Desai S, Crum B, Linton-Reid K, Chen M, Li D, Ip J, Mauri F, Pinato DJ, Rockall A, Copley SJ, Ghaem-Maghami S, Aboagye EO. Tumor and local lymphoid tissue interaction determines prognosis in high-grade serous ovarian cancer. Cell Rep Med 2023:101092. [PMID: 37348499 PMCID: PMC10394173 DOI: 10.1016/j.xcrm.2023.101092] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/29/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023]
Abstract
Tertiary lymphoid structure (TLS) is associated with prognosis in copy-number-driven tumors, including high-grade serous ovarian cancer (HGSOC), although the function of TLS and its interaction with copy-number alterations in HGSOC are not fully understood. In the current study, we confirm that TLS-high HGSOC patients show significantly better progression-free survival (PFS). We show that the presence of TLS in HGSOC tumors is associated with B cell maturation and cytotoxic tumor-specific T cell activation and proliferation. In addition, the copy-number loss of IL15 and CXCL10 may limit TLS formation in HGSOC; a list of genes that may dysregulate TLS function is also proposed. Last, a radiomics-based signature is developed to predict the presence of TLS, which independently predicts PFS in both HGSOC patients and immune checkpoint inhibitor (ICI)-treated non-small cell lung cancer (NSCLC) patients. Overall, we reveal that TLS coordinates intratumoral B cell and T cell response to HGSOC tumor, while the cancer genome evolves to counteract TLS formation and function.
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Affiliation(s)
- Haonan Lu
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK
| | - Hantao Lou
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
| | - Georg Wengert
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK
| | - Reema Paudel
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK
| | - Naina Patel
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK
| | - Saral Desai
- Imperial College Healthcare NHS Trust, Du Cane Road, W12 0HS London, UK
| | - Bill Crum
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK
| | - Kristofer Linton-Reid
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK
| | - Mitchell Chen
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK; Imperial College Healthcare NHS Trust, Du Cane Road, W12 0HS London, UK
| | - Dongyang Li
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK
| | - Jacey Ip
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK; Imperial College Healthcare NHS Trust, Du Cane Road, W12 0HS London, UK
| | - Francesco Mauri
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK
| | - David J Pinato
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK; Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Andrea Rockall
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK
| | - Susan J Copley
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK; Imperial College Healthcare NHS Trust, Du Cane Road, W12 0HS London, UK
| | - Sadaf Ghaem-Maghami
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK; Imperial College Healthcare NHS Trust, Du Cane Road, W12 0HS London, UK
| | - Eric O Aboagye
- Department of Surgery and Cancer, Imperial College, Hammersmith Campus, The Commonwealth Building, Du Cane Road, W12 0NN London, UK.
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20
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Cui Y, Li J, Zhang P, Yin D, Wang Z, Dai J, Wang W, Zhang E, Guo R. B4GALT1 promotes immune escape by regulating the expression of PD-L1 at multiple levels in lung adenocarcinoma. J Exp Clin Cancer Res 2023; 42:146. [PMID: 37303063 DOI: 10.1186/s13046-023-02711-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023] Open
Abstract
BACKGROUND Invasive adenocarcinoma (IAC), which is typically preceded by minimally invasive adenocarcinoma (MIA), is the dominant pathological subtype of early-stage lung adenocarcinoma (LUAD). Identifying the molecular events underlying the progression from MIA to IAC may provide a crucial perspective and boost the exploration of novel strategies for early-stage LUAD diagnosis and treatment. METHODS Transcriptome sequencing of four pairs of MIA and IAC tumours obtained from four multiple primary lung cancer patients was performed to screen out beta-1,4-galactosyltransferase1 (B4GALT1). Function and mechanism experiments in vitro and in vivo were performed to explore the regulatory mechanism of B4GALT1-mediated immune evasion by regulating programmed cell death ligand 1 (PD-L1). RESULTS B4GALT1, a key gene involved in N-glycan biosynthesis, was highly expressed in IAC samples. Further experiments revealed that B4GALT1 regulated LUAD cell proliferation and invasion both in vitro and in vivo and was related to the impaired antitumour capacity of CD8 + T cells. Mechanistically, B4GALT1 directly mediates the N-linked glycosylation of PD-L1 protein, thus preventing PD-L1 degradation at the posttranscriptional level. In addition, B4GALT1 stabilized the TAZ protein via glycosylation, which activated CD274 at the transcriptional level. These factors lead to lung cancer immune escape. Importantly, inhibition of B4GALT1 increased CD8 + T-cell abundance and activity and enhanced the antitumour immunity of anti-PD-1 therapy in vivo. CONCLUSION B4GALT1 is a critical molecule in the development of early-stage LUAD and may be a novel target for LUAD intervention and immunotherapy.
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Affiliation(s)
- Yanan Cui
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Jun Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Dandan Yin
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Zhong Fu Road, Gulou District, Nanjing, Jiangsu, 210003, P. R. China
| | - Ziyu Wang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jiali Dai
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Wei Wang
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China.
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Renhua Guo
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China.
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21
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Kato S, Maeda Y, Sugiyama D, Watanabe K, Nishikawa H, Hinohara K. The cancer epigenome: Non-cell autonomous player in tumor immunity. Cancer Sci 2023; 114:730-740. [PMID: 36468774 PMCID: PMC9986067 DOI: 10.1111/cas.15681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Dysregulation of the tumor-intrinsic epigenetic circuit is a key driver event for the development of cancer. Accumulating evidence suggests that epigenetic and/or genetic drivers stimulate intrinsic oncogenic pathways as well as extrinsic factors that modulate the immune system. These modulations indeed shape the tumor microenvironment (TME), allowing pro-oncogenic factors to become oncogenic, thereby contributing to cancer development and progression. Here we review the epigenetic dysregulation arising in cancer cells that disseminates throughout the TME and beyond. Recent CRISPR screening has elucidated key epigenetic drivers that play important roles in the proliferation of cancer cells (intrinsic) and inhibition of antitumor immunity (extrinsic), which lead to the development and progression of cancer. These epigenetic players can serve as promising targets for cancer therapy as a dual (two-in-one)-targeted approach. Considering the interplay between cancer and the immune system as a key determinant of immunotherapy, we discuss a novel lineage-tracing technology that enables longitudinal monitoring of cancer and immune phenotypic heterogeneity and fate paths during cancer development, progression, and therapeutic interventions.
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Affiliation(s)
- Shinichiro Kato
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Maeda
- Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan
| | - Daisuke Sugiyama
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keisuke Watanabe
- Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Cancer Immunology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Research Institute, Tokyo, Japan.,Institute for Advanced Study, Nagoya University, Nagoya, Japan
| | - Kunihiko Hinohara
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Advanced Study, Nagoya University, Nagoya, Japan
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22
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Sahu A, Wang X, Munson P, Klomp JP, Wang X, Gu SS, Han Y, Qian G, Nicol P, Zeng Z, Wang C, Tokheim C, Zhang W, Fu J, Wang J, Nair NU, Rens JA, Bourajjaj M, Jansen B, Leenders I, Lemmers J, Musters M, van Zanten S, van Zelst L, Worthington J, Liu JS, Juric D, Meyer CA, Oubrie A, Liu XS, Fisher DE, Flaherty KT. Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha. Cancer Discov 2023; 13:672-701. [PMID: 36745048 PMCID: PMC9975674 DOI: 10.1158/2159-8290.cd-22-0244] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 09/13/2022] [Accepted: 11/23/2022] [Indexed: 02/07/2023]
Abstract
Drugs that kill tumors through multiple mechanisms have the potential for broad clinical benefits. Here, we first developed an in silico multiomics approach (BipotentR) to find cancer cell-specific regulators that simultaneously modulate tumor immunity and another oncogenic pathway and then used it to identify 38 candidate immune-metabolic regulators. We show the tumor activities of these regulators stratify patients with melanoma by their response to anti-PD-1 using machine learning and deep neural approaches, which improve the predictive power of current biomarkers. The topmost identified regulator, ESRRA, is activated in immunotherapy-resistant tumors. Its inhibition killed tumors by suppressing energy metabolism and activating two immune mechanisms: (i) cytokine induction, causing proinflammatory macrophage polarization, and (ii) antigen-presentation stimulation, recruiting CD8+ T cells into tumors. We also demonstrate a wide utility of BipotentR by applying it to angiogenesis and growth suppressor evasion pathways. BipotentR (http://bipotentr.dfci.harvard.edu/) provides a resource for evaluating patient response and discovering drug targets that act simultaneously through multiple mechanisms. SIGNIFICANCE BipotentR presents resources for evaluating patient response and identifying targets for drugs that can kill tumors through multiple mechanisms concurrently. Inhibition of the topmost candidate target killed tumors by suppressing energy metabolism and effects on two immune mechanisms. This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Avinash Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, Colorado
| | - Xiaoman Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Phillip Munson
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | | | - Xiaoqing Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Cardiology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shengqing Stan Gu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ya Han
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Gege Qian
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Phillip Nicol
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chenfei Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Wubing Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | | | - Bas Jansen
- Lead Pharma, Kloosterstraat, Oss, the Netherlands
| | | | - Jaap Lemmers
- Lead Pharma, Kloosterstraat, Oss, the Netherlands
| | - Mark Musters
- Lead Pharma, Kloosterstraat, Oss, the Netherlands
| | | | | | | | - Jun S. Liu
- Department of Statistics, Harvard University, Cambridge, Massachusetts
| | - Dejan Juric
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Clifford A. Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - X. Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David E. Fisher
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
| | - Keith T. Flaherty
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
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23
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Hou J, Liang S, Xu C, Wei Y, Wang Y, Tan Y, Sahni N, McGrail D, Bernatchez C, Davies M, Li Y, Chen R, Yi S, Chen Y, Yee C, Chen K, Peng W. Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors. NAR Cancer 2022; 4:zcac038. [PMID: 36518525 PMCID: PMC9732527 DOI: 10.1093/narcan/zcac038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Genetic screens are widely exploited to develop novel therapeutic approaches for cancer treatment. With recent advances in single-cell technology, single-cell CRISPR screen (scCRISPR) platforms provide opportunities for target validation and mechanistic studies in a high-throughput manner. Here, we aim to establish scCRISPR platforms which are suitable for immune-related screens involving multiple cell types. We integrated two scCRISPR platforms, namely Perturb-seq and CROP-seq, with both in vitro and in vivo immune screens. By leveraging previously generated resources, we optimized experimental conditions and data analysis pipelines to achieve better consistency between results from high-throughput and individual validations. Furthermore, we evaluated the performance of scCRISPR immune screens in determining underlying mechanisms of tumor intrinsic immune regulation. Our results showed that scCRISPR platforms can simultaneously characterize gene expression profiles and perturbation effects present in individual cells in different immune screen conditions. Results from scCRISPR immune screens also predict transcriptional phenotype associated with clinical responses to cancer immunotherapy. More importantly, scCRISPR screen platforms reveal the interactive relationship between targeting tumor intrinsic factors and T cell-mediated antitumor immune response which cannot be easily assessed by bulk RNA-seq. Collectively, scCRISPR immune screens provide scalable and reliable platforms to elucidate molecular determinants of tumor immune resistance.
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Affiliation(s)
- Jiakai Hou
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Chunyu Xu
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yunfei Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yukun Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nidhi Sahni
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - S Stephen Yi
- Department of Oncology, Livestrong Cancer Institutes, and Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs (ILSGP) and Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiyi Peng
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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24
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German B, Ellis L. Polycomb Directed Cell Fate Decisions in Development and Cancer. EPIGENOMES 2022; 6:28. [PMID: 36135315 PMCID: PMC9497807 DOI: 10.3390/epigenomes6030028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
The polycomb group (PcG) proteins are a subset of transcription regulators highly conserved throughout evolution. Their principal role is to epigenetically modify chromatin landscapes and control the expression of master transcriptional programs to determine cellular identity. The two mayor PcG protein complexes that have been identified in mammals to date are Polycomb Repressive Complex 1 (PRC1) and 2 (PRC2). These protein complexes selectively repress gene expression via the induction of covalent post-translational histone modifications, promoting chromatin structure stabilization. PRC2 catalyzes the histone H3 methylation at lysine 27 (H3K27me1/2/3), inducing heterochromatin structures. This activity is controlled by the formation of a multi-subunit complex, which includes enhancer of zeste (EZH2), embryonic ectoderm development protein (EED), and suppressor of zeste 12 (SUZ12). This review will summarize the latest insights into how PRC2 in mammalian cells regulates transcription to orchestrate the temporal and tissue-specific expression of genes to determine cell identity and cell-fate decisions. We will specifically describe how PRC2 dysregulation in different cell types can promote phenotypic plasticity and/or non-mutational epigenetic reprogramming, inducing the development of highly aggressive epithelial neuroendocrine carcinomas, including prostate, small cell lung, and Merkel cell cancer. With this, EZH2 has emerged as an important actionable therapeutic target in such cancers.
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Affiliation(s)
- Beatriz German
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Leigh Ellis
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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25
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Song J, Lan J, Tang J, Luo N. PTPN2 in the Immunity and Tumor Immunotherapy: A Concise Review. Int J Mol Sci 2022; 23:ijms231710025. [PMID: 36077422 PMCID: PMC9456094 DOI: 10.3390/ijms231710025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
PTPN2 (protein tyrosine phosphatase non-receptor 2), also called TCPTP (T cell protein tyrosine phosphatase), is a member of the PTP family signaling proteins. Phosphotyrosine-based signaling of this non-transmembrane protein is essential for regulating cell growth, development, differentiation, survival, and migration. In particular, PTPN2 received researchers’ attention when Manguso et al. identified PTPN2 as a cancer immunotherapy target using in vivo CRISPR library screening. In this review, we attempt to summarize the important functions of PTPN2 in terms of its structural and functional properties, inflammatory reactions, immunomodulatory properties, and tumor immunity. PTPN2 exerts synergistic anti-inflammatory effects in various inflammatory cells and regulates the developmental differentiation of immune cells. The diversity of PTPN2 effects in different types of tumors makes it a potential target for tumor immunotherapy.
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26
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Cook AL, Wyhs N, Sur S, Ptak B, Popoli M, Dobbyn L, Papadopoulos T, Bettegowda C, Papadopoulos N, Vogelstein B, Zhou S, Kinzler KW. An isogenic cell line panel for sequence-based screening of targeted anticancer drugs. iScience 2022; 25:104437. [PMID: 35692635 PMCID: PMC9184558 DOI: 10.1016/j.isci.2022.104437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/11/2022] [Accepted: 05/18/2022] [Indexed: 12/05/2022] Open
Abstract
We describe the creation of an isogenic cell line panel representing common cancer pathways, with features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cell lines were generated using CRISPR technologies. Surprisingly, most of these lines did not result in complete gene inactivation despite integration of sgRNA at the desired genomic site. A subset of the lines harbored biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterized lines covering 19 frequently lost cancer pathways. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of TP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena. Creation of an isogenic cell line panel representing the loss of 19 cancer pathways HTS confirmed MK-1775 as a selective inhibitor of cells with loss of TP53 These cell lines are useful for studying a variety of cellular biochemical phenomena
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Affiliation(s)
- Ashley L. Cook
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicolas Wyhs
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Surojit Sur
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Blair Ptak
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Laura Dobbyn
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Tasos Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shibin Zhou
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Corresponding author
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Corresponding author
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Li F, Aljahdali IAM, Ling X. Molecular Glues: Capable Protein-Binding Small Molecules That Can Change Protein-Protein Interactions and Interactomes for the Potential Treatment of Human Cancer and Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23116206. [PMID: 35682885 PMCID: PMC9181451 DOI: 10.3390/ijms23116206] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 12/29/2022] Open
Abstract
Molecular glue (MG) compounds are a type of unique small molecule that can change the protein–protein interactions (PPIs) and interactomes by degrading, stabilizing, or activating the target protein after their binging. These small-molecule MGs are gradually being recognized for their potential application in treating human diseases, including cancer. Evidence suggests that small-molecule MG compounds could essentially target any proteins, which play critical roles in human disease etiology, where many of these protein targets were previously considered undruggable. Intriguingly, most MG compounds with high efficacy for cancer treatment can glue on and control multiple key protein targets. On the other hand, a single key protein target can also be glued by multiple MG compounds with distinct chemical structures. The high flexibility of MG–protein interaction profiles provides rich soil for the growth and development of small-molecule MG compounds that can be used as molecular tools to assist in unraveling disease mechanisms, and they can also facilitate drug development for the treatment of human disease, especially human cancer. In this review, we elucidate this concept by using various types of small-molecule MG compounds and their corresponding protein targets that have been documented in the literature.
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Affiliation(s)
- Fengzhi Li
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (I.A.M.A.); (X.L.)
- Developmental Therapeutics (DT) Program, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Gastrointestinal Translational Research Group (GI TRG), Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Correspondence: ; Tel.: +1-(716)-845-4398; Fax: +1-(716)-845-8857
| | - Ieman A. M. Aljahdali
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (I.A.M.A.); (X.L.)
- Department of Cellular & Molecular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Xiang Ling
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (I.A.M.A.); (X.L.)
- Canget BioTekpharma LLC, Buffalo, NY 14203, USA
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28
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Kermi C, Lau L, Asadi Shahmirzadi A, Classon M. Disrupting Mechanisms that Regulate Genomic Repeat Elements to Combat Cancer and Drug Resistance. Front Cell Dev Biol 2022; 10:826461. [PMID: 35602594 PMCID: PMC9114874 DOI: 10.3389/fcell.2022.826461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Despite advancements in understanding cancer pathogenesis and the development of many effective therapeutic agents, resistance to drug treatment remains a widespread challenge that substantially limits curative outcomes. The historical focus on genetic evolution under drug “pressure” as a key driver of resistance has uncovered numerous mechanisms of therapeutic value, especially with respect to acquired resistance. However, recent discoveries have also revealed a potential role for an ancient evolutionary balance between endogenous “viral” elements in the human genome and diverse factors involved in their restriction in tumor evolution and drug resistance. It has long been appreciated that the stability of genomic repeats such as telomeres and centromeres affect tumor fitness, but recent findings suggest that de-regulation of other repetitive genome elements, including retrotransposons, might also be exploited as cancer therapy. This review aims to present an overview of these recent findings.
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29
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Abstract
Over the past decade, CRISPR has become as much a verb as it is an acronym, transforming biomedical research and providing entirely new approaches for dissecting all facets of cell biology. In cancer research, CRISPR and related tools have offered a window into previously intractable problems in our understanding of cancer genetics, the noncoding genome and tumour heterogeneity, and provided new insights into therapeutic vulnerabilities. Here, we review the progress made in the development of CRISPR systems as a tool to study cancer, and the emerging adaptation of these technologies to improve diagnosis and treatment.
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Affiliation(s)
- Alyna Katti
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Bianca J Diaz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Christina M Caragine
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- Department of Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | - Lukas E Dow
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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30
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Bernareggi D, Xie Q, Prager BC, Yun J, Cruz LS, Pham TV, Kim W, Lee X, Coffey M, Zalfa C, Azmoon P, Zhu H, Tamayo P, Rich JN, Kaufman DS. CHMP2A regulates tumor sensitivity to natural killer cell-mediated cytotoxicity. Nat Commun 2022; 13:1899. [PMID: 35393416 PMCID: PMC8990014 DOI: 10.1038/s41467-022-29469-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/09/2022] [Indexed: 02/08/2023] Open
Abstract
Natural killer (NK) cells are known to mediate killing of various cancer types, but tumor cells can develop resistance mechanisms to escape NK cell-mediated killing. Here, we use a "two cell type" whole genome CRISPR-Cas9 screening system to discover key regulators of tumor sensitivity and resistance to NK cell-mediated cytotoxicity in human glioblastoma stem cells (GSC). We identify CHMP2A as a regulator of GSC resistance to NK cell-mediated cytotoxicity and we confirm these findings in a head and neck squamous cells carcinoma (HNSCC) model. We show that deletion of CHMP2A activates NF-κB in tumor cells to mediate increased chemokine secretion that promotes NK cell migration towards tumor cells. In the HNSCC model we demonstrate that CHMP2A mediates tumor resistance to NK cells via secretion of extracellular vesicles (EVs) that express MICA/B and TRAIL. These secreted ligands induce apoptosis of NK cells to inhibit their antitumor activity. To confirm these in vitro studies, we demonstrate that deletion of CHMP2A in CAL27 HNSCC cells leads to increased NK cell-mediated killing in a xenograft immunodeficient mouse model. These findings illustrate a mechanism of tumor immune escape through EVs secretion and identify inhibition of CHMP2A and related targets as opportunities to improve NK cell-mediated immunotherapy.
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Affiliation(s)
- Davide Bernareggi
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qi Xie
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Briana C Prager
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Cleveland Clinic Lerner College of Medicine at Cleveland Clinic & Case Western Reserve University, Cleveland, OH, USA
| | - Jiyoung Yun
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Luisjesus S Cruz
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Timothy V Pham
- Center for Novel Therapeutics and Moores Cancer Center, UCSD, San Diego, CA, USA
| | - William Kim
- Center for Novel Therapeutics and Moores Cancer Center, UCSD, San Diego, CA, USA.,Division of Medical Genetics, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Xiqing Lee
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan, China
| | - Michael Coffey
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cristina Zalfa
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Pardis Azmoon
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Huang Zhu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Pablo Tamayo
- Center for Novel Therapeutics and Moores Cancer Center, UCSD, San Diego, CA, USA.,Division of Medical Genetics, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Jeremy N Rich
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Dan S Kaufman
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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31
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Dong MB, Tang K, Zhou X, Zhou JJ, Chen S. Tumor immunology CRISPR screening: present, past, and future. Trends Cancer 2022; 8:210-225. [PMID: 34920978 PMCID: PMC8854335 DOI: 10.1016/j.trecan.2021.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 02/08/2023]
Abstract
Recent advances in immunotherapy have fundamentally changed the landscape of cancer treatment by leveraging the specificity and selectivity of the adaptive immune system to kill cancer cells. These successes have ushered in a new wave of research aimed at understanding immune recognition with the hope of developing newer immunotherapies. The advent of clustered regularly interspaced short palindromic repeats (CRISPR) technologies and advancement of multiomics modalities have greatly accelerated the discovery process. Here, we review the current literature surrounding CRISPR screens within the context of tumor immunology, provide essential components needed to conduct immune-specific CRISPR screens, and present avenues for future research.
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Affiliation(s)
- Matthew B. Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,System Biology Institute, Yale University, West Haven, CT, USA,Center for Cancer Systems Biology, Yale University, West Haven, CT, USA,Immunobiology Program, Yale University, New Haven, CT, USA,Department of Immunobiology, Yale University, New Haven, CT, USA,M.D.-Ph.D. Program, Yale University, West Haven, CT, USA
| | - Kaiyuan Tang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,System Biology Institute, Yale University, West Haven, CT, USA,Center for Cancer Systems Biology, Yale University, West Haven, CT, USA,Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Xiaoyu Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,System Biology Institute, Yale University, West Haven, CT, USA,Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Jingjia J. Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,System Biology Institute, Yale University, West Haven, CT, USA,Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; Immunobiology Program, Yale University, New Haven, CT, USA; M.D.-Ph.D. Program, Yale University, West Haven, CT, USA; Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA.
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32
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Yang H, Choi K, Kim KJ, Park SY, Jeon JY, Kim BG, Kim JY. Immunoenhancing Effects of Euglena gracilis on a Cyclophosphamide-Induced Immunosuppressive Mouse Model. J Microbiol Biotechnol 2022; 32:228-237. [PMID: 35001010 PMCID: PMC9628845 DOI: 10.4014/jmb.2112.12035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/15/2022]
Abstract
In this study, the effects of the immune stimulator Euglena gracilis (Euglena) in cyclophosphamide (CCP)-induced immunocompromised mice were assessed. The key component β-1,3-glucan (paramylon) constitutes 50% of E. gracilis. Mice were orally administered Euglena powder (250 and 500 mg/kg body weight (B.W.)) or β-glucan powder (250 mg/kg B.W.) for 19 days. In a preliminary immunology experiment, ICR mice were intraperitoneally injected with 80 mg of CCP/kg B.W. during the final 3 consecutive days. In the main experiment, BALB/c mice were treated with CCP for the final 5 days. To evaluate the enhancing effects of Euglena on the immune system, mouse B.W., the spleen index, natural killer (NK) cell activity and mRNA expression in splenocytes lungs and livers were determined. To detect cytokine and receptor expression, splenocytes were treated with 5 μg/ml concanavalin A or 1 μg/ml lipopolysaccharide. The B.W. and spleen index were significantly increased and NK cell activity was slightly enhanced in all the experimental groups compared to the CCP group. In splenocytes, the gene expression levels of tumor necrosis factor-α, interferon-γ, interleukin (IL)-10, IL-6, and IL-12 receptor were increased in the E. gracilis and β-glucan groups compared to the CCP group, but there was no significant difference. Treatment with 500mg of Euglena/kg B.W. significantly upregulated dectin-1 mRNA expression in the lung and liver compared to the CCP group. These results suggest that Euglena may enhance the immune system by strengthening innate immunity through immunosuppression.
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Affiliation(s)
- Hyeonji Yang
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Kwanyong Choi
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Kyeong Jin Kim
- Department of Nano Bio Engineering, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Soo-yeon Park
- Lab of Nanobio, Seoul National University of Science and Technology, Seoul 08826, Republic of Korea
| | - Jin-Young Jeon
- BIO R&D center, Daesang Corp., Icheon 17384, Republic of Korea
| | - Byung-Gon Kim
- BIO R&D center, Daesang Corp., Icheon 17384, Republic of Korea
| | - Ji Yeon Kim
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea,Department of Nano Bio Engineering, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea,Corresponding author Phone: +82-2-970-6740 E-mail:
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33
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Kerrison WGJ, Lee ATJ, Thway K, Jones RL, Huang PH. Current Status and Future Directions of Immunotherapies in Soft Tissue Sarcomas. Biomedicines 2022; 10:573. [PMID: 35327375 PMCID: PMC8945421 DOI: 10.3390/biomedicines10030573] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/15/2022] Open
Abstract
Immunotherapy in soft tissue sarcoma (STS) has experienced a surge of interest in the past decade, contributing to an expanding number of therapeutic options for this extremely heterogenous group of rare malignancies. Immune checkpoint inhibitors (CPIs) targeting the PD-1 and CTLA-4 axes have demonstrated promising responses in a select number of STS subtypes, including rarer subtypes, such as alveolar soft part sarcoma, SWI/SNF-deficient sarcomas, clear cell sarcoma, and angiosarcoma. Multiple pan-subtype sarcoma trials have facilitated the study of possible predictive biomarkers of the CPI response. It has also become apparent that certain therapies, when combined with CPIs, can enhance response rates, although the specific mechanisms of this possible synergy remain unconfirmed in STS. In addition to CPIs, several other immune targeting agents, including anti-tumour-associated macrophage and antigen-directed therapies, are now under assessment in STS with promising efficacy in some subtypes. In this article, we review the state of the art in immunotherapy in STS, highlighting the pre-clinical and clinical data available for this promising therapeutic strategy.
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Affiliation(s)
- William G. J. Kerrison
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton SM2 5NG, UK; (W.G.J.K.); (K.T.)
| | | | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton SM2 5NG, UK; (W.G.J.K.); (K.T.)
- The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK;
| | - Robin L. Jones
- The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK;
- Division of Clinical Studies, The Institute of Cancer Research, London SW3 6JB, UK
| | - Paul H. Huang
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton SM2 5NG, UK; (W.G.J.K.); (K.T.)
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34
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Yamanaka S, Horiuchi Y, Matsuoka S, Kido K, Nishino K, Maeno M, Shibata N, Kosako H, Sawasaki T. A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues. Nat Commun 2022; 13:183. [PMID: 35013300 PMCID: PMC8748630 DOI: 10.1038/s41467-021-27818-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
Proteolysis-targeting chimaeras (PROTACs) as well as molecular glues such as immunomodulatory drugs (IMiDs) and indisulam are drugs that induce interactions between substrate proteins and an E3 ubiquitin ligases for targeted protein degradation. Here, we develop a workflow based on proximity-dependent biotinylation by AirID to identify drug-induced neo-substrates of the E3 ligase cereblon (CRBN). Using AirID-CRBN, we detect IMiD-dependent biotinylation of CRBN neo-substrates in vitro and identify biotinylated peptides of well-known neo-substrates by mass spectrometry with high specificity and selectivity. Additional analyses reveal ZMYM2 and ZMYM2-FGFR1 fusion protein-responsible for the 8p11 syndrome involved in acute myeloid leukaemia-as CRBN neo-substrates. Furthermore, AirID-DCAF15 and AirID-CRBN biotinylate neo-substrates targeted by indisulam and PROTACs, respectively, suggesting that this approach has the potential to serve as a general strategy for characterizing drug-inducible protein-protein interactions in cells.
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Affiliation(s)
- Satoshi Yamanaka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Yuto Horiuchi
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Saya Matsuoka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Kohki Kido
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Mayaka Maeno
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Norio Shibata
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan.
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35
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Zhuang X, Long EO. CRISPR Screen to Identify Factors that Render Tumor Cells Sensitive or Resistant to Killing by NK Cells. Methods Mol Biol 2022; 2463:269-288. [PMID: 35344181 DOI: 10.1007/978-1-0716-2160-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Natural killer (NK) cells are an important component of the cancer immune surveillance system. They are regulated by germline-encoded receptors that activate and inhibit their effector function, such as secretion of cytokines and direct lysis of tumor cells and virus-infected cells. Without the need to be primed by prior exposure to tumor antigen, NK cells can detect ligands expressed on tumor cells and selectively kill these cells. NK cells are under strict control by inhibitory receptors that bind to HLA class I on target cells and block early activation signals, thus preventing lysis of target cells. The sensitivity to lysis by NK cells is therefore determined to a large extent by the expression of HLA class I molecules on tumor cells. In addition to receptor-ligand interactions that occur at NK-target cell synapses, many other factors determine the sensitivity of tumor cells to lysis by NK. Intrinsic properties of tumor cells, such as their metabolism and signaling networks establish a threshold above which they will succumb to the death pathways triggered by NK cell attack. Here we provide a protocol for a genome-wide CRISPR screen in tumor cells to identify factors that regulate their sensitivity to primary human NK cells. Tumor cells first transduced for expression of Cas9 are then transduced with a guide RNA (gRNA) library and co-cultured with NK cells. Deep sequencing of the library generated from the genome of tumor cells that survived the selection by NK cells and analysis of the distribution of guide RNAs is performed to identify genes that promote either sensitivity or resistance to NK-mediated killing. The contribution of individual genes to tumor sensitivity can be validated by knockouts using individual gRNAs. The techniques and workflow described here could be applied to primary tumors from cancer patients and reveal tumor-specific points of vulnerability that could be exploited for cancer immunotherapy, such as checkpoint blockade or expression of chimeric antigen receptors specifically designed to activate NK cell cytotoxicity.
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Affiliation(s)
- Xiaoxuan Zhuang
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Eric O Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
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36
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Jiang HS, Zhuang SC, Lam CH, Chang LY, Angata T. Recent Progress in the Methodologies to Identify Physiological Ligands of Siglecs. Front Immunol 2021; 12:813082. [PMID: 34956244 PMCID: PMC8702521 DOI: 10.3389/fimmu.2021.813082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/23/2021] [Indexed: 11/28/2022] Open
Abstract
Siglecs, a family of receptor-like lectins, recognize glycoproteins and/or glycolipids containing sialic acid in the extracellular space and transduce intracellular signaling. Recently, researchers uncovered significant contributions of Siglecs in cancer immunity, renewing interest in this family of proteins. Previous extensive studies have defined how Siglecs recognize glycan epitopes (glycotopes). Nevertheless, the biological role of these glycotopes has not been fully evaluated. Recent studies using live cells have begun unraveling the constituents of Siglec ligands. These studies demonstrated that glycoprotein scaffolds (counter-receptors) displaying glycotopes are sometimes just as important as the glycotope itself. These new insights may guide future efforts to develop therapeutic agents to target the Siglec – ligand axis.
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Affiliation(s)
- Huei-Syuan Jiang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Shao-Chien Zhuang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chak Hin Lam
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Lan-Yi Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Takashi Angata
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
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37
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Lu J, Jiang H, Li D, Chen T, Wang Y, Pu Z, Xu G. Proximity Labeling, Quantitative Proteomics, and Biochemical Studies Revealed the Molecular Mechanism for the Inhibitory Effect of Indisulam on the Proliferation of Gastric Cancer Cells. J Proteome Res 2021; 20:4462-4474. [PMID: 34420308 DOI: 10.1021/acs.jproteome.1c00437] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Indisulam exhibits antitumor activity against several cancer cells. Although the DCAF15-indisulam-RBM39 axis has been well documented in the inhibition of cancer cell growth, it is unknown whether RBM39 degradation alone is the mechanism of action of indisulam. Here, we verified the inhibitory effect of indisulam on the proliferation of gastric cancer cells and its dependence on DCAF15. Proximity-dependent biotin labeling with TurboID and quantitative proteomics revealed that indisulam indeed promoted the interaction between DCAF15 and RBM39. Immunoblotting and immunofluorescence also revealed that indisulam promoted the ubiquitin-mediated RBM39 degradation and RBM39 colocalized with DCAF15 in the nucleus. DCAF15 knockdown almost completely abolished the indisulam-mediated RBM39 reduction. Further knockdown of RBM39 eliminated the effect of DCAF15 on the proliferation of gastric cancer cells upon indisulam treatment. Immunoblotting of gastric tumor tissues confirmed the downregulation of RBM39 by indisulam. Database analysis unveiled that RBM39 was highly expressed in gastric cancer tissues and its high expression significantly shortened the survival time of gastric cancer patients. Taken together, we demonstrated that indisulam enhanced RBM39 ubiquitination and degradation by promoting its interaction with DCAF15, thus inhibiting the proliferation of gastric cancer cells. This work may provide valuable information for drug discovery through proteolysis targeting chimeras. MS data were deposited in ProteomeXchange (Dataset identifier: PXD024168).
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Affiliation(s)
- Jiaqi Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Honglv Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Dan Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Tao Chen
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Yuhong Wang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Zhongjian Pu
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, Jiangsu 226600, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
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38
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Sheffer M, Lowry E, Beelen N, Borah M, Amara SNA, Mader CC, Roth JA, Tsherniak A, Freeman SS, Dashevsky O, Gandolfi S, Bender S, Bryan JG, Zhu C, Wang L, Tariq I, Kamath GM, Simoes RDM, Dhimolea E, Yu C, Hu Y, Dufva O, Giannakis M, Syrgkanis V, Fraenkel E, Golub T, Romee R, Mustjoki S, Culhane AC, Wieten L, Mitsiades CS. Genome-scale screens identify factors regulating tumor cell responses to natural killer cells. Nat Genet 2021; 53:1196-1206. [PMID: 34253920 DOI: 10.1038/s41588-021-00889-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/18/2021] [Indexed: 12/26/2022]
Abstract
To systematically define molecular features in human tumor cells that determine their degree of sensitivity to human allogeneic natural killer (NK) cells, we quantified the NK cell responsiveness of hundreds of molecularly annotated 'DNA-barcoded' solid tumor cell lines in multiplexed format and applied genome-scale CRISPR-based gene-editing screens in several solid tumor cell lines, to functionally interrogate which genes in tumor cells regulate the response to NK cells. In these orthogonal studies, NK cell-sensitive tumor cells tend to exhibit 'mesenchymal-like' transcriptional programs; high transcriptional signature for chromatin remodeling complexes; high levels of B7-H6 (NCR3LG1); and low levels of HLA-E/antigen presentation genes. Importantly, transcriptional signatures of NK cell-sensitive tumor cells correlate with immune checkpoint inhibitor (ICI) resistance in clinical samples. This study provides a comprehensive map of mechanisms regulating tumor cell responses to NK cells, with implications for future biomarker-driven applications of NK cell immunotherapies.
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MESH Headings
- Allogeneic Cells/physiology
- Animals
- B7 Antigens/genetics
- Cell Line, Tumor
- Chromatin Assembly and Disassembly/physiology
- Cytotoxicity Tests, Immunologic/methods
- Cytotoxicity, Immunologic/genetics
- Cytotoxicity, Immunologic/physiology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Genome, Human
- Histocompatibility Antigens Class I/genetics
- Histocompatibility Antigens Class I/immunology
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Killer Cells, Natural/physiology
- Mice, Inbred NOD
- Xenograft Model Antitumor Assays
- HLA-E Antigens
- Mice
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Affiliation(s)
- Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center, Harvard Medical School, Boston, MA, USA.
| | - Emily Lowry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicky Beelen
- Department of Transplantation Immunology, Maastricht University Medical Center+, Maastricht, the Netherlands
- School for Oncology and Developmental Biology, Maastricht University Medical Center+ GROW, Maastricht, the Netherlands
| | - Minasri Borah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Chris C Mader
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jennifer A Roth
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Samantha Bender
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jordan G Bryan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Cong Zhu
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Li Wang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Ifrah Tariq
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Ricardo De Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Channing Yu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Sichuan University, Chengdu, China
| | - Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Ernest Fraenkel
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Todd Golub
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Aedin C Culhane
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Lotte Wieten
- Department of Transplantation Immunology, Maastricht University Medical Center+, Maastricht, the Netherlands
- School for Oncology and Developmental Biology, Maastricht University Medical Center+ GROW, Maastricht, the Netherlands
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center, Harvard Medical School, Boston, MA, USA.
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39
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Kannt A, Đikić I. Expanding the arsenal of E3 ubiquitin ligases for proximity-induced protein degradation. Cell Chem Biol 2021; 28:1014-1031. [PMID: 33945791 DOI: 10.1016/j.chembiol.2021.04.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Efficacy and selectivity of molecules inducing protein degradation depend on their affinity to the target protein but also on the type of E3 ubiquitin ligase that is recruited to trigger proteasomal degradation. While tremendous progress has been made on the former, the latter-the arsenal of E3 ligases that can be hijacked for targeted protein degradation-is still largely unexplored. Only about 2% of the more than 600 E3 ligases have been utilized to date. Exploiting additional E3 ligases that are, for example, selectively expressed in specific tissues or cells, or regulated under certain conditions, can considerably broaden the applicability of molecular degraders as a therapeutic modality. Here, we provide an overview of major classes of E3 ligases, review the enzymes that have been exploited for induced protein degradation and approaches used to identify or design E3 ligands, and highlight challenges and opportunities for targeting new E3 ligases.
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Affiliation(s)
- Aimo Kannt
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Clinical Pharmacology, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Ivan Đikić
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
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40
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Buquicchio FA, Satpathy AT. Interrogating immune cells and cancer with CRISPR-Cas9. Trends Immunol 2021; 42:432-446. [PMID: 33812776 DOI: 10.1016/j.it.2021.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas9 technologies have transformed the study of genetic pathways governing cellular differentiation and function. Recent advances have adapted these methods to immune cells, which has accelerated the pace of functional genomics in immunology and enabled new avenues for the design of cellular immunotherapies for cancer. In this review, we summarize recent developments in CRISPR-Cas9 technology and discuss how they have been leveraged to discover and manipulate novel genetic regulators of the immune system. We envision that these results will provide a valuable resource to aid in the design, implementation, and interpretation of CRISPR-Cas9-based screens in immunology and immuno-oncology.
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Affiliation(s)
- Frank A Buquicchio
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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41
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Jongsma MLM, de Waard AA, Raaben M, Zhang T, Cabukusta B, Platzer R, Blomen VA, Xagara A, Verkerk T, Bliss S, Kong X, Gerke C, Janssen L, Stickel E, Holst S, Plomp R, Mulder A, Ferrone S, Claas FHJ, Heemskerk MHM, Griffioen M, Halenius A, Overkleeft H, Huppa JB, Wuhrer M, Brummelkamp TR, Neefjes J, Spaapen RM. The SPPL3-Defined Glycosphingolipid Repertoire Orchestrates HLA Class I-Mediated Immune Responses. Immunity 2021; 54:132-150.e9. [PMID: 33271119 PMCID: PMC8722104 DOI: 10.1016/j.immuni.2020.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/25/2020] [Accepted: 11/06/2020] [Indexed: 12/26/2022]
Abstract
HLA class I (HLA-I) glycoproteins drive immune responses by presenting antigens to cognate CD8+ T cells. This process is often hijacked by tumors and pathogens for immune evasion. Because options for restoring HLA-I antigen presentation are limited, we aimed to identify druggable HLA-I pathway targets. Using iterative genome-wide screens, we uncovered that the cell surface glycosphingolipid (GSL) repertoire determines effective HLA-I antigen presentation. We show that absence of the protease SPPL3 augmented B3GNT5 enzyme activity, resulting in upregulation of surface neolacto-series GSLs. These GSLs sterically impeded antibody and receptor interactions with HLA-I and diminished CD8+ T cell activation. Furthermore, a disturbed SPPL3-B3GNT5 pathway in glioma correlated with decreased patient survival. We show that the immunomodulatory effect could be reversed through GSL synthesis inhibition using clinically approved drugs. Overall, our study identifies a GSL signature that inhibits immune recognition and represents a potential therapeutic target in cancer, infection, and autoimmunity.
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Affiliation(s)
- Marlieke L M Jongsma
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands; Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - Antonius A de Waard
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Matthijs Raaben
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tao Zhang
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Birol Cabukusta
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - René Platzer
- Institut für Hygiene und Angewandte Immunologie, Vienna, Austria
| | - Vincent A Blomen
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Anastasia Xagara
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Tamara Verkerk
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Sophie Bliss
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Xiangrui Kong
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Carolin Gerke
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lennert Janssen
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - Elmer Stickel
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Stephanie Holst
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Rosina Plomp
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Arend Mulder
- Department of Immunology, LUMC, Leiden, the Netherlands
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne Halenius
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hermen Overkleeft
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Johannes B Huppa
- Institut für Hygiene und Angewandte Immunologie, Vienna, Austria
| | - Manfred Wuhrer
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Cancer Genomics Center, Amsterdam, the Netherlands
| | - Jacques Neefjes
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - Robbert M Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands.
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42
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Potts MA, McDonald JA, Sutherland KD, Herold MJ. Critical cancer vulnerabilities identified by unbiased CRISPR/Cas9 screens inform on efficient cancer Immunotherapy. Eur J Immunol 2020; 50:1871-1884. [PMID: 33202035 DOI: 10.1002/eji.202048712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/21/2020] [Accepted: 11/12/2020] [Indexed: 12/19/2022]
Abstract
The mutational landscape of human cancers is highly complex. While next generation sequencing aims to comprehensively catalogue somatic alterations in tumor cells, it fails to delineate driver from passenger mutations. Functional genomic approaches, particularly CRISPR/Cas9, enable both gene discovery, and annotation of gene function. Indeed, recent CRISPR/Cas9 technologies have flourished with the development of more sophisticated and versatile platforms capable of gene knockouts to high throughput genome wide editing of a single nucleotide base. With new platforms constantly emerging, it can be challenging to navigate what CRISPR tools are available and how they can be effectively applied to understand cancer biology. This review provides an overview of current and emerging CRISPR technologies and their power to model cancer and identify novel treatments. Specifically, how CRISPR screening approaches have been exploited to enhance immunotherapies through the identification of tumor intrinsic and extrinsic mechanisms to escape immune recognition will be discussed.
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Affiliation(s)
- Margaret A Potts
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jackson A McDonald
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kate D Sutherland
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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43
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Nguyen KM, Busino L. Targeting the E3 ubiquitin ligases DCAF15 and cereblon for cancer therapy. Semin Cancer Biol 2020; 67:53-60. [DOI: 10.1016/j.semcancer.2020.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/22/2022]
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44
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Li Z, Fei T. Improving Cancer Immunotherapy with CRISPR-Based Technology. ACTA ACUST UNITED AC 2020; 4:e1900253. [PMID: 33245213 DOI: 10.1002/adbi.201900253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/29/2019] [Indexed: 12/19/2022]
Abstract
The rapidly evolving field of immunotherapy has attracted great attention in the field of cancer research and already revolutionized the clinical practice standard for treating cancer. Genetically engineered T cells expressing either T cell receptors or chimeric antigen receptors represent novel treatment modalities and are considered powerful weapons to fight cancer. The immune checkpoint blockade, which harnesses the negative control signaling behind the anti-tumor immune response with therapeutic antibodies by blocking cytotoxic T lymphocyte-associated protein 4 or the programmed cell death 1 pathways are another mainstream direction for cancer immunotherapy. In addition to cytotoxic T cells, other immune cell types such as nature killer cells and macrophages also possess the ability to eradicate cancer cells, which may serve as the basis to develop novel cancer immunotherapies. The advent of cutting-edge genome editing technology, especially clustered regularly interspaced palindromic repeats (CRISPR)-based tools, has greatly expedited many biomedical research areas, including cancer immunology and immunotherapy. In this review, the contribution of current CRISPR techniques to basic and translational cancer immunology research is discussed, and the future for cancer immunotherapy in the age of CRISPR is predicted.
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Affiliation(s)
- Zexu Li
- College of Life and Health Sciences, Northeastern University, Shenyang, 110819, P. R. China.,Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, 110819, P. R. China
| | - Teng Fei
- College of Life and Health Sciences, Northeastern University, Shenyang, 110819, P. R. China.,Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, 110819, P. R. China
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45
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Xu Y, Nijhuis A, Keun HC. RNA-binding motif protein 39 (RBM39): An emerging cancer target. Br J Pharmacol 2020; 179:2795-2812. [PMID: 33238031 DOI: 10.1111/bph.15331] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/13/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
RNA-binding motif protein 39 (RBM39) is an RNA-binding protein involved in transcriptional co-regulation and alternative RNA splicing. Recent studies have revealed that RBM39 is the unexpected target of aryl sulphonamides, which act as molecular glues between RBM39 and the DCAF15-associated E3 ubiquitin ligase complex leading to selective degradation of the target. Loss of RBM39 leads to aberrant splicing events and differential gene expression, thereby inhibiting cell cycle progression and causing tumour regression in a number of preclinical models. Many clinical studies have shown that aryl sulphonamides were well tolerated, but their clinical performance was limited due to an insufficient understanding of the target, RBM39 biology and a lack of predictive biomarkers. This review summarises the current knowledge of RBM39 function and discusses the therapeutic potential of this spliceosome target in cancer therapy.
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Affiliation(s)
- Yuewei Xu
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Anke Nijhuis
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Hector C Keun
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
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46
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Jammal N, Rausch CR, Kadia TM, Pemmaraju N. Cell cycle inhibitors for the treatment of acute myeloid leukemia: a review of phase 2 & 3 clinical trials. Expert Opin Emerg Drugs 2020; 25:491-499. [PMID: 33161749 DOI: 10.1080/14728214.2020.1847272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Introduction: Acute myeloid leukemia (AML) is a clinically heterogeneous hematologic malignancy with poor long term outcomes. Cytotoxic chemotherapy remains the backbone of therapy especially among younger patients; however the effective incorporation of targeted therapies continues to be an area of active research in an effort to improve response durations and survival. Cell cycle inhibitors (CCI) are a novel class of agents which may be of particular interest for development in patients with AML. Areas covered: We will review the concept of CCIs along with available pre-clinical and clinical data in the treatment of AML both in North America and abroad. Specific drug targets reviewed include cyclin D kinase, Aurora kinase, CHK1, and WEE1. Expert opinion: Utilization of CCIs in patients with AML is an emerging approach that has shown promise in pre-clinical models. It has been challenging to translate this concept into clinical success thus far, due to marginal single-agent activity and significant toxicity profiles, however clinical evaluation is ongoing. Addition of these agents to cytotoxic chemotherapy and other targeted therapies provides a potential combinatorial path forward for this novel class of therapies. Developing optimal combinations while balancing toxicity are among the top clinical challenges that must be overcome before we can anticipate adoption of these agents into the armamentarium of AML therapy.
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Affiliation(s)
- Nadya Jammal
- Department of Leukemia, University of Texas, MD Anderson Cancer Center , Houston, Texas, USA
| | - Caitlin R Rausch
- Department of Leukemia, University of Texas, MD Anderson Cancer Center , Houston, Texas, USA
| | - Tapan M Kadia
- Department of Leukemia, University of Texas, MD Anderson Cancer Center , Houston, Texas, USA
| | - Naveen Pemmaraju
- Department of Leukemia, University of Texas, MD Anderson Cancer Center , Houston, Texas, USA
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47
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Menasche BL, Davis EM, Wang S, Ouyang Y, Li S, Yu H, Shen J. PBRM1 and the glycosylphosphatidylinositol biosynthetic pathway promote tumor killing mediated by MHC-unrestricted cytotoxic lymphocytes. SCIENCE ADVANCES 2020; 6:eabc3243. [PMID: 33246952 PMCID: PMC7695474 DOI: 10.1126/sciadv.abc3243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/14/2020] [Indexed: 06/12/2023]
Abstract
Major histocompatibility complex (MHC)-unrestricted cytotoxic lymphocytes (CLs) such as natural killer (NK) cells can detect and destroy tumor and virus-infected cells resistant to T cell-mediated killing. Here, we performed genome-wide genetic screens to identify tumor-intrinsic genes regulating killing by MHC-unrestricted CLs. A group of genes identified in our screens encode enzymes for the biosynthesis of the glycosylphosphatidylinositol (GPI) anchor, which is not involved in tumor response to T cell-mediated cytotoxicity. Another gene identified in the screens was PBRM1, which encodes a subunit of the PBAF form of the SWI/SNF chromatin-remodeling complex. PBRM1 mutations in tumor cells cause resistance to MHC-unrestricted killing, in contrast to their sensitizing effects on T cell-mediated killing. PBRM1 and the GPI biosynthetic pathway regulate the ligands of NK cell receptors in tumor cells and promote cytolytic granule secretion in CLs. The regulators identified in this work represent potential targets for cancer immunotherapy.
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Affiliation(s)
- Bridget L Menasche
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Eric M Davis
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Shifeng Wang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- Department of Chinese Medicine Information Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yan Ouyang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Suzhao Li
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Haijia Yu
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jingshi Shen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
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48
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Single-cell derived tumor organoids display diversity in HLA class I peptide presentation. Nat Commun 2020; 11:5338. [PMID: 33087703 PMCID: PMC7577990 DOI: 10.1038/s41467-020-19142-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
Tumor heterogeneity is a major cause of therapeutic resistance. Immunotherapy may exploit alternative vulnerabilities of drug-resistant cells, where tumor-specific human leukocyte antigen (HLA) peptide ligands are promising leads to invoke targeted anti-tumor responses. Here, we investigate the variability in HLA class I peptide presentation between different clonal cells of the same colorectal cancer patient, using an organoid system. While clone-specific differences in HLA peptide presentation were observed, broad inter-clone variability was even more prevalent (15–25%). By coupling organoid proteomics and HLA peptide ligandomics, we also found that tumor-specific ligands from DNA damage control and tumor suppressor source proteins were prominently presented by tumor cells, coinciding likely with the silencing of such cytoprotective functions. Collectively, these data illustrate the heterogeneous HLA peptide presentation landscape even within one individual, and hint that a multi-peptide vaccination approach against highly conserved tumor suppressors may be a viable option in patients with low tumor-mutational burden. Immunotherapy may exploit alternative vulnerabilities of drug resistant cells. Here, the authors show that the HLA peptide presentation landscape is heterogeneous even within one individual, hinting that a multi-peptide vaccination approach against highly conserved tumor suppressors may be needed.
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49
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Khalaf K, Janowicz K, Dyszkiewicz-Konwińska M, Hutchings G, Dompe C, Moncrieff L, Jankowski M, Machnik M, Oleksiewicz U, Kocherova I, Petitte J, Mozdziak P, Shibli JA, Iżycki D, Józkowiak M, Piotrowska-Kempisty H, Skowroński MT, Antosik P, Kempisty B. CRISPR/Cas9 in Cancer Immunotherapy: Animal Models and Human Clinical Trials. Genes (Basel) 2020; 11:E921. [PMID: 32796761 PMCID: PMC7463827 DOI: 10.3390/genes11080921] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Even though chemotherapy and immunotherapy emerged to limit continual and unregulated proliferation of cancer cells, currently available therapeutic agents are associated with high toxicity levels and low success rates. Additionally, ongoing multi-targeted therapies are limited only for few carcinogenesis pathways, due to continually emerging and evolving mutations of proto-oncogenes and tumor-suppressive genes. CRISPR/Cas9, as a specific gene-editing tool, is used to correct causative mutations with minimal toxicity, but is also employed as an adjuvant to immunotherapy to achieve a more robust immunological response. Some of the most critical limitations of the CRISPR/Cas9 technology include off-target mutations, resulting in nonspecific restrictions of DNA upstream of the Protospacer Adjacent Motifs (PAM), ethical agreements, and the lack of a scientific consensus aiming at risk evaluation. Currently, CRISPR/Cas9 is tested on animal models to enhance genome editing specificity and induce a stronger anti-tumor response. Moreover, ongoing clinical trials use the CRISPR/Cas9 system in immune cells to modify genomes in a target-specific manner. Recently, error-free in vitro systems have been engineered to overcome limitations of this gene-editing system. The aim of the article is to present the knowledge concerning the use of CRISPR Cas9 technique in targeting treatment-resistant cancers. Additionally, the use of CRISPR/Cas9 is aided as an emerging supplementation of immunotherapy, currently used in experimental oncology. Demonstrating further, applications and advances of the CRISPR/Cas9 technique are presented in animal models and human clinical trials. Concluding, an overview of the limitations of the gene-editing tool is proffered.
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Affiliation(s)
- Khalil Khalaf
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (K.K.); (K.J.); (M.D.-K.); (G.H.); (M.J.); (I.K.)
| | - Krzysztof Janowicz
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (K.K.); (K.J.); (M.D.-K.); (G.H.); (M.J.); (I.K.)
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (C.D.); (L.M.)
| | - Marta Dyszkiewicz-Konwińska
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (K.K.); (K.J.); (M.D.-K.); (G.H.); (M.J.); (I.K.)
- Department of Biomaterials and Experimental Dentistry, Poznan University of Medical Sciences, 60-812 Poznań, Poland
| | - Greg Hutchings
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (K.K.); (K.J.); (M.D.-K.); (G.H.); (M.J.); (I.K.)
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (C.D.); (L.M.)
| | - Claudia Dompe
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (C.D.); (L.M.)
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznań, Poland
| | - Lisa Moncrieff
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (C.D.); (L.M.)
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznań, Poland
| | - Maurycy Jankowski
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (K.K.); (K.J.); (M.D.-K.); (G.H.); (M.J.); (I.K.)
| | - Marta Machnik
- Department of Cancer Immunology, Poznan University of Medical Sciences, 60-408 Poznan, Poland; (M.M.); (U.O.); (D.I.)
- Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 60-408 Poznan, Poland; (M.M.); (U.O.); (D.I.)
- Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Ievgeniia Kocherova
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (K.K.); (K.J.); (M.D.-K.); (G.H.); (M.J.); (I.K.)
| | - Jim Petitte
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA;
| | - Paul Mozdziak
- Physiology Graduate Program, North Carolina State University, Raleigh, NC 27695, USA;
| | - Jamil A. Shibli
- Department of Periodontology and Oral Implantology, Dental Research Division, University of Guarulhos, Guarulhos 07023-070, Brazil;
| | - Dariusz Iżycki
- Department of Cancer Immunology, Poznan University of Medical Sciences, 60-408 Poznan, Poland; (M.M.); (U.O.); (D.I.)
| | - Małgorzata Józkowiak
- Department of Toxicology, Poznan University of Medical Sciences, 61-631 Poznań, Poland; (M.J.); (H.P.-K.)
| | - Hanna Piotrowska-Kempisty
- Department of Toxicology, Poznan University of Medical Sciences, 61-631 Poznań, Poland; (M.J.); (H.P.-K.)
| | - Mariusz T. Skowroński
- Department of Basic and Preclinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Toruń, Poland;
| | - Paweł Antosik
- Department of Veterinary Surgery, Nicolaus Copernicus University in Torun, 87-100 Toruń, Poland;
| | - Bartosz Kempisty
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznań, Poland; (K.K.); (K.J.); (M.D.-K.); (G.H.); (M.J.); (I.K.)
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznań, Poland
- Department of Veterinary Surgery, Nicolaus Copernicus University in Torun, 87-100 Toruń, Poland;
- Department of Obstetrics and Gynecology, University Hospital and Masaryk University, 601 77 Brno, Czech Republic
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50
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Navarrete-Bernal MGC, Cervantes-Badillo MG, Martínez-Herrera JF, Lara-Torres CO, Gerson-Cwilich R, Zentella-Dehesa A, Ibarra-Sánchez MDJ, Esparza-López J, Montesinos JJ, Cortés-Morales VA, Osorio-Pérez D, Villegas-Osorno DA, Reyes-Sánchez E, Salazar-Sojo P, Tallabs-Utrilla LF, Romero-Córdoba S, Rocha-Zavaleta L. Biological Landscape of Triple Negative Breast Cancers Expressing CTLA-4. Front Oncol 2020; 10:1206. [PMID: 32850353 PMCID: PMC7419680 DOI: 10.3389/fonc.2020.01206] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Patients with triple-negative breast cancer (TNBC) have a poor prognosis, partly because of the absence of targeted therapies. Recognition of the key role of immune responses against cancer has allowed the advent of immunotherapy, focused on the inhibition of negative immune checkpoints, such as CTLA-4. CTLA-4 is also expressed in some cancer cells, but its activity in tumor cells is not completely understood. Thus, the aim of the present work was to determine the biological landscape and functions of CTLA-4 expressed in TNBC cells through preclinical and in silico analysis. Exploration of CTLA-4 by immunohistochemistry in 50 TNBC tumors revealed membrane and cytoplasmic expression at different intensities. Preclinical experiments, using TNBC cell lines, showed that stimulation of CTLA-4 with CD80 enhances activation of the ERK1/2 signaling pathway, while CTLA-4 blockade by Ipilimumab induces the activation of AKT and reduces cell proliferation in vitro. We then developed an analytic pipeline to define the effects of CTLA-4 in available public data that allowed us to identify four distinct tumor clusters associated with CTLA-4 activation, which are characterized by enrichment of distinctive pathways associated with cell adhesion, MAPK signaling, TGF-ß, VEGF, TNF-α, drug metabolism, ion and amino acid transport, and KRAS signaling, among others. In addition, blockade of CTLA-4 induced increased secretion of IL-2 by tumor cells, suggesting that the receptor regulates cellular functions that may impact the immune microenvironment. This is relevant because a deep characterization of immune infiltrate, conducted using public data to estimate the abundancies of immune-cell types, showed that CTLA-4-activated-like tumors present a conditional immune state similar to an escape phenotype exploited by cancer cells. Finally, by interrogating transcriptional predictors of immunotherapy response, we defined that CTLA-4 activation correlates with high immune scores related to good clinical predicted responses to anti-CTLA-4 therapy. This work sheds new light on the roles of activated CLTA-4 in the tumor compartment and suggests an important interplay between tumor CLTA-4-activated portraits and immune-infiltrating cell populations.
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Affiliation(s)
- María G C Navarrete-Bernal
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico
| | - Mayte G Cervantes-Badillo
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico.,Programa Institucional de Cáncer de Mama, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico
| | | | - César O Lara-Torres
- American British Cowdray Medical Center, Pathology Service, Ciudad de Mexico, Mexico
| | | | - Alejandro Zentella-Dehesa
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico.,Programa Institucional de Cáncer de Mama, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico.,Biochemistry Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico
| | - María de Jesús Ibarra-Sánchez
- Biochemistry Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico.,Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de Mexico-Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - José Esparza-López
- Biochemistry Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico.,Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de Mexico-Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Juan J Montesinos
- Laboratorio de Células Troncales Mesenquimales, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Ciudad de Mexico, Mexico
| | - Víctor Adrián Cortés-Morales
- Laboratorio de Células Troncales Mesenquimales, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Ciudad de Mexico, Mexico
| | - Diego Osorio-Pérez
- American British Cowdray Medical Center, Cancer Center, Ciudad de Mexico, Mexico
| | | | | | | | | | - Sandra Romero-Córdoba
- Programa Institucional de Cáncer de Mama, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico.,Biochemistry Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico
| | - Leticia Rocha-Zavaleta
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico.,Programa Institucional de Cáncer de Mama, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de Mexico, Mexico
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