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Mullen NJ, Shukla SK, Thakur R, Kollala SS, Wang D, Chaika N, Santana JF, Miklavcic WR, LaBreck DA, Mallareddy JR, Price DH, Natarajan A, Mehla K, Sykes DB, Hollingsworth MA, Singh PK. DHODH inhibition enhances the efficacy of immune checkpoint blockade by increasing cancer cell antigen presentation. eLife 2024; 12:RP87292. [PMID: 38973593 PMCID: PMC11230627 DOI: 10.7554/elife.87292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
Pyrimidine nucleotide biosynthesis is a druggable metabolic dependency of cancer cells, and chemotherapy agents targeting pyrimidine metabolism are the backbone of treatment for many cancers. Dihydroorotate dehydrogenase (DHODH) is an essential enzyme in the de novo pyrimidine biosynthesis pathway that can be targeted by clinically approved inhibitors. However, despite robust preclinical anticancer efficacy, DHODH inhibitors have shown limited single-agent activity in phase 1 and 2 clinical trials. Therefore, novel combination therapy strategies are necessary to realize the potential of these drugs. To search for therapeutic vulnerabilities induced by DHODH inhibition, we examined gene expression changes in cancer cells treated with the potent and selective DHODH inhibitor brequinar (BQ). This revealed that BQ treatment causes upregulation of antigen presentation pathway genes and cell surface MHC class I expression. Mechanistic studies showed that this effect is (1) strictly dependent on pyrimidine nucleotide depletion, (2) independent of canonical antigen presentation pathway transcriptional regulators, and (3) mediated by RNA polymerase II elongation control by positive transcription elongation factor B (P-TEFb). Furthermore, BQ showed impressive single-agent efficacy in the immunocompetent B16F10 melanoma model, and combination treatment with BQ and dual immune checkpoint blockade (anti-CTLA-4 plus anti-PD-1) significantly prolonged mouse survival compared to either therapy alone. Our results have important implications for the clinical development of DHODH inhibitors and provide a rationale for combination therapy with BQ and immune checkpoint blockade.
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Affiliation(s)
- Nicholas J Mullen
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Surendra K Shukla
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
| | - Ravi Thakur
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
| | - Sai Sundeep Kollala
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Dezhen Wang
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Nina Chaika
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Juan F Santana
- Department of Biochemistry and Molecular Biology, University of IowaIowa CityUnited States
| | - William R Miklavcic
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Drew A LaBreck
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
| | - Jayapal Reddy Mallareddy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - David H Price
- Department of Biochemistry and Molecular Biology, University of IowaIowa CityUnited States
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Kamiya Mehla
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General HospitalBostonUnited States
- Harvard Stem Cell InstituteCambridgeUnited States
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Pankaj K Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
- Department of Oncology Science, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
- OU Health Stephenson Cancer Center, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
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2
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Mullen NJ, Shukla SK, Thakur R, Kollala SS, Wang D, Chaika N, Santana JF, Miklavcic WR, LaBreck DA, Mallareddy JR, Price DH, Natarajan A, Mehla K, Sykes DB, Hollingsworth MA, Singh PK. DHODH inhibition enhances the efficacy of immune checkpoint blockade by increasing cancer cell antigen presentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.03.535399. [PMID: 37066260 PMCID: PMC10103971 DOI: 10.1101/2023.04.03.535399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Pyrimidine nucleotide biosynthesis is a druggable metabolic dependency of cancer cells, and chemotherapy agents targeting pyrimidine metabolism are the backbone of treatment for many cancers. Dihydroorotate dehydrogenase (DHODH) is an essential enzyme in the de novo pyrimidine biosynthesis pathway that can be targeted by clinically approved inhibitors. However, despite robust preclinical anticancer efficacy, DHODH inhibitors have shown limited single-agent activity in phase 1 and 2 clinical trials. Therefore, novel combination therapy strategies are necessary to realize the potential of these drugs. To search for therapeutic vulnerabilities induced by DHODH inhibition, we examined gene expression changes in cancer cells treated with the potent and selective DHODH inhibitor brequinar (BQ). This revealed that BQ treatment causes upregulation of antigen presentation pathway genes and cell surface MHC class I expression. Mechanistic studies showed that this effect is 1) strictly dependent on pyrimidine nucleotide depletion, 2) independent of canonical antigen presentation pathway transcriptional regulators, and 3) mediated by RNA polymerase II elongation control by positive transcription elongation factor B (P-TEFb). Furthermore, BQ showed impressive single-agent efficacy in the immunocompetent B16F10 melanoma model, and combination treatment with BQ and dual immune checkpoint blockade (anti-CTLA-4 plus anti-PD-1) significantly prolonged mouse survival compared to either therapy alone. Our results have important implications for the clinical development of DHODH inhibitors and provide a rationale for combination therapy with BQ and immune checkpoint blockade.
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Affiliation(s)
- Nicholas J. Mullen
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Surendra K. Shukla
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
| | - Ravi Thakur
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
| | - Sai Sundeep Kollala
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Dezhen Wang
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Nina Chaika
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Juan F. Santana
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa, USA
| | - William R. Miklavcic
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Drew A. LaBreck
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
| | - Jayapal Reddy Mallareddy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - David H. Price
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Kamiya Mehla
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
| | - David B. Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Michael A. Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
| | - Pankaj K. Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA
- Department of Oncology Science, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73014, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
- OU Health Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
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3
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Sarapultsev A, Gusev E, Komelkova M, Utepova I, Luo S, Hu D. JAK-STAT signaling in inflammation and stress-related diseases: implications for therapeutic interventions. MOLECULAR BIOMEDICINE 2023; 4:40. [PMID: 37938494 PMCID: PMC10632324 DOI: 10.1186/s43556-023-00151-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
The Janus kinase-signal transducer and transcription activator pathway (JAK-STAT) serves as a cornerstone in cellular signaling, regulating physiological and pathological processes such as inflammation and stress. Dysregulation in this pathway can lead to severe immunodeficiencies and malignancies, and its role extends to neurotransduction and pro-inflammatory signaling mechanisms. Although JAK inhibitors (Jakinibs) have successfully treated immunological and inflammatory disorders, their application has generally been limited to diseases with similar pathogenic features. Despite the modest expression of JAK-STAT in the CNS, it is crucial for functions in the cortex, hippocampus, and cerebellum, making it relevant in conditions like Parkinson's disease and other neuroinflammatory disorders. Furthermore, the influence of the pathway on serotonin receptors and phospholipase C has implications for stress and mood disorders. This review expands the understanding of JAK-STAT, moving beyond traditional immunological contexts to explore its role in stress-related disorders and CNS function. Recent findings, such as the effectiveness of Jakinibs in chronic conditions such as rheumatoid arthritis, expand their therapeutic applicability. Advances in isoform-specific inhibitors, including filgotinib and upadacitinib, promise greater specificity with fewer off-target effects. Combination therapies, involving Jakinibs and monoclonal antibodies, aiming to enhance therapeutic specificity and efficacy also give great hope. Overall, this review bridges the gap between basic science and clinical application, elucidating the complex influence of the JAK-STAT pathway on human health and guiding future interventions.
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Affiliation(s)
- Alexey Sarapultsev
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080, Chelyabinsk, Russia.
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049, Ekaterinburg, Russia.
| | - Evgenii Gusev
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080, Chelyabinsk, Russia
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049, Ekaterinburg, Russia
| | - Maria Komelkova
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080, Chelyabinsk, Russia
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049, Ekaterinburg, Russia
| | - Irina Utepova
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049, Ekaterinburg, Russia
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002, Ekaterinburg, Russian Federation
| | - Shanshan Luo
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Desheng Hu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, Wuhan, 430022, China
- Clinical Research Center of Cancer Immunotherapy, Hubei Wuhan, 430022, China
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4
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Rabaan AA, AlSaihati H, Bukhamsin R, Bakhrebah MA, Nassar MS, Alsaleh AA, Alhashem YN, Bukhamseen AY, Al-Ruhimy K, Alotaibi M, Alsubki RA, Alahmed HE, Al-Abdulhadi S, Alhashem FA, Alqatari AA, Alsayyah A, Farahat RA, Abdulal RH, Al-Ahmed AH, Imran M, Mohapatra RK. Application of CRISPR/Cas9 Technology in Cancer Treatment: A Future Direction. Curr Oncol 2023; 30:1954-1976. [PMID: 36826113 PMCID: PMC9955208 DOI: 10.3390/curroncol30020152] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Gene editing, especially with clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9), has advanced gene function science. Gene editing's rapid advancement has increased its medical/clinical value. Due to its great specificity and efficiency, CRISPR/Cas9 can accurately and swiftly screen the whole genome. This simplifies disease-specific gene therapy. To study tumor origins, development, and metastasis, CRISPR/Cas9 can change genomes. In recent years, tumor treatment research has increasingly employed this method. CRISPR/Cas9 can treat cancer by removing genes or correcting mutations. Numerous preliminary tumor treatment studies have been conducted in relevant fields. CRISPR/Cas9 may treat gene-level tumors. CRISPR/Cas9-based personalized and targeted medicines may shape tumor treatment. This review examines CRISPR/Cas9 for tumor therapy research, which will be helpful in providing references for future studies on the pathogenesis of malignancy and its treatment.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Hajir AlSaihati
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Rehab Bukhamsin
- Dammam Regional Laboratory and Blood Bank, Dammam 31411, Saudi Arabia
| | - Muhammed A. Bakhrebah
- Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Majed S. Nassar
- Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Abdulmonem A. Alsaleh
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Yousef N. Alhashem
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Ammar Y. Bukhamseen
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Khalil Al-Ruhimy
- Department of Public Health, Ministry of Health, Riyadh 14235, Saudi Arabia
| | - Mohammed Alotaibi
- Department of Public Health, Ministry of Health, Riyadh 14235, Saudi Arabia
| | - Roua A. Alsubki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Hejji E. Alahmed
- Department of Laboratory and Blood Bank, King Fahad Hospital, Al Hofuf 36441, Saudi Arabia
| | - Saleh Al-Abdulhadi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Riyadh 11942, Saudi Arabia
- Saleh Office for Medical Genetic and Genetic Counseling Services, The House of Expertise, Prince Sattam Bin Abdulaziz University, Dammam 32411, Saudi Arabia
| | - Fatemah A. Alhashem
- Laboratory Medicine Department, Hematopathology Division, King Fahad Hospital of the University, Al-Khobar 31441, Saudi Arabia
| | - Ahlam A. Alqatari
- Hematopathology Department, Clinical Pathology, Al-Dorr Specialist Medical Center, Qatif 31911, Saudi Arabia
| | - Ahmed Alsayyah
- Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | - Rwaa H. Abdulal
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ali H. Al-Ahmed
- Dammam Health Network, Eastern Health Cluster, Dammam 31444, Saudi Arabia
| | - Mohd. Imran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Ranjan K. Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, India
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5
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Muto S, Enta A, Maruya Y, Inomata S, Yamaguchi H, Mine H, Takagi H, Ozaki Y, Watanabe M, Inoue T, Yamaura T, Fukuhara M, Okabe N, Matsumura Y, Hasegawa T, Osugi J, Hoshino M, Higuchi M, Shio Y, Hamada K, Suzuki H. Wnt/β-Catenin Signaling and Resistance to Immune Checkpoint Inhibitors: From Non-Small-Cell Lung Cancer to Other Cancers. Biomedicines 2023; 11:biomedicines11010190. [PMID: 36672698 PMCID: PMC9855612 DOI: 10.3390/biomedicines11010190] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. The standard of care for advanced non-small-cell lung cancer (NSCLC) without driver-gene mutations is a combination of an anti-PD-1/PD-L1 antibody and chemotherapy, or an anti-PD-1/PD-L1 antibody and an anti-CTLA-4 antibody with or without chemotherapy. Although there were fewer cases of disease progression in the early stages of combination treatment than with anti-PD-1/PD-L1 antibodies alone, only approximately half of the patients had a long-term response. Therefore, it is necessary to elucidate the mechanisms of resistance to immune checkpoint inhibitors. Recent reports of such mechanisms include reduced cancer-cell immunogenicity, loss of major histocompatibility complex, dysfunctional tumor-intrinsic interferon-γ signaling, and oncogenic signaling leading to immunoediting. Among these, the Wnt/β-catenin pathway is a notable potential mechanism of immune escape and resistance to immune checkpoint inhibitors. In this review, we will summarize findings on these resistance mechanisms in NSCLC and other cancers, focusing on Wnt/β-catenin signaling. First, we will review the molecular biology of Wnt/β-catenin signaling, then discuss how it can induce immunoediting and resistance to immune checkpoint inhibitors. We will also describe other various mechanisms of immune-checkpoint-inhibitor resistance. Finally, we will propose therapeutic approaches to overcome these mechanisms.
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Affiliation(s)
- Satoshi Muto
- Correspondence: ; Tel.: +81-24-547-1252; Fax: +81-24-548-2735
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6
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Shi H, Doench JG, Chi H. CRISPR screens for functional interrogation of immunity. Nat Rev Immunol 2022:10.1038/s41577-022-00802-4. [DOI: 10.1038/s41577-022-00802-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
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7
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Hou J, He Z, Liu T, Chen D, Wang B, Wen Q, Zheng X. Evolution of Molecular Targeted Cancer Therapy: Mechanisms of Drug Resistance and Novel Opportunities Identified by CRISPR-Cas9 Screening. Front Oncol 2022; 12:755053. [PMID: 35372044 PMCID: PMC8970599 DOI: 10.3389/fonc.2022.755053] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/17/2022] [Indexed: 12/14/2022] Open
Abstract
Molecular targeted therapy has revolutionized the landscape of cancer treatment due to better therapeutic responses and less systemic toxicity. However, therapeutic resistance is a major challenge in clinical settings that hinders continuous clinical benefits for cancer patients. In this regard, unraveling the mechanisms of drug resistance may identify new druggable genetic alterations for molecularly targeted therapies, thus contributing to improved therapeutic efficacies. The recent rapid development of novel methodologies including CRISPR-Cas9 screening technology and patient-derived models provides powerful tools to dissect the underlying mechanisms of resistance to targeted cancer therapies. In this review, we updated therapeutic targets undergoing preclinical and clinical evaluation for various cancer types. More importantly, we provided comprehensive elaboration of high throughput CRISPR-Cas9 screening in deciphering potential mechanisms of unresponsiveness to molecularly targeted therapies, which will shed light on the discovery of novel opportunities for designing next-generation anti-cancer drugs.
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Affiliation(s)
- Jue Hou
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zongsheng He
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Tian Liu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Dongfeng Chen
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Bin Wang
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Xi Zheng, ; Qinglian Wen, ; Bin Wang,
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Xi Zheng, ; Qinglian Wen, ; Bin Wang,
| | - Xi Zheng
- Department of Gastroenterology, Chongqing University Cancer Hospital, Chongqing, China
- *Correspondence: Xi Zheng, ; Qinglian Wen, ; Bin Wang,
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8
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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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9
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Darbeheshti F. The Immunogenetics of Melanoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:383-396. [DOI: 10.1007/978-3-030-92616-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Martin TD, Patel RS, Cook DR, Choi MY, Patil A, Liang AC, Li MZ, Haigis KM, Elledge SJ. The adaptive immune system is a major driver of selection for tumor suppressor gene inactivation. Science 2021; 373:1327-1335. [PMID: 34529489 DOI: 10.1126/science.abg5784] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During tumorigenesis, tumors must evolve to evade the immune system and do so by disrupting the genes involved in antigen processing and presentation or up-regulating inhibitory immune checkpoint genes. We performed in vivo CRISPR screens in syngeneic mouse tumor models to examine requirements for tumorigenesis both with and without adaptive immune selective pressure. In each tumor type tested, we found a marked enrichment for the loss of tumor suppressor genes (TSGs) in the presence of an adaptive immune system relative to immunocompromised mice. Nearly one-third of TSGs showed preferential enrichment, often in a cancer- and tissue-specific manner. These results suggest that clonal selection of recurrent mutations found in cancer is driven largely by the tumor’s requirement to avoid the adaptive immune system.
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MESH Headings
- Animals
- CRISPR-Cas Systems
- Carcinogenesis
- Cell Line, Tumor
- Chemokine CCL2/metabolism
- Female
- GTP-Binding Protein alpha Subunits, G12-G13/genetics
- GTP-Binding Protein alpha Subunits, G12-G13/metabolism
- Gene Silencing
- Genes, Tumor Suppressor
- Humans
- Immune Evasion/genetics
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/immunology
- Mammary Neoplasms, Experimental/pathology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, SCID
- Neoplasm Transplantation
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/immunology
- Neoplasms, Experimental/pathology
- Selection, Genetic
- Tumor Microenvironment
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Affiliation(s)
- Timothy D Martin
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rupesh S Patel
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Danielle R Cook
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mei Yuk Choi
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ajinkya Patil
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony C Liang
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mamie Z Li
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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11
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CRISPR-based screens uncover determinants of immunotherapy response in multiple myeloma. Blood Adv 2021; 4:2899-2911. [PMID: 32589729 DOI: 10.1182/bloodadvances.2019001346] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/11/2020] [Indexed: 02/01/2023] Open
Abstract
Cancer cells commonly develop resistance to immunotherapy by loss of antigen expression. Combinatorial treatments that increase levels of the target antigen on the surface of cancer cells have the potential to restore efficacy to immunotherapy. Here, we use our CRISPR interference- and CRISPR activation-based functional genomics platform to systematically identify pathways controlling cell surface expression of the multiple myeloma immunotherapy antigen B-cell maturation antigen (BCMA). We discovered that pharmacologic inhibition of HDAC7 and the Sec61 complex increased cell surface BCMA, including in primary patient cells. Pharmacologic Sec61 inhibition enhanced the antimyeloma efficacy of a BCMA-targeted antibody-drug conjugate. A CRISPR interference chimeric antigen receptor T cells (CAR-T cells) coculture screen enabled us to identify both antigen-dependent and antigen-independent mechanisms controlling response of myeloma cells to BCMA-targeted CAR-T cells. Thus, our study shows the potential of CRISPR screens to uncover mechanisms controlling response of cancer cells to immunotherapy and to suggest potential combination therapies.
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12
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Li M, Xu Y, Liang J, Lin H, Qi X, Li F, Han P, Gao Y, Yang X. USP22 deficiency in melanoma mediates resistance to T cells through IFNγ-JAK1-STAT1 signal axis. Mol Ther 2021; 29:2108-2120. [PMID: 33601053 DOI: 10.1016/j.ymthe.2021.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/12/2020] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
Genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated 9 (Cas9)-mediated loss-of-function screens are powerful tools for identifying genes responsible for diverse phenotypes. Here, we perturbed genes in melanoma cells to screen for genes involved in tumor escape from T cell-mediated killing. Multiple interferon gamma (IFNγ) signaling-related genes were enriched in melanoma cells resistant to T cell killing. In addition, deletion of the deubiquitinating protease ubiquitin specific peptidase 22 (USP22) in mouse melanoma (B16-OVA) cells decreased the efficacy of T cell-mediated killing, both in vitro and in vivo, while overexpression enhanced tumor-cell sensitivity to T (OT-I) cell-mediated killing. USP22 deficiency in both mouse and human melanoma cells showed impaired sensitivity to interferon pathway and USP22 was positively correlated with key molecules of interferon pathway in clinical melanoma samples. Mechanistically, USP22 may directly interact with signal transducer and activator of transcription 1 (STAT1), deubiquitinate it, and improve its stability in both human and mouse melanoma cells. Our findings identified a previously unknown function of USP22 and linked the loss of genes in tumor cells that are essential for escaping the effector function of CD8+ T cells during immunotherapy.
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Affiliation(s)
- Min Li
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yanqin Xu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jie Liang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hao Lin
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xinyue Qi
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Fanlin Li
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ping Han
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yanfeng Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, People's Republic of China
| | - Xuanming Yang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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13
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Sena LA, Fountain J, Isaacsson Velho P, Lim SJ, Wang H, Nizialek E, Rathi N, Nussenzveig R, Maughan BL, Velez MG, Ashkar R, Larson AC, Pritchard CC, Adra N, Bryce AH, Agarwal N, Pardoll DM, Eshleman JR, Lotan TL, Antonarakis ES. Tumor Frameshift Mutation Proportion Predicts Response to Immunotherapy in Mismatch Repair-Deficient Prostate Cancer. Oncologist 2020; 26:e270-e278. [PMID: 33215787 PMCID: PMC7873327 DOI: 10.1002/onco.13601] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Background Genomic biomarkers that predict response to anti‐PD1 therapy in prostate cancer are needed. Frameshift mutations are predicted to generate more neoantigens than missense mutations; therefore, we hypothesized that the number or proportion of tumor frameshift mutations would correlate with response to anti‐PD1 therapy in prostate cancer. Methods To enrich for response to anti‐PD1 therapy, we assembled a multicenter cohort of 65 men with mismatch repair‐deficient (dMMR) prostate cancer. Patient characteristics and outcomes were determined by retrospective chart review. Clinical somatic DNA sequencing was used to determine tumor mutational burden (TMB), frameshift mutation burden, and frameshift mutation proportion (FSP), which were correlated to outcomes on anti‐PD1 treatment. We subsequently used data from a clinical trial of pembrolizumab in patients with nonprostatic dMMR cancers of various histologies as a biomarker validation cohort. Results Nineteen of 65 patients with dMMR metastatic castration‐resistant prostate cancer were treated with anti‐PD1 therapy. The PSA50 response rate was 65%, and the median progression‐free survival (PFS) was 24 (95% confidence interval 16–54) weeks. Tumor FSP, more than overall TMB, correlated most strongly with prolonged PFS and overall survival (OS) on anti‐PD1 treatment and with density of CD8+ tumor‐infiltrating lymphocytes. High FSP similarly identified patients with longer PFS as well as OS on anti‐PD1 therapy in a validation cohort. Conclusion Tumor FSP correlated with prolonged efficacy of anti‐PD1 treatment among patients with dMMR cancers and may represent a new biomarker of immune checkpoint inhibitor sensitivity. Implications for Practice Given the modest efficacy of immune checkpoint inhibition (ICI) in unselected patients with advanced prostate cancer, biomarkers of ICI sensitivity are needed. To facilitate biomarker discovery, a cohort of patients with DNA mismatch repair‐deficient (dMMR) prostate cancer was assembled, as these patients are enriched for responses to ICI. A high response rate to anti‐PD1 therapy in these patients was observed; however, these responses were not durable in most patients. Notably, tumor frameshift mutation proportion (FSP) was identified as a novel biomarker that was associated with prolonged response to anti‐PD1 therapy in this cohort. This finding was validated in a separate cohort of patients with nonprostatic dMMR cancers of various primary histologies. This works suggests that FSP predicts response to anti‐PD1 therapy in dMMR cancers, which should be validated prospectively in larger independent cohorts. Biomarkers of immune checkpoint inhibition sensitivity are needed. This article reports on genomic biomarkers that may predict response to anti‐PD1 therapy in prostate cancer.
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Affiliation(s)
- Laura A Sena
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julia Fountain
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Pedro Isaacsson Velho
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Su Jin Lim
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Wang
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emily Nizialek
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nityam Rathi
- Division of Medical Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Roberto Nussenzveig
- Division of Medical Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Benjamin L Maughan
- Division of Medical Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | | | - Ryan Ashkar
- Division of Hematology-Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Amanda C Larson
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Nabil Adra
- Division of Hematology-Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Alan H Bryce
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, Arizona, USA
| | - Neeraj Agarwal
- Division of Medical Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Drew M Pardoll
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - James R Eshleman
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tamara L Lotan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emmanuel S Antonarakis
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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14
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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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15
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韩 萍, 杨 选. 胞内染色法检测T细胞活化产生的细胞因子. Bio Protoc 2019. [DOI: 10.21769/bioprotoc.1010314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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