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Li Y, Li C, Yan J, Liao Y, Qin C, Wang L, Huang Y, Yang C, Wang J, Ding X, Yang YY, Yuan P. Polymeric micellar nanoparticles for effective CRISPR/Cas9 genome editing in cancer. Biomaterials 2024; 309:122573. [PMID: 38677222 DOI: 10.1016/j.biomaterials.2024.122573] [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: 11/12/2023] [Revised: 03/21/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9) gene editing has attracted extensive attentions in various fields, however, its clinical application is hindered by the lack of effective and safe delivery system. Herein, we reported a cationic micelle nanoparticle composed of cholesterol-modified branched small molecular PEI (PEI-CHO) and biodegradable PEG-b-polycarbonate block copolymer (PEG-PC), denoted as PEG-PC/PEI-CHO/pCas9, for the CRISPR/Cas9 delivery to realize genomic editing in cancer. Specifically, PEI-CHO condensed pCas9 into nanocomplexes, which were further encapsulated into PEG-PC nanoparticles (PEG-PC/PEI-CHO/pCas9). PEG-PC/PEI-CHO/pCas9 had a PEG shell, protecting DNA from degradation by nucleases. Enhanced cellular uptake of PEG-PC/PEI-CHO/pCas9 nanoparticles was observed as compared to that mediated by Lipo2k/pCas9 nanoparticles, thus leading to significantly elevated transfection efficiency after escaping from endosomes via the proton sponge effect of PEI. In addition, the presence of PEG shell greatly improved biocompatibility, and significantly enhanced the in vivo tumor retention of pCas9 compared to PEI-CHO/pCas9. Notably, apparent downregulation of GFP expression could be achieved both in vitro and in vivo by using PEG-PC/PEI-CHO/pCas9-sgGFP nanoparticles. Furthermore, PEG-PC/PEI-CHO/pCas9-sgMcl1 induced effective apoptosis and tumor suppression in a HeLa tumor xenograft mouse model by downregulating Mcl1 expression. This work may provide an alternative paradigm for the efficient and safe genome editing in cancer.
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Affiliation(s)
- Yuzhen Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chun Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Jiachang Yan
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Chengyuan Qin
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Lingyin Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Yi Huang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chuan Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Jianwei Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Xin Ding
- School of Medicine, Sun Yat-sen University, Shenzhen, 518107, China.
| | - Yi Yan Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore.
| | - Peiyan Yuan
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China.
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2
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Fang T, Chen G. Non-viral vector-based genome editing for cancer immunotherapy. Biomater Sci 2024; 12:3068-3085. [PMID: 38716572 DOI: 10.1039/d4bm00286e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Despite the exciting promise of cancer immunotherapy in the clinic, immune checkpoint blockade therapy and T cell-based therapies are often associated with low response rates, intrinsic and adaptive immune resistance, and systemic side effects. CRISPR-Cas-based genome editing appears to be an effective strategy to overcome these unmet clinical needs. As a safer delivery platform for the CRISPR-Cas system, non-viral nanoformulations have been recently explored to target tumor cells and immune cells, aiming to improve cancer immunotherapy on a gene level. In this review, we summarized the efforts of non-viral vector-based CRISPR-Cas-mediated genome editing in tumor cells and immune cells for cancer immunotherapy. Their design rationale and specific applications were highlighted.
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Affiliation(s)
- Tianxu Fang
- Department of Biomedical Engineering, McGill University, Montreal, QC, H3G 0B1, Canada.
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Guojun Chen
- Department of Biomedical Engineering, McGill University, Montreal, QC, H3G 0B1, Canada.
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3G 0B1, Canada
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3
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Mou Y, Chen Y, Fan Z, Ye L, Hu B, Han B, Wang G. Discovery of a novel small-molecule activator of SIRT3 that inhibits cell proliferation and migration by apoptosis and autophagy-dependent cell death pathways in colorectal cancer. Bioorg Chem 2024; 146:107327. [PMID: 38579616 DOI: 10.1016/j.bioorg.2024.107327] [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: 02/27/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
Colorectal cancer (CRC) is well known as a prevalent malignancy affecting the digestive tract, yet its precise etiological determinants remain to be elusive. Accordingly, identifying specific molecular targets for colorectal cancer and predicting potential malignant tumor behavior are potential strategies for therapeutic interventions. Of note, apoptosis (type I programmed cell death) has been widely reported to play a pivotal role in tumorigenesis by exerting a suppressive effect on cancer development. Moreover, autophagy-dependent cell death (type II programmed cell death) has been implicated in different types of human cancers. Thus, investigating the molecular mechanisms underlying apoptosis and autophagy-dependent cell death is paramount in treatment modalities of colorectal cancer. In this study, we uncovered that a new small-molecule activator of SIRT3, named MY-13, triggered both autophagy-dependent cell death and apoptosis by modulating the SIRT3/Hsp90/AKT signaling pathway. Consequently, this compound inhibited tumor cell proliferation and migration in RKO and HCT-116 cell lines. Moreover, we further demonstrated that the small-molecule activator significantly suppressed tumor growth in vivo. In conclusion, these findings demonstrate that the novel small-molecule activator of SIRT3 may hold a therapeutic potential as a drug candidate in colorectal cancer.
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Affiliation(s)
- Yi Mou
- Department of Gastroenterology, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Yanmei Chen
- Department of Gastroenterology, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhichao Fan
- Department of Gastroenterology, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Liansong Ye
- Department of Gastroenterology, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Bing Hu
- Department of Gastroenterology, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China.
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Guan Wang
- Department of Gastroenterology, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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Papakyriacou I, Kutkaite G, Rúbies Bedós M, Nagarajan D, Alford LP, Menden MP, Mao Y. Loss of NEDD8 in cancer cells causes vulnerability to immune checkpoint blockade in triple-negative breast cancer. Nat Commun 2024; 15:3581. [PMID: 38678024 PMCID: PMC11055868 DOI: 10.1038/s41467-024-47987-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: 03/22/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
Immune checkpoint blockade therapy aims to activate the immune system to eliminate cancer cells. However, clinical benefits are only recorded in a subset of patients. Here, we leverage genome-wide CRISPR/Cas9 screens in a Tumor-Immune co-Culture System focusing on triple-negative breast cancer (TNBC). We reveal that NEDD8 loss in cancer cells causes a vulnerability to nivolumab (anti-PD-1). Genetic deletion of NEDD8 only delays cell division initially but cell proliferation is unaffected after recovery. Since the NEDD8 gene is commonly essential, we validate this observation with additional CRISPR screens and uncover enhanced immunogenicity in NEDD8 deficient cells using proteomics. In female immunocompetent mice, PD-1 blockade lacks efficacy against established EO771 breast cancer tumors. In contrast, we observe tumor regression mediated by CD8+ T cells against Nedd8 deficient EO771 tumors after PD-1 blockade. In essence, we provide evidence that NEDD8 is conditionally essential in TNBC and presents as a synergistic drug target for PD-1/L1 blockade therapy.
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Affiliation(s)
- Irineos Papakyriacou
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ginte Kutkaite
- Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, Martinsried, Germany
| | - Marta Rúbies Bedós
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Divya Nagarajan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Liam P Alford
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Michael P Menden
- Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Yumeng Mao
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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Zhuang X, Woods J, Ji Y, Scheich S, Mo F, Rajagopalan S, Coulibaly ZA, Voss M, Urlaub H, Staudt LM, Pan KT, Long EO. Functional genomics identifies N-acetyllactosamine extension of complex N-glycans as a mechanism to evade lysis by natural killer cells. Cell Rep 2024; 43:114105. [PMID: 38619967 PMCID: PMC11170631 DOI: 10.1016/j.celrep.2024.114105] [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: 05/04/2023] [Revised: 12/31/2023] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
Natural killer (NK) cells are primary defenders against cancer precursors, but cancer cells can persist by evading immune surveillance. To investigate the genetic mechanisms underlying this evasion, we perform a genome-wide CRISPR screen using B lymphoblastoid cells. SPPL3, a peptidase that cleaves glycosyltransferases in the Golgi, emerges as a top hit facilitating evasion from NK cytotoxicity. SPPL3-deleted cells accumulate glycosyltransferases and complex N-glycans, disrupting not only binding of ligands to NK receptors but also binding of rituximab, a CD20 antibody approved for treating B cell cancers. Notably, inhibiting N-glycan maturation restores receptor binding and sensitivity to NK cells. A secondary CRISPR screen in SPPL3-deficient cells identifies B3GNT2, a transferase-mediating poly-LacNAc extension, as crucial for resistance. Mass spectrometry confirms enrichment of N-glycans bearing poly-LacNAc upon SPPL3 loss. Collectively, our study shows the essential role of SPPL3 and poly-LacNAc in cancer immune evasion, suggesting a promising target for cancer treatment.
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Affiliation(s)
- Xiaoxuan Zhuang
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - James Woods
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Yanlong Ji
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Sebastian Scheich
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fei Mo
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sumati Rajagopalan
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Zana A Coulibaly
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthias Voss
- Institute of Biochemistry, Kiel University, 24118 Kiel, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kuan-Ting Pan
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Eric O Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.
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6
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Xiang M, Li H, Zhan Y, Ma D, Gao Q, Fang Y. Functional CRISPR screens in T cells reveal new opportunities for cancer immunotherapies. Mol Cancer 2024; 23:73. [PMID: 38581063 PMCID: PMC10996278 DOI: 10.1186/s12943-024-01987-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: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
T cells are fundamental components in tumour immunity and cancer immunotherapies, which have made immense strides and revolutionized cancer treatment paradigm. However, recent studies delineate the predicament of T cell dysregulation in tumour microenvironment and the compromised efficacy of cancer immunotherapies. CRISPR screens enable unbiased interrogation of gene function in T cells and have revealed functional determinators, genetic regulatory networks, and intercellular interactions in T cell life cycle, thereby providing opportunities to revamp cancer immunotherapies. In this review, we briefly described the central roles of T cells in successful cancer immunotherapies, comprehensively summarised the studies of CRISPR screens in T cells, elaborated resultant master genes that control T cell activation, proliferation, fate determination, effector function, and exhaustion, and highlighted genes (BATF, PRDM1, and TOX) and signalling cascades (JAK-STAT and NF-κB pathways) that extensively engage in multiple branches of T cell responses. In conclusion, this review bridged the gap between discovering element genes to a specific process of T cell activities and apprehending these genes in the global T cell life cycle, deepened the understanding of T cell biology in tumour immunity, and outlined CRISPR screens resources that might facilitate the development and implementation of cancer immunotherapies in the clinic.
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Affiliation(s)
- Minghua Xiang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huayi Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zhan
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinglei Gao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yong Fang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Čaval T, Xu G, Baniasad M, Chu CW, Rice R, Hundal I, Czerwieniec G, Schwarz F. Mass Spectrometry Analysis of Glycopeptides Enriched by Anion Exchange-Mediated Methods Reveals PolyLacNAc-Extended N-Glycans in Integrins and Tetraspanins in Melanoma Cells. Anal Chem 2024; 96:5086-5094. [PMID: 38513651 PMCID: PMC10993200 DOI: 10.1021/acs.analchem.3c04045] [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: 09/08/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
Glycosylation is a key modulator of the functional state of proteins. Recent developments in large-scale analysis of intact glycopeptides have enabled the identification of numerous glycan structures that are relevant in pathophysiological processes. However, one motif found in N-glycans, poly-N-acetyllactosamine (polyLacNAc), still poses a substantial challenge to mass spectrometry-based glycoproteomic analysis due to its relatively low abundance and large size. In this work, we developed approaches for the systematic mapping of polyLacNAc-elongated N-glycans in melanoma cells. We first evaluated five anion exchange-based matrices for enriching intact glycopeptides and selected two materials that provided better overall enrichment efficiency. We then tested the robustness of the methodology by quantifying polyLacNAc-containing glycopeptides as well as changes in protein fucosylation and sialylation. Finally, we applied the optimal enrichment methods to discover glycopeptides containing polyLacNAc motifs in melanoma cells and found that integrins and tetraspanins are substantially modified with these structures. This study demonstrates the feasibility of glycoproteomic approaches for identification of glycoproteins with polyLacNAc motifs.
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Affiliation(s)
| | | | - Maryam Baniasad
- InterVenn Biosciences, 2 Tower Place Fifth Floor, South San Francisco, California 94080, United States
| | - Chih-Wei Chu
- InterVenn Biosciences, 2 Tower Place Fifth Floor, South San Francisco, California 94080, United States
| | - Rachel Rice
- InterVenn Biosciences, 2 Tower Place Fifth Floor, South San Francisco, California 94080, United States
| | - Itati Hundal
- InterVenn Biosciences, 2 Tower Place Fifth Floor, South San Francisco, California 94080, United States
| | - Gregg Czerwieniec
- InterVenn Biosciences, 2 Tower Place Fifth Floor, South San Francisco, California 94080, United States
| | - Flavio Schwarz
- InterVenn Biosciences, 2 Tower Place Fifth Floor, South San Francisco, California 94080, United States
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8
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Quintero-Ruiz N, Oliveira WDL, Esteca MV, Granato DC, Simabuco FM. Uncovering the bookshelves of CRISPR-based libraries: Advances and applications in cancer studies. Crit Rev Oncol Hematol 2024; 196:104287. [PMID: 38342473 DOI: 10.1016/j.critrevonc.2024.104287] [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: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/13/2024] Open
Abstract
The advent of CRISPR/Cas9 technology has revolutionized the genome editing field. CRISPR-based libraries have become powerful tools for high-throughput functional genomics and genetic screening. CRISPR-based libraries can represent a powerful approach to uncovering genes related to chemoresistance and therapy efficacy and to studying cancer cells' fitness. In this review, we conducted an extensive literature search and summarized multiple studies that utilized these libraries in both in vitro and in vivo research, emphasizing their key findings. We provide an overview of the design, construction, and applications of CRISPR-based libraries in different cancer-focused studies and discuss the different types of CRISPR-based libraries. We finally point out the challenges associated with library design, including guide RNA selection, off-target effects, and library complexity. This review provides an overview of the work conducted with CRISPR libraries in the search for new targets that could potentially assist in cancer therapy by contributing to functional approaches.
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Affiliation(s)
- Nathalia Quintero-Ruiz
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil
| | - Wesley de Lima Oliveira
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil; Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa Em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Marcos Vinicius Esteca
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil
| | - Daniela Campos Granato
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa Em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Fernando Moreira Simabuco
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil; Department of Biochemistry, Federal University of São Paulo, São Paulo, SP 04044-020, Brazil.
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9
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Xie A, Wang J, Liu Y, Li G, Yang N. Impacts of β-1, 3-N-acetylglucosaminyltransferases (B3GNTs) in human diseases. Mol Biol Rep 2024; 51:476. [PMID: 38553573 DOI: 10.1007/s11033-024-09405-9] [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: 12/04/2023] [Accepted: 02/29/2024] [Indexed: 04/02/2024]
Abstract
Glycosylation modification of proteins is a common post-translational modification that exists in various organisms and has rich biological functions. It is usually catalyzed by multiple glycosyltransferases located in the Golgi apparatus. β-1,3-N-acetylglucosaminyltransferases (B3GNTs) are members of the glycosyltransferases and have been found to be involved in the occurrence and development of a variety of diseases including autoimmunity diseases, cancers, neurodevelopment, musculoskeletal system, and metabolic diseases. The functions of B3GNTs represent the glycosylation of proteins is a crucial and frequently life-threatening step in progression of most diseases. In this review, we give an overview about the roles of B3GNTs in tumor, nervous system, musculoskeletal and metabolic diseases, describing the recent results about B3GNTs, in order to provide a research direction and exploration value for the prevention, diagnosis and treatment of these diseases.
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Affiliation(s)
- Anna Xie
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Jingjing Wang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Yi Liu
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Guoqing Li
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Nanyang Yang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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10
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Ito Y, Inoue S, Kagoya Y. Gene editing technology to improve antitumor T-cell functions in adoptive immunotherapy. Inflamm Regen 2024; 44:13. [PMID: 38468282 PMCID: PMC10926667 DOI: 10.1186/s41232-024-00324-7] [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: 01/05/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Adoptive immunotherapy, in which tumor-reactive T cells are prepared in vitro for adoptive transfer to the patient, can induce an objective clinical response in specific types of cancer. In particular, chimeric antigen receptor (CAR)-redirected T-cell therapy has shown robust responses in hematologic malignancies. However, its efficacy against most of the other tumors is still insufficient, which remains an unmet medical need. Accumulating evidence suggests that modifying specific genes can enhance antitumor T-cell properties. Epigenetic factors have been particularly implicated in the remodeling of T-cell functions, including changes to dysfunctional states such as terminal differentiation and exhaustion. Genetic ablation of key epigenetic molecules prevents the dysfunctional reprogramming of T cells and preserves their functional properties.Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-based gene editing is a valuable tool to enable efficient and specific gene editing in cultured T cells. A number of studies have already identified promising targets to improve the therapeutic efficacy of CAR-T cells using genome-wide or focused CRISPR screening. In this review, we will present recent representative findings on molecular insights into T-cell dysfunction and how genetic modification contributes to overcoming it. We will also discuss several technical advances to achieve efficient gene modification using the CRISPR and other novel platforms.
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Affiliation(s)
- Yusuke Ito
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Satoshi Inoue
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yuki Kagoya
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, 160-8582, Japan.
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11
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Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [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: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
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Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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12
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Li YR, Lyu Z, Tian Y, Fang Y, Zhu Y, Chen Y, Yang L. Advancements in CRISPR screens for the development of cancer immunotherapy strategies. Mol Ther Oncolytics 2023; 31:100733. [PMID: 37876793 PMCID: PMC10591018 DOI: 10.1016/j.omto.2023.100733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
CRISPR screen technology enables systematic and scalable interrogation of gene function by using the CRISPR-Cas9 system to perturb gene expression. In the field of cancer immunotherapy, this technology has empowered the discovery of genes, biomarkers, and pathways that regulate tumor development and progression, immune reactivity, and the effectiveness of immunotherapeutic interventions. By conducting large-scale genetic screens, researchers have successfully identified novel targets to impede tumor growth, enhance anti-tumor immune responses, and surmount immunosuppression within the tumor microenvironment (TME). Here, we present an overview of CRISPR screens conducted in tumor cells for the purpose of identifying novel therapeutic targets. We also explore the application of CRISPR screens in immune cells to propel the advancement of cell-based therapies, encompassing T cells, natural killer cells, dendritic cells, and macrophages. Furthermore, we outline the crucial components necessary for the successful implementation of immune-specific CRISPR screens and explore potential directions for future research.
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Affiliation(s)
- Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zibai Lyu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yanxin Tian
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ying Fang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yichen Zhu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuning Chen
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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13
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Wang Y, Khalil A, Kamar A, Du M, Dinh T, McFarland C, Wang Z. Unveiling immune checkpoint regulation: exploring the power of in vivo CRISPR screenings in cancer immunotherapy. Front Genet 2023; 14:1304425. [PMID: 38162677 PMCID: PMC10755878 DOI: 10.3389/fgene.2023.1304425] [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: 09/29/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized cancer immunotherapy by reinvigorating antitumor immune responses, but their efficacy remains limited in most patients. To address this challenge and optimize Immune check inhibitor treatment, understanding the underlying molecular intricacies involved is crucial. The emergence of CRISPR-Cas9 technology has empowered researchers to precisely investigate gene function and has introduced transformative shifts in identifying key genes for various physiological and pathological processes. CRISPR screenings, particularly in vivo CRISPR screenings, have become invaluable tools in deciphering molecular networks and signaling pathways governing suppressive immune checkpoint molecules. In this review, we provide a comprehensive overview of in vivo CRISPR screenings in cancer immunotherapy, exploring how this cutting-edge technology has unraveled potential novel therapeutic targets and combination strategies. We delve into the latest findings and advancements, shedding light on immune checkpoint regulation and offering exciting prospects for the development of innovative and effective treatments for cancer patients.
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Affiliation(s)
- Yuxiang Wang
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Athar Khalil
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Amina Kamar
- Centre for Digital Transformation, Imperial College, London, United Kingdom
| | - Mengyan Du
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Trang Dinh
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Christopher McFarland
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Zhenghe Wang
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
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14
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Jackson JJ, Siegmund AC, Bai WJ, Reed AB, Birkholz AB, Campuzano IDG, Créquer-Grandhomme A, Hu R, Modak RV, Sudom A, Javier N, Sanders C, Lo MC, Xie F, Cee VJ, Manzanillo P, Allen JG. Imidazolone as an Amide Bioisostere in the Development of β-1,3- N-Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors. J Med Chem 2023; 66:16120-16140. [PMID: 37988652 DOI: 10.1021/acs.jmedchem.3c01517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
B3GNT2 is responsible for elongation of cell surface long-chain polylactosamine, which influences the regulation of the immune response, making it an attractive target for immunomodulation. In the development of amide containing B3GNT2 inhibitors guided by structure-based drug design, imidazolones were found to successfully serve as amide bioisosteres. This novel imidazolone isosteric strategy alleviated torsional strain of the amide bond on binding to B3GNT2 and improved potency, isoform selectivity, as well as certain physicochemical and pharmacokinetic properties. Herein, we present the synthesis, SAR, X-ray cocrystal structures, and in vivo PK properties of imidazol-4-ones in the context of B3GNT2 inhibition.
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Affiliation(s)
- Jeffrey J Jackson
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Aaron C Siegmund
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Wen-Ju Bai
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Anthony B Reed
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Adam B Birkholz
- Center for Research Acceleration by Digital Innovation, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Iain D G Campuzano
- Center for Research Acceleration by Digital Innovation, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Amandine Créquer-Grandhomme
- Inflammation, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Ruozhen Hu
- Inflammation, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Rucha V Modak
- Inflammation, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Athena Sudom
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Noelle Javier
- Lead Discovery & Characterization, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Christiana Sanders
- Lead Discovery & Characterization, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Mei-Chu Lo
- Lead Discovery & Characterization, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Fang Xie
- Pharmacokinetics & Drug Metabolism, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Victor J Cee
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Paolo Manzanillo
- Inflammation, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - John G Allen
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
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15
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Lakhani AA, Thompson SL, Sheltzer JM. Aneuploidy in human cancer: new tools and perspectives. Trends Genet 2023; 39:968-980. [PMID: 37778926 PMCID: PMC10715718 DOI: 10.1016/j.tig.2023.09.002] [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: 05/25/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
Chromosome copy number imbalances, otherwise known as aneuploidies, are a common but poorly understood feature of cancer. Here, we describe recent advances in both detecting and manipulating aneuploidies that have greatly advanced our ability to study their role in tumorigenesis. In particular, new clustered regularly interspaced short palindromic repeats (CRISPR)-based techniques have been developed that allow the creation of isogenic cell lines with specific chromosomal changes, thereby facilitating experiments in genetically controlled backgrounds to uncover the consequences of aneuploidy. These approaches provide increasing evidence that aneuploidy is a key driver of cancer development and enable the identification of multiple dosage-sensitive genes encoded on aneuploid chromosomes. Consequently, measuring aneuploidy may inform clinical prognosis, while treatment strategies that target aneuploidy could represent a novel method to counter malignant growth.
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Affiliation(s)
- Asad A Lakhani
- Cold Spring Harbor Laboratory School of Biological Sciences, Cold Spring, Harbor, NY 11724, USA
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16
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Ding S, Liu J, Han X, Tang M. CRISPR/Cas9-Mediated Genome Editing in Cancer Therapy. Int J Mol Sci 2023; 24:16325. [PMID: 38003514 PMCID: PMC10671490 DOI: 10.3390/ijms242216325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system, an RNA-based adaptive immune system found in bacteria and archaea, has catalyzed the development and application of a new generation of gene editing tools. Numerous studies have shown that this system can precisely target a wide range of human genes, including those associated with diseases such as cancer. In cancer research, the intricate genetic mutations in tumors have promoted extensive utilization of the CRISPR/Cas9 system due to its efficient and accurate gene editing capabilities. This includes improvements in Chimeric Antigen Receptor (CAR)-T-cell therapy, the establishment of tumor models, and gene and drug target screening. Such progress has propelled the investigation of cancer molecular mechanisms and the advancement of precision medicine. However, the therapeutic potential of genome editing remains underexplored, and lingering challenges could elevate the risk of additional genetic mutations. Here, we elucidate the fundamental principles of CRISPR/Cas9 gene editing and its practical applications in tumor research. We also briefly discuss the primary challenges faced by CRISPR technology and existing solutions, intending to enhance the efficacy of this gene editing therapy and shed light on the underlying mechanisms of tumors.
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Affiliation(s)
- Shuai Ding
- Department of Biochemistry and Molecular Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Jinfeng Liu
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Xin Han
- Department of Biochemistry and Molecular Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Mengfan Tang
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
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17
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Lee DH, Ahn H, Sim HI, Choi E, Choi S, Jo Y, Yun B, Song HK, Oh SJ, Denda-Nagai K, Park CS, Irimura T, Park Y, Jin HS. A CRISPR activation screen identifies MUC-21 as critical for resistance to NK and T cell-mediated cytotoxicity. J Exp Clin Cancer Res 2023; 42:272. [PMID: 37858248 PMCID: PMC10588101 DOI: 10.1186/s13046-023-02840-9] [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] [Received: 07/27/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Immunotherapy has significantly advanced cancer treatments, but many patients do not respond to it, partly due to immunosuppressive mechanisms used by tumor cells. These cells employ immunosuppressive ligands to evade detection and elimination by the immune system. Therefore, the discovery and characterization of novel immunosuppressive ligands that facilitate immune evasion are crucial for developing more potent anti-cancer therapies. METHODS We conducted gain-of-function screens using a CRISPRa (CRISPR activation) library that covered the entire human transmembrane sub-genome to identify surface molecules capable of hindering NK-mediated cytotoxicity. The immunosuppressive role and mechanism of MUC21 were validated using NK and T cell mediated cytotoxicity assays. Bioinformatics tools were employed to assess the clinical implications of mucin-21 (MUC21) in cancer cell immunity. RESULTS Our genetic screens revealed that MUC21 expression on cancer cell surfaces inhibits both the cytotoxic activity of NK cells and antibody-dependent cellular cytotoxicity, but not affecting complement-dependent cytotoxicity. Additionally, MUC21 expression hinders T cell activation by impeding antigen recognition, thereby diminishing the effectiveness of the immune checkpoint inhibitor, anti-PD-L1. Moreover, MUC21 expression suppress the antitumor function of both CAR-T cells and CAR-NK cells. Mechanistically, MUC21 facilitates immune evasion by creating steric hindrance, preventing interactions between cancer and immune cells. Bioinformatics analysis revealed elevated MUC21 expression in lung cancer, which correlated with reduced infiltration and activation of cytotoxic immune cells. Intriguingly, MUC21 expression was higher in non-small cell lung cancer (NSCLC) tumors that were non-responsive to anti-PD-(L)1 treatment compared to responsive tumors. CONCLUSIONS These findings indicate that surface MUC21 serves as a potent immunosuppressive ligand, shielding cancer cells from NK and CD8+T cell attacks. This suggests that inhibiting MUC21 could be a promising strategy to improve cancer immunotherapy.
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Affiliation(s)
- Dong-Hee Lee
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Hyejin Ahn
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Hye-In Sim
- Chemical and Biological Integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
- Department of Life Sciences, Korea University, Seoul, 02481, South Korea
| | - Eunji Choi
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Seunghyun Choi
- Chemical and Biological Integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
- Department of Life Sciences, Korea University, Seoul, 02481, South Korea
| | - Yunju Jo
- Chemical and Biological Integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
- Department of Life Sciences, Korea University, Seoul, 02481, South Korea
| | - Bohwan Yun
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul, 02481, South Korea
| | - Soo Jin Oh
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Kaori Denda-Nagai
- Division of Glycobiologics, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Chan-Sik Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
| | - Tatsuro Irimura
- Division of Glycobiologics, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoon Park
- Chemical and Biological Integrative Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea.
| | - Hyung-Seung Jin
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea.
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18
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Herzfeldt AK, Gamez MP, Martin E, Boryn LM, Baskaran P, Huber HJ, Schuler M, Park JE, Swee LK. Complementary CRISPR screen highlights the contrasting role of membrane-bound and soluble ICAM-1 in regulating antigen-specific tumor cell killing by cytotoxic T cells. eLife 2023; 12:e84314. [PMID: 37732732 PMCID: PMC10586807 DOI: 10.7554/elife.84314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 09/20/2023] [Indexed: 09/22/2023] Open
Abstract
Cytotoxic CD8 +T lymphocytes (CTLs) are key players of adaptive anti-tumor immunity based on their ability to specifically recognize and destroy tumor cells. Many cancer immunotherapies rely on unleashing CTL function. However, tumors can evade killing through strategies which are not yet fully elucidated. To provide deeper insight into tumor evasion mechanisms in an antigen-dependent manner, we established a human co-culture system composed of tumor and primary immune cells. Using this system, we systematically investigated intrinsic regulators of tumor resistance by conducting a complementary CRISPR screen approach. By harnessing CRISPR activation (CRISPRa) and CRISPR knockout (KO) technology in parallel, we investigated gene gain-of-function as well as loss-of-function across genes with annotated function in a colon carcinoma cell line. CRISPRa and CRISPR KO screens uncovered 187 and 704 hits, respectively, with 60 gene hits overlapping between both. These data confirmed the role of interferon-γ (IFN-γ), tumor necrosis factor α (TNF-α) and autophagy pathways and uncovered novel genes implicated in tumor resistance to killing. Notably, we discovered that ILKAP encoding the integrin-linked kinase-associated serine/threonine phosphatase 2 C, a gene previously unknown to play a role in antigen specific CTL-mediated killing, mediate tumor resistance independently from regulating antigen presentation, IFN-γ or TNF-α responsiveness. Moreover, our work describes the contrasting role of soluble and membrane-bound ICAM-1 in regulating tumor cell killing. The deficiency of membrane-bound ICAM-1 (mICAM-1) or the overexpression of soluble ICAM-1 (sICAM-1) induced resistance to CTL killing, whereas PD-L1 overexpression had no impact. These results highlight the essential role of ICAM-1 at the immunological synapse between tumor and CTL and the antagonist function of sICAM-1.
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Affiliation(s)
- Ann-Kathrin Herzfeldt
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Marta Puig Gamez
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Eva Martin
- Department of Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | | | - Praveen Baskaran
- Department of Global Computational Biology and Digital Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - Heinrich J Huber
- Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - Michael Schuler
- Department of Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - John E Park
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Lee Kim Swee
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
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19
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Chen X, Wang S, Chen Y, Xin H, Zhang S, Wu D, Xue Y, Zha M, Li H, Li K, Gu Z, Wei W, Ping Y. Non-invasive activation of intratumoural gene editing for improved adoptive T-cell therapy in solid tumours. NATURE NANOTECHNOLOGY 2023; 18:933-944. [PMID: 37188968 DOI: 10.1038/s41565-023-01378-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/14/2023] [Indexed: 05/17/2023]
Abstract
Adoptive T-cell therapy against solid tumours is limited by the apoptosis resistance mechanisms of tumour cells and by the extracellular, immunosuppressive tumour microenvironment. Here we report a temperature-sensitive genome-editing nanodevice that can deliver a Cas9 editor with an external trigger which can be used to edit the genome of tumour cells to reduce resistance to apoptosis and modulate the tumour microenvironment via a mild heating trigger. After local or systemic delivery of Cas9, mild heating is induced by non-invasive near-infrared (NIR) light or focused ultrasound (FUS) to activate Cas9, which initiates simultaneous genome editing of HSP70 (HSPA1A) and BAG3 in tumour cells. This disrupts the apoptotic resistance machinery of the tumour cells against adoptive T cells. At the same time, an NIR- or FUS-induced mild thermal effect reshapes the extracellular tumour microenvironment by disrupting the physical barriers and immune suppression. This facilitates the infiltration of adoptive T cells and enhances their therapeutic activity. Mild thermal Cas9 delivery is demonstrated in different murine tumour models which mimic a range of clinical indications, including a tumour model based on humanized patient-derived xenografts. As a result, the non-invasive thermal delivery of Cas9 significantly enhances the therapeutic efficacies of tumour-infiltrating lymphocytes and chimeric antigen receptor T and shows potential for clinical application.
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Affiliation(s)
- Xiaohong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shuang Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxuan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Huhu Xin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shuaishuai Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Di Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yanan Xue
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Menglei Zha
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Hongjun Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Kai Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhen Gu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China.
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China.
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
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20
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Yi M, Wang M, Xu Y, Cao Z, Ling Y, Zhang Z, Cao H. CRISPR-based m 6A modification and its potential applications in telomerase regulation. Front Cell Dev Biol 2023; 11:1200734. [PMID: 37519297 PMCID: PMC10382234 DOI: 10.3389/fcell.2023.1200734] [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: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Telomerase determines cell lifespan by controlling chromosome stability and cell viability, m6A epigenetic modification plays an important role in the regulation of telomerase activity. Using CRISPR epigenome editing to analyze specific m6A modification sites in telomerase will provide an important tool for analyzing the molecular mechanism of m6A modification regulating telomerase activity. In this review, we clarified the relevant applications of CRISPR system, paid special attention to the regulation of m6A modification in stem cells and cancer cells based on CRISPR system, emphasized the regulation of m6A modification on telomerase activity, pointed out that m6A modification sites regulate telomerase activity, and discussed strategies based on telomerase activity and disease treatment, which are helpful to promote the research of anti-aging and tumor related diseases.
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Affiliation(s)
- Mingliang Yi
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Mingyue Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Yongjie Xu
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Zhikun Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Yinghui Ling
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zijun Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Hongguo Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
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21
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Cao F, Jiang Y, Chang L, Du H, Chang D, Pan C, Huang X, Yu D, Zhang M, Fan Y, Bian X, Li K. High-throughput functional screen identifies YWHAZ as a key regulator of pancreatic cancer metastasis. Cell Death Dis 2023; 14:431. [PMID: 37452033 PMCID: PMC10349114 DOI: 10.1038/s41419-023-05951-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Pancreatic cancer is a leading cause of cancer death due to its early metastasis and limited response to the current therapies. Metastasis is a complicated multistep process, which is determined by complex genetic alterations. Despite the identification of many metastasis-related genes, distinguishing the drivers from numerous passengers and establishing the causality in cancer pathophysiology remains challenging. Here, we established a high-throughput and piggyBac transposon-based genetic screening platform, which enables either reduced or increased expression of chromosomal genes near the incorporation site of the gene search vector cassette that contains a doxycycline-regulated promoter. Using this strategy, we identified YWHAZ as a key regulator of pancreatic cancer metastasis. We demonstrated that functional activation of Ywhaz by the gene search vector led to enhanced metastatic capability in mouse pancreatic cancer cells. The metastasis-promoting role of YWHAZ was further validated in human pancreatic cancer cells. Overexpression of YWHAZ resulted in more aggressive metastatic phenotypes in vitro and a shorter survival rate in vivo by modulating epithelial-to-mesenchymal transition. Hence, our study established a high-throughput screening method to investigate the functional relevance of novel genes and validated YWHAZ as a key regulator of pancreatic cancer metastasis.
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Affiliation(s)
- Fang Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yunpeng Jiang
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lin Chang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Endoscopy Center, Peking University Cancer Hospital & Institute, Beijing, China
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Hongzhen Du
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - De Chang
- Department of Pulmonary and Critical Care Medicine, 7th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chunxiao Pan
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Xiaozheng Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Donglin Yu
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Mi Zhang
- Department of Pulmonary and Critical Care Medicine, 7th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yongna Fan
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Xiaocui Bian
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China.
| | - Kailong Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
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22
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Tang YJ, Shuldiner EG, Karmakar S, Winslow MM. High-Throughput Identification, Modeling, and Analysis of Cancer Driver Genes In Vivo. Cold Spring Harb Perspect Med 2023; 13:a041382. [PMID: 37277208 PMCID: PMC10317066 DOI: 10.1101/cshperspect.a041382] [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] [Indexed: 06/07/2023]
Abstract
The vast number of genomic and molecular alterations in cancer pose a substantial challenge to uncovering the mechanisms of tumorigenesis and identifying therapeutic targets. High-throughput functional genomic methods in genetically engineered mouse models allow for rapid and systematic investigation of cancer driver genes. In this review, we discuss the basic concepts and tools for multiplexed investigation of functionally important cancer genes in vivo using autochthonous cancer models. Furthermore, we highlight emerging technical advances in the field, potential opportunities for future investigation, and outline a vision for integrating multiplexed genetic perturbations with detailed molecular analyses to advance our understanding of the genetic and molecular basis of cancer.
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Affiliation(s)
- Yuning J Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Emily G Shuldiner
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Saswati Karmakar
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
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23
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Ma Y, Du J, Chen M, Gao N, Wang S, Mi Z, Wei X, Zhao J. Mitochondrial DNA methylation is a predictor of immunotherapy response and prognosis in breast cancer: scRNA-seq and bulk-seq data insights. Front Immunol 2023; 14:1219652. [PMID: 37457713 PMCID: PMC10339346 DOI: 10.3389/fimmu.2023.1219652] [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: 05/09/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Background Alterations in Mitochondrial DNA methylation (MTDM) exist in many tumors, but their role in breast cancer (BC) development remains unclear. Methods We analyzed BC patient data by combining scRNA-seq and bulk sequencing. Weighted co-expression network analysis (WGCNA) of TCGA data identified mitochondrial DNA methylation (MTDM)-associated genes in BC. COX regression and LASSO regression were used to build prognostic models. The biological function of MTDM was assessed using various methods, such as signaling pathway enrichment analysis, copynumber karyotyping analysis, and quantitative analysis of the cell proliferation rate. We also evaluated MTDM-mediated alterations in the immune microenvironment using immune microenvironment, microsatellite instability, mutation, unsupervised clustering, malignant cell subtype differentiation, immune cell subtype differentiation, and cell-communication signature analyses. Finally, we performed cellular experiments to validate the role of the MTDM-associated prognostic gene NCAPD3 in BC. Results In this study, MTDM-associated prognostic models divided BC patients into high/low MTDM groups in TCGA/GEO datasets. The difference in survival time between the two groups was statistically significant (P<0.001). We found that high MTDM status was positively correlated with tumor cell proliferation. We analyzed the immune microenvironment and found that low-MTDM group had higher immune checkpoint gene expression/immune cell infiltration, which could lead to potential benefits from immunotherapy. In contrast, the high MTDM group had higher proliferation rates and levels of CD8+T cell exhaustion, which may be related to the secretion of GDF15 by malignant breast epithelial cells with a high MTDM status. Cellular experiments validated the role of the MTDM-associated prognostic gene NCAPD3 (the gene most positively correlated with epithelial malignant cell proliferation in the model) in BC. Knockdown of NCAPD3 significantly reduced the activity and proliferation of MDA-MB-231 and BCAP-37 cells, and significantly reduced their migration ability of BCAP-37 cell line. Conclusion This study presented a holistic evaluation of the multifaceted roles of MTDM in BC. The analysis of MTDM levels not only enables the prediction of response to immunotherapy but also serves as an accurate prognostic indicator for patients with BC. These insightful discoveries provide novel perspectives on tumor immunity and have the potentially to revolutionize the diagnosis and treatment of BC.
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24
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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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25
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Brown AC, Cohen CJ, Mielczarek O, Migliorini G, Costantino F, Allcock A, Davidson C, Elliott KS, Fang H, Lledó Lara A, Martin AC, Osgood JA, Sanniti A, Scozzafava G, Vecellio M, Zhang P, Black MH, Li S, Truong D, Molineros J, Howe T, Wordsworth BP, Bowness P, Knight JC. Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis. CELL GENOMICS 2023; 3:100306. [PMID: 37388915 PMCID: PMC10300554 DOI: 10.1016/j.xgen.2023.100306] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/30/2023] [Accepted: 03/27/2023] [Indexed: 07/01/2023]
Abstract
Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis characterized by enthesitis of the spine and sacroiliac joints. Genome-wide association studies (GWASs) have revealed more than 100 genetic associations whose functional effects remain largely unresolved. Here, we present a comprehensive transcriptomic and epigenomic map of disease-relevant blood immune cell subsets from AS patients and healthy controls. We find that, while CD14+ monocytes and CD4+ and CD8+ T cells show disease-specific differences at the RNA level, epigenomic differences are only apparent upon multi-omics integration. The latter reveals enrichment at disease-associated loci in monocytes. We link putative functional SNPs to genes using high-resolution Capture-C at 10 loci, including PTGER4 and ETS1, and show how disease-specific functional genomic data can be integrated with GWASs to enhance therapeutic target discovery. This study combines epigenetic and transcriptional analysis with GWASs to identify disease-relevant cell types and gene regulation of likely pathogenic relevance and prioritize drug targets.
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Affiliation(s)
- Andrew C. Brown
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Carla J. Cohen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Olga Mielczarek
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Horizon Discovery (PerkinElmer) Cambridge Research Park, 8100 Beach Dr., Waterbeach, Cambridge CB25 9TL, UK
| | - Gabriele Migliorini
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Félicie Costantino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- UVSQ, INSERM UMR1173, Infection et Inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Paris, France
- Rheumatology Department, AP-HP, Ambroise Paré Hospital, Paris, France
| | - Alice Allcock
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Connor Davidson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | | | - Hai Fang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Alicia Lledó Lara
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Alice C. Martin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Julie A. Osgood
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Anna Sanniti
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Giuseppe Scozzafava
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- Centro Ricerche Fondazione Italiana Ricerca sull’Artrite (FIRA), Fondazione Pisana per la Scienza ONLUS, Via Ferruccio Giovannini 13, 56017 San Giuliano Terme (Pisa), Italy
| | - Ping Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Mary Helen Black
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Shuwei Li
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Dongnhu Truong
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Julio Molineros
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Trevor Howe
- Data Science, External Innovation, Janssen R&D, London W1G 0BG, UK
| | - B. Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Julian C. Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
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Li F, Tarkington J, Sherlock G. Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays. J Mol Evol 2023; 91:334-344. [PMID: 36877292 PMCID: PMC10276102 DOI: 10.1007/s00239-023-10098-0] [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: 10/26/2022] [Accepted: 02/02/2023] [Indexed: 03/07/2023]
Abstract
The fitness of a genotype is defined as its lifetime reproductive success, with fitness itself being a composite trait likely dependent on many underlying phenotypes. Measuring fitness is important for understanding how alteration of different cellular components affects a cell's ability to reproduce. Here, we describe an improved approach, implemented in Python, for estimating fitness in high throughput via pooled competition assays.
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Affiliation(s)
- Fangfei Li
- Department of Genetics, Stanford University, Stanford, USA
| | | | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, USA.
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27
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Li YR, Dunn ZS, Yu Y, Li M, Wang P, Yang L. Advancing cell-based cancer immunotherapy through stem cell engineering. Cell Stem Cell 2023; 30:592-610. [PMID: 36948187 PMCID: PMC10164150 DOI: 10.1016/j.stem.2023.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/04/2023] [Accepted: 02/22/2023] [Indexed: 03/24/2023]
Abstract
Advances in cell-based therapy, particularly CAR-T cell therapy, have transformed the treatment of hematological malignancies. Although an important step forward for the field, autologous CAR-T therapies are hindered by high costs, manufacturing challenges, and limited efficacy against solid tumors. With ongoing progress in gene editing and culture techniques, engineered stem cells and their application in cell therapy are poised to address some of these challenges. Here, we review stem cell-based immunotherapy approaches, stem cell sources, gene engineering and manufacturing strategies, therapeutic platforms, and clinical trials, as well as challenges and future directions for the field.
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Affiliation(s)
- Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zachary Spencer Dunn
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Yanqi Yu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Miao Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pin Wang
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA; Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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28
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Čaval T, Alisson-Silva F, Schwarz F. Roles of glycosylation at the cancer cell surface: opportunities for large scale glycoproteomics. Theranostics 2023; 13:2605-2615. [PMID: 37215580 PMCID: PMC10196828 DOI: 10.7150/thno.81760] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Cell surface glycosylation has a variety of functions, and its dysregulation in cancer contributes to impaired signaling, metastasis and the evasion of the immune responses. Recently, a number of glycosyltransferases that lead to altered glycosylation have been linked to reduced anti-tumor immune responses: B3GNT3, which is implicated in PD-L1 glycosylation in triple negative breast cancer, FUT8, through fucosylation of B7H3, and B3GNT2, which confers cancer resistance to T cell cytotoxicity. Given the increased appreciation of the relevance of protein glycosylation, there is a critical need for the development of methods that allow for an unbiased interrogation of cell surface glycosylation status. Here we provide an overview of the broad changes in glycosylation at the surface of cancer cell and describe selected examples of receptors with aberrant glycosylation leading to functional changes, with emphasis on immune checkpoint inhibitors, growth-promoting and growth-arresting receptors. Finally, we posit that the field of glycoproteomics has matured to an extent where large-scale profiling of intact glycopeptides from the cell surface is feasible and is poised for discovery of new actionable targets against cancer.
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29
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N-Glycosylation of LRP6 by B3GnT2 Promotes Wnt/β-Catenin Signalling. Cells 2023; 12:cells12060863. [PMID: 36980204 PMCID: PMC10047360 DOI: 10.3390/cells12060863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Reception of Wnt signals by cells is predominantly mediated by Frizzled receptors in conjunction with a co-receptor, the latter being LRP6 or LRP5 for the Wnt/β-catenin signalling pathway. It is important that cells maintain precise control of receptor activation events in order to properly regulate Wnt/β-catenin signalling as aberrant signalling can result in disease in humans. Phosphorylation of the intracellular domain (ICD) of LRP6 is well known to regulate Wntβ-catenin signalling; however, less is known for regulatory post-translational modification events within the extracellular domain (ECD). Using a cell culture-based expression screen for functional regulators of LRP6, we identified a glycosyltransferase, B3GnT2-like, from a teleost fish (medaka) cDNA library, that modifies LRP6 and regulates Wnt/β-catenin signalling. We provide both gain-of-function and loss-of-function evidence that the single human homolog, B3GnT2, promotes extension of polylactosamine chains at multiple N-glycans on LRP6, thereby enhancing trafficking of LRP6 to the plasma membrane and promoting Wnt/β-catenin signalling. Our findings further highlight the importance of LRP6 as a regulatory hub in Wnt signalling and provide one of the few examples of how a specific glycosyltransferase appears to selectively target a signalling pathway component to alter cellular signalling events.
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30
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Hargadon KM. Genetic dysregulation of immunologic and oncogenic signaling pathways associated with tumor-intrinsic immune resistance: a molecular basis for combination targeted therapy-immunotherapy for cancer. Cell Mol Life Sci 2023; 80:40. [PMID: 36629955 PMCID: PMC11072992 DOI: 10.1007/s00018-023-04689-9] [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: 10/01/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023]
Abstract
Since the turn of the century, advances in targeted therapy and immunotherapy have revolutionized the treatment of cancer. Although these approaches have far outperformed traditional therapies in various clinical settings, both remain plagued by mechanisms of innate and acquired resistance that limit therapeutic efficacy in many patients. With a focus on tumor-intrinsic resistance to immunotherapy, this review highlights our current understanding of the immunologic and oncogenic pathways whose genetic dysregulation in cancer cells enables immune escape. Emphasis is placed on genomic, epigenomic, transcriptomic, and proteomic aberrations that influence the activity of these pathways in the context of immune resistance. Specifically, the role of pathways that govern interferon signaling, antigen processing and presentation, and immunologic cell death as determinants of tumor immune susceptibility are discussed. Likewise, mechanisms of tumor immune resistance mediated by dysregulated RAS-MAPK, WNT, PI3K-AKT-mTOR, and cell cycle pathways are described. Finally, this review highlights the ways in which recent insight into genetic dysregulation of these immunologic and oncogenic signaling pathways is informing the design of combination targeted therapy-immunotherapy regimens that aim to restore immune susceptibility of cancer cells by overcoming resistance mechanisms that often limit the success of monotherapies.
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Affiliation(s)
- Kristian M Hargadon
- Hargadon Laboratory, Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA, 23943, USA.
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31
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Comprehensive Analysis Identified Glycosyltransferase Signature to Predict Glioma Prognosis and TAM Phenotype. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6082635. [PMID: 36685667 PMCID: PMC9859707 DOI: 10.1155/2023/6082635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/09/2022] [Accepted: 11/23/2022] [Indexed: 01/15/2023]
Abstract
Glycosylation is the most common posttranslational modification of proteins. Glycosyltransferase gene differential expression dictates the glycosylation model and is epigenetically regulating glioma progression and immunity. This study is aimed at identifying the glycosyltransferase gene signature to predict the prognosis and immune characteristics of glioma. The glycosyltransferase gene signature of glioma was identified in the TCGA database and validated in the CGGA database. Glioma patients were then divided into high- and low-risk groups based on risk scores to compare survival differences and predictive capacity. Subsequently, validation of glycosyltransferase gene signature merits by comparing with other signatures and utility in clinical judgment. The immune cell infiltration, immune pathways, and immune checkpoint expression level were also analyzed and compared in the high- and low-risk groups. Finally, the signature and its gene function were tested in our cohort and in vitro experiments. Eight glycosyltransferase genes were identified to establish the glycosyltransferase signature to predict the prognosis of glioma patients. The survival time was shorter in the high-risk group compared to the low-risk group based on glycosyltransferase signature and was confirmed in an independent external cohort. The glycosyltransferase signature displayed outstanding predictive capacity than other signatures in the TCGA and CGGA database cohorts. Furthermore, patients in the high-risk group were positively correlated with TAM infiltration, immune checkpoint expression level, and protumor immune pathways in TCGA cohorts. Validation of clinical tissue specimens revealed that the high-risk group was closely associated with infiltration of M2 TAMs. High-risk genes in the signature promote glioma proliferation, invasion, and macrophage recruitment in an in vitro validation of U87 and U251 cell lines. This carefully constructed that glycosyltransferase signature can predict the prognosis and immune profile of gliomas and help us evaluate subsequent macrophage-targeted therapies as well as other immune microenvironment modulation therapeutic strategies.
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McLean B, Istadi A, Clack T, Vankan M, Schramek D, Neely GG, Pajic M. A CRISPR Path to Finding Vulnerabilities and Solving Drug Resistance: Targeting the Diverse Cancer Landscape and Its Ecosystem. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200014. [PMID: 36911295 PMCID: PMC9993475 DOI: 10.1002/ggn2.202200014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Cancer is the second leading cause of death globally, with therapeutic resistance being a major cause of treatment failure in the clinic. The dynamic signaling that occurs between tumor cells and the diverse cells of the surrounding tumor microenvironment actively promotes disease progression and therapeutic resistance. Improving the understanding of how tumors evolve following therapy and the molecular mechanisms underpinning de novo or acquired resistance is thus critical for the identification of new targets and for the subsequent development of more effective combination regimens. Simultaneously targeting multiple hallmark capabilities of cancer to circumvent adaptive or evasive resistance may lead to significantly improved treatment response in the clinic. Here, the latest applications of functional genomics tools, such as clustered regularly interspaced short palindromic repeats (CRISPR) editing, to characterize the dynamic cancer resistance mechanisms, from improving the understanding of resistance to classical chemotherapeutics, to deciphering unique mechanisms that regulate tumor responses to new targeted agents and immunotherapies, are discussed. Potential avenues of future research in combating therapeutic resistance, the contribution of tumor-stroma signaling in this setting, and how advanced functional genomics tools can help streamline the identification of key molecular determinants of drug response are explored.
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Affiliation(s)
- Benjamin McLean
- The Kinghorn Cancer Centre The Garvan Institute of Medical Research 384 Victoria St, Darlinghurst Sydney New South Wales 2010 Australia
| | - Aji Istadi
- The Kinghorn Cancer Centre The Garvan Institute of Medical Research 384 Victoria St, Darlinghurst Sydney New South Wales 2010 Australia
| | - Teleri Clack
- Dr. John and Anne Chong Lab for Functional Genomics Charles Perkins Centre Centenary Institute University of Sydney Camperdown New South Wales 2006 Australia
| | - Mezzalina Vankan
- Dr. John and Anne Chong Lab for Functional Genomics Charles Perkins Centre Centenary Institute University of Sydney Camperdown New South Wales 2006 Australia
| | - Daniel Schramek
- Centre for Molecular and Systems Biology Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital Toronto Ontario M5G 1X5 Canada.,Department of Molecular Genetics Faculty of Medicine University of Toronto Toronto Ontario M5S 1A8 Canada
| | - G Gregory Neely
- Dr. John and Anne Chong Lab for Functional Genomics Charles Perkins Centre Centenary Institute University of Sydney Camperdown New South Wales 2006 Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre The Garvan Institute of Medical Research 384 Victoria St, Darlinghurst Sydney New South Wales 2010 Australia.,St Vincent's Clinical School Faculty of Medicine University of NSW Sydney Sydney New South Wales 2052 Australia
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Theivanthiran B, Yarla N, Haykal T, Nguyen YV, Cao L, Ferreira M, Holtzhausen A, Al-Rohil R, Salama AKS, Beasley GM, Plebanek MP, DeVito NC, Hanks BA. Tumor-intrinsic NLRP3-HSP70-TLR4 axis drives premetastatic niche development and hyperprogression during anti-PD-1 immunotherapy. Sci Transl Med 2022; 14:eabq7019. [PMID: 36417489 DOI: 10.1126/scitranslmed.abq7019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The tumor-intrinsic NOD-, LRR- and pyrin domain-containing protein-3 (NLRP3) inflammasome-heat shock protein 70 (HSP70) signaling axis is triggered by CD8+ T cell cytotoxicity and contributes to the development of adaptive resistance to anti-programmed cell death protein 1 (PD-1) immunotherapy by recruiting granulocytic polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) into the tumor microenvironment. Here, we demonstrate that the tumor NLRP3-HSP70 axis also drives the accumulation of PMN-MDSCs into distant lung tissues in a manner that depends on lung epithelial cell Toll-like receptor 4 (TLR4) signaling, establishing a premetastatic niche that supports disease hyperprogression in response to anti-PD-1 immunotherapy. Lung epithelial HSP70-TLR4 signaling induces the downstream Wnt5a-dependent release of granulocyte colony-stimulating factor (G-CSF) and C-X-C motif chemokine ligand 5 (CXCL5), thus promoting myeloid granulopoiesis and recruitment of PMN-MDSCs into pulmonary tissues. Treatment with anti-PD-1 immunotherapy enhanced the activation of this pathway through immunologic pressure and drove disease progression in the setting of Nlrp3 amplification. Genetic and pharmacologic inhibition of NLRP3 and HSP70 blocked PMN-MDSC accumulation in the lung in response to anti-PD-1 therapy and suppressed metastatic progression in preclinical models of melanoma and breast cancer. Elevated baseline concentrations of plasma HSP70 and evidence of NLRP3 signaling activity in tumor tissue specimens correlated with the development of disease hyperprogression and inferior survival in patients with stage IV melanoma undergoing anti-PD-1 immunotherapy. Together, this work describes a pathogenic mechanism underlying the phenomenon of disease hyperprogression in melanoma and offers candidate targets and markers capable of improving the management of patients with melanoma.
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Affiliation(s)
- Balamayooran Theivanthiran
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Nagendra Yarla
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Tarek Haykal
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Y-Van Nguyen
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Linda Cao
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Michelle Ferreira
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Alisha Holtzhausen
- Lineberger Comprehensive Cancer Center, University of North Caroline at Chapel Hill, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rami Al-Rohil
- Department of Pathology, Duke Cancer Institute, Duke University Durham, Durham, NC 27710, USA
| | - April K S Salama
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Georgia M Beasley
- Department of Surgery, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Michael P Plebanek
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Nicholas C DeVito
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Brent A Hanks
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708, USA
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Biederstädt A, Manzar GS, Daher M. Multiplexed engineering and precision gene editing in cellular immunotherapy. Front Immunol 2022; 13:1063303. [PMID: 36483551 PMCID: PMC9723254 DOI: 10.3389/fimmu.2022.1063303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
The advent of cellular immunotherapy in the clinic has entirely redrawn the treatment landscape for a growing number of human cancers. Genetically reprogrammed immune cells, including chimeric antigen receptor (CAR)-modified immune effector cells as well as T cell receptor (TCR) therapy, have demonstrated remarkable responses across different hard-to-treat patient populations. While these novel treatment options have had tremendous success in providing long-term remissions for a considerable fraction of treated patients, a number of challenges remain. Limited in vivo persistence and functional exhaustion of infused immune cells as well as tumor immune escape and on-target off-tumor toxicities are just some examples of the challenges which restrain the potency of today's genetically engineered cell products. Multiple engineering strategies are being explored to tackle these challenges.The advent of multiplexed precision genome editing has in recent years provided a flexible and highly modular toolkit to specifically address some of these challenges by targeted genetic interventions. This class of next-generation cellular therapeutics aims to endow engineered immune cells with enhanced functionality and shield them from immunosuppressive cues arising from intrinsic immune checkpoints as well as the hostile tumor microenvironment (TME). Previous efforts to introduce additional genetic modifications into immune cells have in large parts focused on nuclease-based tools like the CRISPR/Cas9 system or TALEN. However, nuclease-inactive platforms including base and prime editors have recently emerged and promise a potentially safer route to rewriting genetic sequences and introducing large segments of transgenic DNA without inducing double-strand breaks (DSBs). In this review, we discuss how these two exciting and emerging fields-cellular immunotherapy and precision genome editing-have co-evolved to enable a dramatic expansion in the possibilities to engineer personalized anti-cancer treatments. We will lay out how various engineering strategies in addition to nuclease-dependent and nuclease-inactive precision genome editing toolkits are increasingly being applied to overcome today's limitations to build more potent cellular therapeutics. We will reflect on how novel information-rich unbiased discovery approaches are continuously deepening our understanding of fundamental mechanisms governing tumor biology. We will conclude with a perspective of how multiplexed-engineered and gene edited cell products may upend today's treatment paradigms as they evolve into the next generation of more potent cellular immunotherapies.
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Affiliation(s)
- Alexander Biederstädt
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Medicine III, Hematology and Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Gohar Shahwar Manzar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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35
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Chen P, Gao G, Xu Y, Jia P, Li Y, Li Y, Cao J, Du J, Zhang S, Zhang J. Novel gene signature reveals prognostic model in acute lymphoblastic leukemia. Front Cell Dev Biol 2022; 10:1036312. [PMID: 36407095 PMCID: PMC9669305 DOI: 10.3389/fcell.2022.1036312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a type of hematological malignancy and has a poor prognosis. In our study, we aimed to construct a prognostic model of ALL by identifying important genes closely related to ALL prognosis. We obtained transcriptome data (RNA-seq) of ALL samples from the GDC TARGET database and identified differentially expressed genes (DEGs) using the “DESeq” package of R software. We used univariate and multivariate cox regression analyses to screen out the prognostic genes of ALL. In our results, the risk score can be used as an independent prognostic factor to predict the prognosis of ALL patients [hazard ratio (HR) = 2.782, 95% CI = 1.903–4.068, p < 0.001]. Risk score in clinical parameters has high diagnostic sensitivity and specificity for predicting overall survival of ALL patients, and the area under curve (AUC) is 0.864 in the receiver operating characteristic (ROC) analysis results. Our study evaluated a potential prognostic signature with six genes and constructed a risk model significantly related to the prognosis of ALL patients. The results of this study can help clinicians to adjust the treatment plan and distinguish patients with good and poor prognosis for targeted treatment.
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36
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Chandrasekar AP, Badley AD. Prime, shock and kill: BCL-2 inhibition for HIV cure. Front Immunol 2022; 13:1033609. [PMID: 36341439 PMCID: PMC9631312 DOI: 10.3389/fimmu.2022.1033609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/07/2022] [Indexed: 05/30/2024] Open
Abstract
While modern HIV therapy can effectively suppress viral replication, the persistence of the latent reservoir posits the greatest hurdle to complete cure. The "shock and kill" strategy is under investigation for HIV therapy, aiming to reactivate latent HIV, and subsequently eliminate it through anti-retroviral therapy and host immune function. However, thus far, studies have yielded suboptimal results, stemming from a combination of ineffective latency reversal and poor immune clearance. Concomitantly, studies have now revealed the importance of the BCL-2 anti-apoptotic protein as a critical mediator of infected cell survival, reservoir maintenance and immune evasion in HIV. Furthermore, BCL-2 inhibitors are now recognized for their anti-HIV effects in pre-clinical studies. This minireview aims to examine the intersection of BCL-2 inhibition and current shock and kill efforts, hoping to inform future studies which may ultimately yield a cure for HIV.
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Affiliation(s)
- Aswath P. Chandrasekar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, United States
| | - Andrew D. Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, United States
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, United States
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37
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Wang H, Li S, Yang Y, Zhang L, Zhang Y, Wei T. Perspectives of metal-organic framework nanosystem to overcome tumor drug resistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:954-970. [PMID: 36627891 PMCID: PMC9771744 DOI: 10.20517/cdr.2022.76] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/14/2022] [Accepted: 08/09/2022] [Indexed: 12/23/2022]
Abstract
Cancer is one of the most harmful diseases in the world, which causes huge numbers of deaths every year. Many drugs have been developed to treat tumors. However, drug resistance usually develops after a period of time, which greatly weakens the therapeutic effect. Tumor drug resistance is characterized by blocking the action of anticancer drugs, resisting apoptosis and DNA repair, and evading immune recognition. To tackle tumor drug resistance, many engineered drug delivery systems (DDS) have been developed. Metal-organic frameworks (MOFs) are one kind of emerging and promising nanocarriers for DDS with high surface area and abundant active sites that make the functionalization simpler and more efficient. These features enable MOFs to achieve advantages easily towards other materials. In this review, we highlight the main mechanisms of tumor drug resistance and the characteristics of MOFs. The applications and opportunities of MOF-based DDS to overcome tumor drug resistance are also discussed, shedding light on the future development of MOFs to address tumor drug resistance.
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Affiliation(s)
- Huafeng Wang
- School of Environment, Nanjing Normal University, Nanjing 210023, Jiangsu, China.,School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Shi Li
- School of Environment, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Yiting Yang
- School of Environment, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lei Zhang
- School of Environment, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Yinghao Zhang
- School of Environment, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Tianxiang Wei
- School of Environment, Nanjing Normal University, Nanjing 210023, Jiangsu, China.,Correspondence to: Dr. Tianxiang Wei, School of Environment, Nanjing Normal University, Nanjing 210023, Jiangsu, China. E-mail:
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38
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Li X, Liang W, Yu C, Meng Q, Zhang W, Wu X, Xue J, Deng S, Wang H. Potential therapeutic strategies for quercetin targeting critical pathological mechanisms associated with colon adenocarcinoma and COVID-19. Front Pharmacol 2022; 13:988153. [PMID: 36249762 PMCID: PMC9557079 DOI: 10.3389/fphar.2022.988153] [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: 07/07/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Patients with colon adenocarcinoma (COAD) are at a higher probability of infection with COVID-19 than healthy individuals. However, there is no globally accepted treatment protocol for patients with COAD/COVID-19. Quercetin has been found to have significant antitumor, antiviral and anti-inflammatory effects in several studies. Therefore, this study sought to evaluate the potential of quercetin as the agent for COAD/COVID-19 and to explore its mechanisms. We used bioinformatics algorithms to obtain COAD/COVID-19-related genes (CCRG) from COAD-related transcriptome data and COVID-related transcriptome sequencing data, and used these genes to construct a COAD prognostic model. We intersected the CCRG with the therapeutic target genes of quercetin and obtained a total of 105 genes (potential target genes of quercetin for the treatment of COAD/COVID-19). By constructing a protein-protein interaction (PPI) network, we ascertained FOS, NFKB1, NFKB1A, JUNB, and JUN as possible core target genes of quercetin for the treatment of COAD/COVID-19. Bioinformatic analysis of these 105 genes revealed that the mechanisms for quercetin the treatment of COAD/COVID-19 may be associated with oxidative stress, apoptosis, anti-inflammatory, immune, anti-viral and multiple pathways containing IL-17, TNF, HIF-1. In this study, we constructed a prognostic model of COAD/COVID19 patients by using CCRG and elucidated for the first time the potential target genes and molecular mechanisms of quercetin for the treatment of COAD/COVID-19, which may benefit the clinical treatment of COAD/COVID-19 patients. However, no clinical trials have yet been conducted to further validate the findings, but this will be the future direction of our research.
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Affiliation(s)
- Xiushen Li
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Key Laboratory, Shenzhen University General Hospital, Shenzhen, China
| | - Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Chengwei Yu
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Qingxue Meng
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Weiwen Zhang
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, China
| | - Xueliang Wu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Jun Xue
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
- *Correspondence: Jun Xue, ; Shoulong Deng, ; Hao Wang,
| | - Shoulong Deng
- National Health Commission of China (NHC) Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
- *Correspondence: Jun Xue, ; Shoulong Deng, ; Hao Wang,
| | - Hao Wang
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Key Laboratory, Shenzhen University General Hospital, Shenzhen, China
- *Correspondence: Jun Xue, ; Shoulong Deng, ; Hao Wang,
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Sorrentino A, Menevse AN, Michels T, Volpin V, Durst FC, Sax J, Xydia M, Hussein A, Stamova S, Spoerl S, Heuschneider N, Muehlbauer J, Jeltsch KM, Rathinasamy A, Werner-Klein M, Breinig M, Mikietyn D, Kohler C, Poschke I, Purr S, Reidell O, Martins Freire C, Offringa R, Gebhard C, Spang R, Rehli M, Boutros M, Schmidl C, Khandelwal N, Beckhove P. Salt-inducible kinase 3 protects tumor cells from cytotoxic T-cell attack by promoting TNF-induced NF-κB activation. J Immunother Cancer 2022; 10:jitc-2021-004258. [PMID: 35606086 PMCID: PMC9174898 DOI: 10.1136/jitc-2021-004258] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Cancer immunotherapeutic strategies showed unprecedented results in the clinic. However, many patients do not respond to immuno-oncological treatments due to the occurrence of a plethora of immunological obstacles, including tumor intrinsic mechanisms of resistance to cytotoxic T-cell (TC) attack. Thus, a deeper understanding of these mechanisms is needed to develop successful immunotherapies. METHODS To identify novel genes that protect tumor cells from effective TC-mediated cytotoxicity, we performed a genetic screening in pancreatic cancer cells challenged with tumor-infiltrating lymphocytes and antigen-specific TCs. RESULTS The screening revealed 108 potential genes that protected tumor cells from TC attack. Among them, salt-inducible kinase 3 (SIK3) was one of the strongest hits identified in the screening. Both genetic and pharmacological inhibitions of SIK3 in tumor cells dramatically increased TC-mediated cytotoxicity in several in vitro coculture models, using different sources of tumor and TCs. Consistently, adoptive TC transfer of TILs led to tumor growth inhibition of SIK3-depleted cancer cells in vivo. Mechanistic analysis revealed that SIK3 rendered tumor cells susceptible to tumor necrosis factor (TNF) secreted by tumor-activated TCs. SIK3 promoted nuclear factor kappa B (NF-κB) nuclear translocation and inhibited caspase-8 and caspase-9 after TNF stimulation. Chromatin accessibility and transcriptome analyses showed that SIK3 knockdown profoundly impaired the expression of prosurvival genes under the TNF-NF-κB axis. TNF stimulation led to SIK3-dependent phosphorylation of the NF-κB upstream regulators inhibitory-κB kinase and NF-kappa-B inhibitor alpha on the one side, and to inhibition of histone deacetylase 4 on the other side, thus sustaining NF-κB activation and nuclear stabilization. A SIK3-dependent gene signature of TNF-mediated NF-κB activation was found in a majority of pancreatic cancers where it correlated with increased cytotoxic TC activity and poor prognosis. CONCLUSION Our data reveal an abundant molecular mechanism that protects tumor cells from cytotoxic TC attack and demonstrate that pharmacological inhibition of this pathway is feasible.
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Affiliation(s)
- Antonio Sorrentino
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ayse Nur Menevse
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Tillmann Michels
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Valentina Volpin
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Julian Sax
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Maria Xydia
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Abir Hussein
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Slava Stamova
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Steffen Spoerl
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Nicole Heuschneider
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Jasmin Muehlbauer
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | | | - Anchana Rathinasamy
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Melanie Werner-Klein
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany
| | - Marco Breinig
- Signalling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Damian Mikietyn
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Christian Kohler
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Isabel Poschke
- Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKTK CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Sabrina Purr
- Joint Immunotherapeutics Laboratory, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olivia Reidell
- Research Department, iOmx Therapeutics, Munich/Martinsried, Germany
| | | | - Rienk Offringa
- Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Gebhard
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Rainer Spang
- Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Michael Rehli
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Michael Boutros
- Signalling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Schmidl
- Junior Group 'Epigenetic Immunooncology', Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Nisit Khandelwal
- Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Research Department, iOmx Therapeutics, Munich/Martinsried, Germany
| | - Philipp Beckhove
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
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40
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Advances in Chimeric Antigen Receptor (CAR) T-Cell Therapies for the Treatment of Primary Brain Tumors. Antibodies (Basel) 2022; 11:antib11020031. [PMID: 35645204 PMCID: PMC9149956 DOI: 10.3390/antib11020031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022] Open
Abstract
Immunotherapy has revolutionized the care of cancer patients. A diverse set of strategies to overcome cancer immunosuppression and enhance the tumor-directed immune response are in clinical use, but have not achieved transformative benefits for brain tumor patients. Adoptive cell therapies, which employ a patient’s own immune cells to generate directed anti-tumor activity, are emerging technologies that hold promise to improve the treatment of primary brain tumors in children and adults. Here, we review recent advances in chimeric antigen receptor (CAR) T-cell therapies for the treatment of aggressive primary brain tumors, including glioblastoma and diffuse midline glioma, H3 K27M-mutant. We highlight current approaches, discuss encouraging investigational data, and describe key challenges in the development and implementation of these types of therapies in the neuro-oncology setting.
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41
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CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity. Nat Commun 2022; 13:1606. [PMID: 35338135 PMCID: PMC8956604 DOI: 10.1038/s41467-022-29205-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/25/2022] [Indexed: 12/28/2022] Open
Abstract
The cellular processes that govern tumor resistance to immunotherapy remain poorly understood. To gain insight into these processes, here we perform a genome-scale CRISPR activation screen for genes that enable human melanoma cells to evade cytotoxic T cell killing. Overexpression of four top candidate genes (CD274 (PD-L1), MCL1, JUNB, and B3GNT2) conferred resistance in diverse cancer cell types and mouse xenografts. By investigating the resistance mechanisms, we find that MCL1 and JUNB modulate the mitochondrial apoptosis pathway. JUNB encodes a transcription factor that downregulates FasL and TRAIL receptors, upregulates the MCL1 relative BCL2A1, and activates the NF-κB pathway. B3GNT2 encodes a poly-N-acetyllactosamine synthase that targets >10 ligands and receptors to disrupt interactions between tumor and T cells and reduce T cell activation. Inhibition of candidate genes sensitized tumor models to T cell cytotoxicity. Our results demonstrate that systematic gain-of-function screening can elucidate resistance pathways and identify potential targets for cancer immunotherapy. Loss-of-function CRISPR-based screens have identified several genes associated with cancer resistance to T cell-induced cytotoxicity. Here the authors perform a genome-scale, gain-of-function CRISPR screen and identify candidate genes, including the poly-N-acetyllactosamine synthase B3GNT2, whose overexpression confers tumor cell resistance to T cell cytotoxicity
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