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Cao Y, Li X, Pan Y, Wang H, Yang S, Hong L, Ye L. CRISPR-based genetic screens advance cancer immunology. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2571-0. [PMID: 39048715 DOI: 10.1007/s11427-023-2571-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/18/2024] [Indexed: 07/27/2024]
Abstract
CRISPR technologies have revolutionized research areas ranging from fundamental science to translational medicine. CRISPR-based genetic screens offer a powerful platform for unbiased screening in various fields, such as cancer immunology. Immune checkpoint blockade (ICB) therapy has been shown to strongly affect cancer treatment. However, the currently available ICBs are limited and do not work in all cancer patients. Pooled CRISPR screens enable the identification of previously unknown immune regulators that can regulate T-cell activation, cytotoxicity, persistence, infiltration into tumors, cytokine secretion, memory formation, T-cell metabolism, and CD4+ T-cell differentiation. These novel targets can be developed as new immunotherapies or used with the current ICBs as new combination therapies that may yield synergistic efficacy. Here, we review the progress made in the development of CRISPR technologies, particularly technological advances in CRISPR screens and their application in novel target identification for immunotherapy.
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Affiliation(s)
- Yuanfang Cao
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Xueting Li
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Yumu Pan
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Huahe Wang
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Siyu Yang
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Lingjuan Hong
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Lupeng Ye
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China.
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2
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Ban GI, Puviindran V, Xiang Y, Nadesan P, Tang J, Ou J, Guardino N, Nakagawa M, Browne M, Wallace A, Ishikawa K, Shimada E, Martin JT, Diao Y, Kirsch DG, Alman BA. The COMPASS complex maintains the metastatic capacity imparted by a subpopulation of cells in UPS. iScience 2024; 27:110187. [PMID: 38989451 PMCID: PMC11233968 DOI: 10.1016/j.isci.2024.110187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/20/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Intratumoral heterogeneity is common in cancer, particularly in sarcomas like undifferentiated pleomorphic sarcoma (UPS), where individual cells demonstrate a high degree of cytogenic diversity. Previous studies showed that a small subset of cells within UPS, known as the metastatic clone (MC), as responsible for metastasis. Using a CRISPR-based genomic screen in-vivo, we identified the COMPASS complex member Setd1a as a key regulator maintaining the metastatic phenotype of the MC in murine UPS. Depletion of Setd1a inhibited metastasis development in the MC. Transcriptome and chromatin sequencing revealed COMPASS complex target genes in UPS, such as Cxcl10, downregulated in the MC. Deleting Cxcl10 in non-MC cells increased their metastatic potential. Treating mice with human UPS xenografts with a COMPASS complex inhibitor suppressed metastasis without affecting tumor growth in the primary tumor. Our data identified an epigenetic program in a subpopulation of sarcoma cells that maintains metastatic potential.
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Affiliation(s)
- Ga I. Ban
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Vijitha Puviindran
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Yu Xiang
- Department of Cell Biology and Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA
| | - Puvi Nadesan
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Jackie Tang
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Jianhong Ou
- Department of Cell Biology and Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas Guardino
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Makoto Nakagawa
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - MaKenna Browne
- Department of Cell Biology and Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA
| | - Asjah Wallace
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Koji Ishikawa
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Eijiro Shimada
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - John T. Martin
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Yarui Diao
- Department of Cell Biology and Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA
| | - David G. Kirsch
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC, USA
- The Princes Margaret Cancer Centre, Department of Radiation Oncology, University Health Network and the University of Toronto, Toronto, ON, Canada
| | - Benjamin A. Alman
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
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3
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Kim TW, Koo SY, Riessland M, Chaudhry F, Kolisnyk B, Cho HS, Russo MV, Saurat N, Mehta S, Garippa R, Betel D, Studer L. TNF-NF-κB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons. Cell 2024; 187:3671-3689.e23. [PMID: 38866017 DOI: 10.1016/j.cell.2024.05.030] [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: 11/20/2022] [Revised: 12/15/2023] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
Ongoing, early-stage clinical trials illustrate the translational potential of human pluripotent stem cell (hPSC)-based cell therapies in Parkinson's disease (PD). However, an unresolved challenge is the extensive cell death following transplantation. Here, we performed a pooled CRISPR-Cas9 screen to enhance postmitotic dopamine neuron survival in vivo. We identified p53-mediated apoptotic cell death as a major contributor to dopamine neuron loss and uncovered a causal link of tumor necrosis factor alpha (TNF-α)-nuclear factor κB (NF-κB) signaling in limiting cell survival. As a translationally relevant strategy to purify postmitotic dopamine neurons, we identified cell surface markers that enable purification without the need for genetic reporters. Combining cell sorting and treatment with adalimumab, a clinically approved TNF-α inhibitor, enabled efficient engraftment of postmitotic dopamine neurons with extensive reinnervation and functional recovery in a preclinical PD mouse model. Thus, transient TNF-α inhibition presents a clinically relevant strategy to enhance survival and enable engraftment of postmitotic hPSC-derived dopamine neurons in PD.
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Affiliation(s)
- Tae Wan Kim
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Interdisciplinary Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - So Yeon Koo
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Markus Riessland
- Department of Neurobiology and Behavior, Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794, USA
| | - Fayzan Chaudhry
- Tri-Institutional PhD program in Computational Biology, New York, NY, USA
| | - Benjamin Kolisnyk
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Hyein S Cho
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Marco Vincenzo Russo
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Nathalie Saurat
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sanjoy Mehta
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Doron Betel
- Division of Hematology & Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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Mondal P, Alyateem G, Mitchell AV, Gottesman MM. A whole-genome CRISPR screen identifies the spindle accessory checkpoint as a locus of nab-paclitaxel resistance in a pancreatic cancer cell line. Sci Rep 2024; 14:15912. [PMID: 38987356 PMCID: PMC11236977 DOI: 10.1038/s41598-024-66244-1] [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: 03/25/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Pancreatic adenocarcinoma is one of the most aggressive and lethal forms of cancer. Chemotherapy is the primary treatment for pancreatic cancer, but resistance to the drugs used remains a major challenge. A genome-wide CRISPR interference and knockout screen in the PANC-1 cell line with the drug nab-paclitaxel has identified a group of spindle assembly checkpoint (SAC) genes that enhance survival in nab-paclitaxel. Knockdown of these SAC genes (BUB1B, BUB3, and TTK) attenuates paclitaxel-induced cell death. Cells treated with the small molecule inhibitors BAY 1217389 or MPI 0479605, targeting the threonine tyrosine kinase (TTK), also enhance survival in paclitaxel. Overexpression of these SAC genes does not affect sensitivity to paclitaxel. These discoveries have helped to elucidate the mechanisms behind paclitaxel cytotoxicity. The outcomes of this investigation may pave the way for a deeper comprehension of the diverse responses of pancreatic cancer to therapies including paclitaxel. Additionally, they could facilitate the formulation of novel treatment approaches for pancreatic cancer.
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Affiliation(s)
- Priya Mondal
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - George Alyateem
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Allison V Mitchell
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Michael M Gottesman
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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Giuliano CJ, Wei KJ, Harling FM, Waldman BS, Farringer MA, Boydston EA, Lan TCT, Thomas RW, Herneisen AL, Sanderlin AG, Coppens I, Dvorin JD, Lourido S. CRISPR-based functional profiling of the Toxoplasma gondii genome during acute murine infection. Nat Microbiol 2024:10.1038/s41564-024-01754-2. [PMID: 38977907 DOI: 10.1038/s41564-024-01754-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/07/2024] [Indexed: 07/10/2024]
Abstract
Examining host-pathogen interactions in animals can capture aspects of infection that are obscured in cell culture. Using CRISPR-based screens, we functionally profile the entire genome of the apicomplexan parasite Toxoplasma gondii during murine infection. Barcoded gRNAs enabled bottleneck detection and mapping of population structures within parasite lineages. Over 300 genes with previously unknown roles in infection were found to modulate parasite fitness in mice. Candidates span multiple axes of host-parasite interaction. Rhoptry Apical Surface Protein 1 was characterized as a mediator of host-cell tropism that facilitates repeated invasion attempts. GTP cyclohydrolase I was also required for fitness in mice and druggable through a repurposed compound, 2,4-diamino-6-hydroxypyrimidine. This compound synergized with pyrimethamine against T. gondii and malaria-causing Plasmodium falciparum parasites. This work represents a complete survey of an apicomplexan genome during infection of an animal host and points to novel interfaces of host-parasite interaction.
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Affiliation(s)
| | - Kenneth J Wei
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, MIT, Cambridge, MA, USA
| | | | - Benjamin S Waldman
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, MIT, Cambridge, MA, USA
| | - Madeline A Farringer
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
- Biological Sciences in Public Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Raina W Thomas
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, MIT, Cambridge, MA, USA
| | - Alice L Herneisen
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, MIT, Cambridge, MA, USA
| | | | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jeffrey D Dvorin
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Sebastian Lourido
- Whitehead Institute, Cambridge, MA, USA.
- Biology Department, MIT, Cambridge, MA, USA.
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Zhang YW, Gvozdenovic A, Aceto N. A Molecular Voyage: Multiomics Insights into Circulating Tumor Cells. Cancer Discov 2024; 14:920-933. [PMID: 38581442 DOI: 10.1158/2159-8290.cd-24-0218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/08/2024]
Abstract
Circulating tumor cells (CTCs) play a pivotal role in metastasis, the leading cause of cancer-associated death. Recent improvements of CTC isolation tools, coupled with a steady development of multiomics technologies at single-cell resolution, have enabled an extensive exploration of CTC biology, unlocking insights into their molecular profiles. A detailed molecular portrait requires CTC interrogation across various levels encompassing genomic, epigenetic, transcriptomic, proteomic and metabolic features. Here, we review how state-of-the-art multiomics applied to CTCs are shedding light on how cancer spreads. Further, we highlight the potential implications of CTC profiling for clinical applications aimed at enhancing cancer diagnosis and treatment. SIGNIFICANCE Exploring the complexity of cancer progression through cutting-edge multiomics studies holds the promise of uncovering novel aspects of cancer biology and identifying therapeutic vulnerabilities to suppress metastasis.
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Affiliation(s)
- Yu Wei Zhang
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Ana Gvozdenovic
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
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Deng L, Zhou J, Sun Y, Hu Y, Qiao J, Liu Z, Gu L, Lin D, Zhang L, Deng D. CDKN2A somatic copy number amplification in normal tissues surrounding gastric carcinoma reduces cancer metastasis risk in droplet digital PCR analysis. Gastric Cancer 2024:10.1007/s10120-024-01515-4. [PMID: 38822931 DOI: 10.1007/s10120-024-01515-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 05/17/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND The CDKN2A gene is frequently affected by somatic copy number variations (SCNVs, including deletions and amplifications [SCNdel and SCNamp]) in the cancer genome. Using surgical gastric margin tissue samples (SMs) as the diploid reference in SCNV analysis via CDKN2A/P16-specific real-time PCR (P16-Light), we previously reported that the CDKN2A SCNdel was associated with a high risk of metastasis of gastric carcinoma (GC). However, the status of CDKN2A SCNVs in SMs and their clinical significance have not been reported. METHODS Peripheral white blood cell (WBC) and frozen GC and SM tissue samples were collected from patients (n = 80). Droplet digital PCR (ddPCR) was used to determine the copy number (CN) of the CDKN2A gene in tissue samples using paired WBCs as the diploid reference. RESULTS A novel P16-ddPCR system was initially established with a minimal proportion (or limit, 10%) of the detection of CDKN2A CN alterations. While CDKN2A SCNamp events were detected in both SMs and GCs, fewer CDKN2A SCNdel events were detected in SMs than in GCs (15.0% vs. 41.3%, P = 4.77E-04). Notably, significantly more SCNamp and fewer SCNdel of the CDKN2A gene were detected in SMs from GC patients without metastasis than in those from patients with lymph node metastasis by P16-ddPCR (P = 0.023). The status of CDKN2A SCNVs in SM samples was significantly associated with overall survival (P = 0.032). No cancer deaths were observed among the 11 patients with CDKN2A SCNamp. CONCLUSION CDKN2A SCNVs in SMs identified by P16-ddPCR are prevalent and significantly associated with GC metastasis and overall survival.
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Affiliation(s)
- Lewen Deng
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yu Sun
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Ying Hu
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Department of Surgery, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Juanli Qiao
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Dongmei Lin
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Lianhai Zhang
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Department of Surgery, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
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Liu S, Zhang Z, Wang Z, Li J, Shen L. Genome-wide CRISPR screening identifies the pivotal role of ANKRD42 in colorectal cancer metastasis through EMT regulation. IUBMB Life 2024. [PMID: 38822625 DOI: 10.1002/iub.2855] [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: 03/11/2024] [Accepted: 04/26/2024] [Indexed: 06/03/2024]
Abstract
Colorectal cancer (CRC), a pervasive and lethal malignancy of gastrointestinal cancer, imposes significant challenges due to the occurrence of distant metastasis in advanced stages. Understanding the intricate regulatory mechanisms driving CRC distant metastasis is of paramount importance. CRISPR-Cas9 screening has emerged as a powerful tool for investigating tumor initiation and progression. However, its application in studying CRC distant metastasis remains largely unexplored. To establish a model that faithfully recapitulates CRC liver metastasis in patients, we developed an in vivo genome-wide CRISPR-Cas9 screening approach using a spleen-injected liver metastasis mouse model. Through comprehensive screening of a whole-genome sgRNA library, we identified ANKRD42 as a pivotal regulatory gene facilitating CRC liver metastasis. Analysis of the TCGA database and our clinical cohorts unveiled heightened ANKRD42 expression in metastases. At the cellular level, the attenuation of ANKRD42 impaired the migration and invasion processes of tumor cells. In vivo experiments further validated these observations, highlighting the diminished liver metastatic capacity of tumor cells upon ANKRD42 knockdown. To unravel the specific mechanisms by which ANKRD42 regulates CRC distant metastasis, we leveraged patient-derived organoid (PDO) models. Depleting ANKRD42 in PDOs sourced from liver metastases precipitated the downregulation of pivotal genes linked to epithelial-mesenchymal transition (EMT), including CDH2 and SNAI2, thereby effectively suppressing tumor metastasis. This study not only establishes a conceptual framework but also identifies potential therapeutic avenues for advanced-stage distant metastasis in CRC patients.
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Affiliation(s)
- Shengde Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zizhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhenghang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jian Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lin Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, China
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Dakal TC, Dhabhai B, Pant A, Moar K, Chaudhary K, Yadav V, Ranga V, Sharma NK, Kumar A, Maurya PK, Maciaczyk J, Schmidt‐Wolf IGH, Sharma A. Oncogenes and tumor suppressor genes: functions and roles in cancers. MedComm (Beijing) 2024; 5:e582. [PMID: 38827026 PMCID: PMC11141506 DOI: 10.1002/mco2.582] [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: 09/18/2023] [Revised: 04/21/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Cancer, being the most formidable ailment, has had a profound impact on the human health. The disease is primarily associated with genetic mutations that impact oncogenes and tumor suppressor genes (TSGs). Recently, growing evidence have shown that X-linked TSGs have specific role in cancer progression and metastasis as well. Interestingly, our genome harbors around substantial portion of genes that function as tumor suppressors, and the X chromosome alone harbors a considerable number of TSGs. The scenario becomes even more compelling as X-linked TSGs are adaptive to key epigenetic processes such as X chromosome inactivation. Therefore, delineating the new paradigm related to X-linked TSGs, for instance, their crosstalk with autosome and involvement in cancer initiation, progression, and metastasis becomes utmost importance. Considering this, herein, we present a comprehensive discussion of X-linked TSG dysregulation in various cancers as a consequence of genetic variations and epigenetic alterations. In addition, the dynamic role of X-linked TSGs in sex chromosome-autosome crosstalk in cancer genome remodeling is being explored thoroughly. Besides, the functional roles of ncRNAs, role of X-linked TSG in immunomodulation and in gender-based cancer disparities has also been highlighted. Overall, the focal idea of the present article is to recapitulate the findings on X-linked TSG regulation in the cancer landscape and to redefine their role toward improving cancer treatment strategies.
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Affiliation(s)
- Tikam Chand Dakal
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Bhanupriya Dhabhai
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Anuja Pant
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kareena Moar
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kanika Chaudhary
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vikas Yadav
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vipin Ranga
- Dearptment of Agricultural BiotechnologyDBT‐NECAB, Assam Agricultural UniversityJorhatAssamIndia
| | | | - Abhishek Kumar
- Manipal Academy of Higher EducationManipalKarnatakaIndia
- Institute of Bioinformatics, International Technology ParkBangaloreIndia
| | - Pawan Kumar Maurya
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Jarek Maciaczyk
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
| | - Ingo G. H. Schmidt‐Wolf
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
| | - Amit Sharma
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
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10
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Finkel Y, Nachshon A, Aharon E, Arazi T, Simonovsky E, Dobešová M, Saud Z, Gluck A, Fisher T, Stanton RJ, Schwartz M, Stern-Ginossar N. A virally encoded high-resolution screen of cytomegalovirus dependencies. Nature 2024; 630:712-719. [PMID: 38839957 DOI: 10.1038/s41586-024-07503-z] [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: 10/30/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Genetic screens have transformed our ability to interrogate cellular factor requirements for viral infections1,2, but most current approaches are limited in their sensitivity, biased towards early stages of infection and provide only simplistic phenotypic information that is often based on survival of infected cells2-4. Here, by engineering human cytomegalovirus to express single guide RNA libraries directly from the viral genome, we developed virus-encoded CRISPR-based direct readout screening (VECOS), a sensitive, versatile, viral-centric approach that enables profiling of different stages of viral infection in a pooled format. Using this approach, we identified hundreds of host dependency and restriction factors and quantified their direct effects on viral genome replication, viral particle secretion and infectiousness of secreted particles, providing a multi-dimensional perspective on virus-host interactions. These high-resolution measurements reveal that perturbations altering late stages in the life cycle of human cytomegalovirus (HCMV) mostly regulate viral particle quality rather than quantity, establishing correct virion assembly as a critical stage that is heavily reliant on virus-host interactions. Overall, VECOS facilitates systematic high-resolution dissection of the role of human proteins during the infection cycle, providing a roadmap for in-depth study of host-herpesvirus interactions.
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Affiliation(s)
- Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Einav Aharon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Arazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elena Simonovsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Martina Dobešová
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Zack Saud
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Avi Gluck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Fisher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Richard J Stanton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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11
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Qin M, Deng C, Wen L, Luo G, Meng Y. CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy. J Transl Med 2024; 22:516. [PMID: 38816739 PMCID: PMC11138051 DOI: 10.1186/s12967-024-05235-2] [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: 01/03/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Target cancer therapy has been developed for clinical cancer treatment based on the discovery of CRISPR (clustered regularly interspaced short palindromic repeat) -Cas system. This forefront and cutting-edge scientific technique improves the cancer research into molecular level and is currently widely utilized in genetic investigation and clinical precision cancer therapy. In this review, we summarized the genetic modification by CRISPR/Cas and CRISPR screening system, discussed key components for successful CRISPR screening, including Cas enzymes, guide RNA (gRNA) libraries, target cells or organs. Furthermore, we focused on the application for CAR-T cell therapy, drug target, drug screening, or drug selection in both ex vivo and in vivo with CRISPR screening system. In addition, we elucidated the advantages and potential obstacles of CRISPR system in precision clinical medicine and described the prospects for future genetic therapy.In summary, we provide a comprehensive and practical perspective on the development of CRISPR/Cas and CRISPR screening system for the treatment of cancer defects, aiming to further improve the precision and accuracy for clinical treatment and individualized gene therapy.
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Affiliation(s)
- Mingming Qin
- Reproductive Medical Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Women and Children Hospital), Foshan, Guangdong, 528000, China
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Chunhao Deng
- Chinese Medicine and Translational Medicine R&D center, Zhuhai UM Science & Technology Research Institute, Zhuhai, Guangdong, 519031, China
| | - Liewei Wen
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai Clinical Medical College of Jinan University, Zhuhai, Guangdong, 519000, China
| | - Guoqun Luo
- Reproductive Medical Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Women and Children Hospital), Foshan, Guangdong, 528000, China.
| | - Ya Meng
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital, Zhuhai Clinical Medical College of Jinan University, Zhuhai, Guangdong, 519000, China.
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12
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Tomić G, Sheridan C, Refermat AY, Baggelaar MP, Sipthorp J, Sudarshan B, Ocasio CA, Suárez-Bonnet A, Priestnall SL, Herbert E, Tate EW, Downward J. Palmitoyl transferase ZDHHC20 promotes pancreatic cancer metastasis. Cell Rep 2024; 43:114224. [PMID: 38733589 DOI: 10.1016/j.celrep.2024.114224] [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: 11/09/2023] [Revised: 03/04/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Metastasis is one of the defining features of pancreatic ductal adenocarcinoma (PDAC) that contributes to poor prognosis. In this study, the palmitoyl transferase ZDHHC20 was identified in an in vivo short hairpin RNA (shRNA) screen as critical for metastatic outgrowth, with no effect on proliferation and migration in vitro or primary PDAC growth in mice. This phenotype is abrogated in immunocompromised animals and animals with depleted natural killer (NK) cells, indicating that ZDHHC20 affects the interaction of tumor cells and the innate immune system. Using a chemical genetics platform for ZDHHC20-specific substrate profiling, a number of substrates of this enzyme were identified. These results describe a role for palmitoylation in enabling distant metastasis that could not have been detected using in vitro screening approaches and identify potential effectors through which ZDHHC20 promotes metastasis of PDAC.
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Affiliation(s)
- Goran Tomić
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Clare Sheridan
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Marc P Baggelaar
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 80 Wood Lane, London W12 0BZ, UK
| | - James Sipthorp
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 80 Wood Lane, London W12 0BZ, UK
| | | | - Cory A Ocasio
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alejandro Suárez-Bonnet
- The Royal Veterinary College, Department of Pathobiology & Population Sciences, Hawkshead Lane, Hatfield AL9 7TA, UK; Experimental Histopathology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Simon L Priestnall
- The Royal Veterinary College, Department of Pathobiology & Population Sciences, Hawkshead Lane, Hatfield AL9 7TA, UK; Experimental Histopathology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eleanor Herbert
- The Royal Veterinary College, Department of Pathobiology & Population Sciences, Hawkshead Lane, Hatfield AL9 7TA, UK; Experimental Histopathology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Edward W Tate
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 80 Wood Lane, London W12 0BZ, UK
| | - Julian Downward
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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13
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Hart SK, Wessels HH, Méndez-Mancilla A, Müller S, Drabavicius G, Choi O, Sanjana NE. Low copy CRISPR-Cas13d mitigates collateral RNA cleavage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.594039. [PMID: 38798586 PMCID: PMC11118291 DOI: 10.1101/2024.05.13.594039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
While CRISPR-Cas13 systems excel in accurately targeting RNA, the potential for collateral RNA degradation poses a concern for therapeutic applications and limits broader adoption for transcriptome perturbations. We evaluate the extent to which collateral RNA cleavage occurs when Rfx Cas13d is delivered via plasmid transfection or lentiviral transduction and find that collateral activity only occurs with high levels of Rfx Cas13d expression. Using transcriptome-scale and combinatorial CRISPR pooled screens in cell lines with low-copy Rfx Cas13d, we find high on-target knockdown, without extensive collateral activity regardless of the expression level of the target gene. In contrast, transfection of Rfx Cas13d, which yields higher nuclease expression, results in collateral RNA degradation. Further, our analysis of a high-fidelity Cas13 variant uncovers a marked decrease in on-target efficiency, suggesting that its reduced collateral activity may be due to an overall diminished nuclease capability.
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14
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Zhang H, Read A, Cataisson C, Yang HH, Lee WC, Turk BE, Yuspa SH, Luo J. Protein phosphatase 6 activates NF-κB to confer sensitivity to MAPK pathway inhibitors in KRAS- and BRAF-mutant cancer cells. Sci Signal 2024; 17:eadd5073. [PMID: 38743809 PMCID: PMC11238902 DOI: 10.1126/scisignal.add5073] [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: 06/16/2022] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
The Ras-mitogen-activated protein kinase (MAPK) pathway is a major target for cancer treatment. To better understand the genetic pathways that modulate cancer cell sensitivity to MAPK pathway inhibitors, we performed a CRISPR knockout screen with MAPK pathway inhibitors on a colorectal cancer (CRC) cell line carrying mutant KRAS. Genetic deletion of the catalytic subunit of protein phosphatase 6 (PP6), encoded by PPP6C, rendered KRAS- and BRAF-mutant CRC and BRAF-mutant melanoma cells more resistant to these inhibitors. In the absence of MAPK pathway inhibition, PPP6C deletion in CRC cells decreased cell proliferation in two-dimensional (2D) adherent cultures but accelerated the growth of tumor spheroids in 3D culture and tumor xenografts in vivo. PPP6C deletion enhanced the activation of nuclear factor κB (NF-κB) signaling in CRC and melanoma cells and circumvented the cell cycle arrest and decreased cyclin D1 abundance induced by MAPK pathway blockade in CRC cells. Inhibiting NF-κB activity by genetic and pharmacological means restored the sensitivity of PPP6C-deficient cells to MAPK pathway inhibition in CRC and melanoma cells in vitro and in CRC cells in vivo. Furthermore, a R264 point mutation in PPP6C conferred loss of function in CRC cells, phenocopying the enhanced NF-κB activation and resistance to MAPK pathway inhibition observed for PPP6C deletion. These findings demonstrate that PP6 constrains the growth of KRAS- and BRAF-mutant cancer cells, implicates the PP6-NF-κB axis as a modulator of MAPK pathway output, and presents a rationale for cotargeting the NF-κB pathway in PPP6C-mutant cancer cells.
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Affiliation(s)
- Haibo Zhang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Abigail Read
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
- Current affiliation: Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Christophe Cataisson
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Howard H. Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Wei-Chun Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Stuart H. Yuspa
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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15
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Simwela NV, Johnston L, Pavinski Bitar P, Jaecklein E, Altier C, Sassetti CM, Russell DG. Genome-wide screen of Mycobacterium tuberculosis- infected macrophages identified the GID/CTLH complex as a determinant of intracellular bacterial growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592714. [PMID: 38766174 PMCID: PMC11100626 DOI: 10.1101/2024.05.06.592714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The eukaryotic GID/CTLH complex is a highly conserved E3 ubiquitin ligase involved in a broad range of biological processes. However, a role of this complex in host antimicrobial defenses has not been described. We exploited Mycobacterium tuberculosis ( Mtb ) induced cytotoxicity in macrophages in a FACS based CRISPR genetic screen to identify host determinants of intracellular Mtb growth restriction. Our screen identified 5 ( GID8 , YPEL5 , WDR26 , UBE2H , MAEA ) of the 10 predicted members of the GID/CTLH complex as determinants of intracellular growth of both Mtb and Salmonella serovar Typhimurium. We show that the antimicrobial properties of the GID/CTLH complex knockdown macrophages are mediated by enhanced GABAergic signaling, activated AMPK, increased autophagic flux and resistance to cell death. Meanwhile, Mtb isolated from GID/CTLH knockdown macrophages are nutritionally starved and oxidatively stressed. Our study identifies the GID/CTLH complex activity as broadly suppressive of host antimicrobial responses against intracellular bacterial infections. Graphical abstract
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16
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Ni Z, Ahmed N, Nabeel-Shah S, Guo X, Pu S, Song J, Marcon E, Burke G, Tong AH, Chan K, Ha KH, Blencowe B, Moffat J, Greenblatt J. Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. Nucleic Acids Res 2024; 52:4483-4501. [PMID: 38587191 PMCID: PMC11077057 DOI: 10.1093/nar/gkae240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024] Open
Abstract
Messenger RNA precursors (pre-mRNA) generally undergo 3' end processing by cleavage and polyadenylation (CPA), which is specified by a polyadenylation site (PAS) and adjacent RNA sequences and regulated by a large variety of core and auxiliary CPA factors. To date, most of the human CPA factors have been discovered through biochemical and proteomic studies. However, genetic identification of the human CPA factors has been hampered by the lack of a reliable genome-wide screening method. We describe here a dual fluorescence readthrough reporter system with a PAS inserted between two fluorescent reporters. This system enables measurement of the efficiency of 3' end processing in living cells. Using this system in combination with a human genome-wide CRISPR/Cas9 library, we conducted a screen for CPA factors. The screens identified most components of the known core CPA complexes and other known CPA factors. The screens also identified CCNK/CDK12 as a potential core CPA factor, and RPRD1B as a CPA factor that binds RNA and regulates the release of RNA polymerase II at the 3' ends of genes. Thus, this dual fluorescence reporter coupled with CRISPR/Cas9 screens reliably identifies bona fide CPA factors and provides a platform for investigating the requirements for CPA in various contexts.
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Affiliation(s)
- Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Nujhat Ahmed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Xinghua Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jingwen Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Giovanni L Burke
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Katherine Chan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Kevin C H Ha
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
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17
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Sánchez Rivera FJ, Dow LE. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Cold Spring Harb Perspect Med 2024; 14:a041384. [PMID: 37487630 PMCID: PMC11065179 DOI: 10.1101/cshperspect.a041384] [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: 07/26/2023]
Abstract
Cancers arise through acquisition of mutations in genes that regulate core biological processes like cell proliferation and cell death. Decades of cancer research have led to the identification of genes and mutations causally involved in disease development and evolution, yet defining their precise function across different cancer types and how they influence therapy responses has been challenging. Mouse models have helped define the in vivo function of cancer-associated alterations, and genome-editing approaches using CRISPR have dramatically accelerated the pace at which these models are developed and studied. Here, we highlight how CRISPR technologies have impacted the development and use of mouse models for cancer research and discuss the many ways in which these rapidly evolving platforms will continue to transform our understanding of this disease.
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Affiliation(s)
- Francisco J Sánchez Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York 10065, USA
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18
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Liu W, Wang W, Wang Z, Fan X, Li W, Huang Y, Yang X, Tang Z. CRISPR Screen Identifies the RNA-Binding Protein Eef1a1 as a Key Regulator of Myogenesis. Int J Mol Sci 2024; 25:4816. [PMID: 38732031 PMCID: PMC11084334 DOI: 10.3390/ijms25094816] [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: 03/19/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Skeletal muscle myogenesis hinges on gene regulation, meticulously orchestrated by molecular mechanisms. While the roles of transcription factors and non-coding RNAs in myogenesis are widely known, the contribution of RNA-binding proteins (RBPs) has remained unclear until now. Therefore, to investigate the functions of post-transcriptional regulators in myogenesis and uncover new functional RBPs regulating myogenesis, we employed CRISPR high-throughput RBP-KO (RBP-wide knockout) library screening. Through this approach, we successfully identified Eef1a1 as a novel regulatory factor in myogenesis. Using CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) technologies, we successfully established cellular models for both CRISPRko and CRISPRi. Our findings demonstrated that Eef1a1 plays a crucial role in promoting proliferation in C2C12 myoblasts. Through siRNA inhibition and overexpression methods, we further elucidated the involvement of Eef1a1 in promoting proliferation and suppressing differentiation processes. RIP (RNA immunoprecipitation), miRNA pull-down, and Dual-luciferase reporter assays confirmed that miR-133a-3p targets Eef1a1. Co-transfection experiments indicated that miR-133a-3p can rescue the effect of Eef1a1 on C2C12 myoblasts. In summary, our study utilized CRISPR library high-throughput screening to unveil a novel RBP, Eef1a1, involved in regulating myogenesis. Eef1a1 promotes the proliferation of myoblasts while inhibiting the differentiation process. Additionally, it acts as an antagonist to miR-133a-3p, thus modulating the process of myogenesis.
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Affiliation(s)
- Weiwei Liu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
| | - Wei Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zishuai Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xinhao Fan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Wangchang Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuxin Huang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaogan Yang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
| | - Zhonglin Tang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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19
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Johnson GA, Gould SI, Sánchez-Rivera FJ. Deconstructing cancer with precision genome editing. Biochem Soc Trans 2024; 52:803-819. [PMID: 38629716 PMCID: PMC11088927 DOI: 10.1042/bst20230984] [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: 02/01/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Recent advances in genome editing technologies are allowing investigators to engineer and study cancer-associated mutations in their endogenous genetic contexts with high precision and efficiency. Of these, base editing and prime editing are quickly becoming gold-standards in the field due to their versatility and scalability. Here, we review the merits and limitations of these precision genome editing technologies, their application to modern cancer research, and speculate how these could be integrated to address future directions in the field.
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Affiliation(s)
- Grace A. Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
| | - Samuel I. Gould
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
| | - Francisco J. Sánchez-Rivera
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
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20
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Wang YF, An ZY, Li JW, Dong ZK, Jin WL. MG53/TRIM72: multi-organ repair protein and beyond. Front Physiol 2024; 15:1377025. [PMID: 38681139 PMCID: PMC11046001 DOI: 10.3389/fphys.2024.1377025] [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: 01/26/2024] [Accepted: 04/01/2024] [Indexed: 05/01/2024] Open
Abstract
MG53, a member of the tripartite motif protein family, possesses multiple functionalities due to its classic membrane repair function, anti-inflammatory ability, and E3 ubiquitin ligase properties. Initially recognized for its crucial role in membrane repair, the therapeutic potential of MG53 has been extensively explored in various diseases including muscle injury, myocardial damage, acute lung injury, and acute kidney injury. However, further research has revealed that the E3 ubiquitin ligase characteristics of MG53 also contribute to the pathogenesis of certain conditions such as diabetic cardiomyopathy, insulin resistance, and metabolic syndrome. Moreover, recent studies have highlighted the anti-tumor effects of MG53 in different types of cancer, such as small cell lung cancer, liver cancer, and colorectal cancer; these effects are closely associated with their E3 ubiquitin ligase activities. In summary, MG53 is a multifunctional protein that participates in important physiological and pathological processes of multiple organs and is a promising therapeutic target for various human diseases. MG53 plays a multi-organ protective role due to its membrane repair function and its exertion of anti-tumor effects due to its E3 ubiquitin ligase properties. In addition, the controversial aspect of MG53's E3 ubiquitin ligase properties potentially causing insulin resistance and metabolic syndrome necessitates further cross-validation for clarity.
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Affiliation(s)
- Yong-Fei Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Zi-Yi An
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Jian-Wen Li
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Zi-Kai Dong
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Wei-Lin Jin
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
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21
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Dong J, Kong L, Wang S, Xia M, Zhang Y, Wu J, Yang F, Zuo S, Wei J. Oncolytic adenovirus encoding apolipoprotein A1 suppresses metastasis of triple-negative breast cancer in mice. J Exp Clin Cancer Res 2024; 43:102. [PMID: 38566092 PMCID: PMC10988920 DOI: 10.1186/s13046-024-03011-0] [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: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Dysregulation of cholesterol metabolism is associated with the metastasis of triple-negative breast cancer (TNBC). Apolipoprotein A1 (ApoA1) is widely recognized for its pivotal role in regulating cholesterol efflux and maintaining cellular cholesterol homeostasis. However, further exploration is needed to determine whether it inhibits TNBC metastasis by affecting cholesterol metabolism. Additionally, it is necessary to investigate whether ApoA1-based oncolytic virus therapy can be used to treat TNBC. METHODS In vitro experiments and mouse breast cancer models were utilized to evaluate the molecular mechanism of ApoA1 in regulating cholesterol efflux and inhibiting breast cancer progression and metastasis. The gene encoding ApoA1 was inserted into the adenovirus genome to construct a recombinant adenovirus (ADV-ApoA1). Subsequently, the efficacy of ADV-ApoA1 in inhibiting the growth and metastasis of TNBC was evaluated in several mouse models, including orthotopic breast cancer, spontaneous breast cancer, and human xenografts. In addition, a comprehensive safety assessment of Syrian hamsters and rhesus monkeys injected with oncolytic adenovirus was conducted. RESULTS This study found that dysregulation of cholesterol homeostasis is critical for the progression and metastasis of TNBC. In a mouse orthotopic model of TNBC, a high-cholesterol diet promoted lung and liver metastasis, which was associated with keratin 14 (KRT14), a protein responsible for TNBC metastasis. Furthermore, studies have shown that ApoA1, a cholesterol reverse transporter, inhibits TNBC metastasis by regulating the cholesterol/IKBKB/FOXO3a/KRT14 axis. Moreover, ADV-ApoA1 was found to promote cholesterol efflux, inhibit tumor growth, reduce lung metastasis, and prolonged the survival of mice with TNBC. Importantly, high doses of ADV-ApoA1 administered intravenously and subcutaneously were well tolerated in rhesus monkeys and Syrian hamsters. CONCLUSIONS This study provides a promising oncolytic virus treatment strategy for TNBC based on targeting dysregulated cholesterol metabolism. It also establishes a basis for subsequent clinical trials of ADV-ApoA1 in the treatment of TNBC.
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Affiliation(s)
- Jie Dong
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 22 Hankou Road, Nanjing, Jiangsu, 210093, P.R. China
| | - Lingkai Kong
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 22 Hankou Road, Nanjing, Jiangsu, 210093, P.R. China
| | - Shiqun Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 22 Hankou Road, Nanjing, Jiangsu, 210093, P.R. China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Mao Xia
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, P.R. China
| | - Yenan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 22 Hankou Road, Nanjing, Jiangsu, 210093, P.R. China
| | - Jingyi Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 22 Hankou Road, Nanjing, Jiangsu, 210093, P.R. China
| | - Fuming Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 22 Hankou Road, Nanjing, Jiangsu, 210093, P.R. China.
| | - Shuguang Zuo
- Liuzhou Key Laboratory of Molecular Diagnosis, Guangxi Key Laboratory of Molecular Diagnosis and Application, Affiliated Liutie Central Hospital of Guangxi Medical University, Liuzhou, Guangxi, China.
| | - Jiwu Wei
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 22 Hankou Road, Nanjing, Jiangsu, 210093, P.R. China.
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22
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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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23
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Wessels HH, Stirn A, Méndez-Mancilla A, Kim EJ, Hart SK, Knowles DA, Sanjana NE. Prediction of on-target and off-target activity of CRISPR-Cas13d guide RNAs using deep learning. Nat Biotechnol 2024; 42:628-637. [PMID: 37400521 DOI: 10.1038/s41587-023-01830-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/16/2023] [Indexed: 07/05/2023]
Abstract
Transcriptome engineering applications in living cells with RNA-targeting CRISPR effectors depend on accurate prediction of on-target activity and off-target avoidance. Here we design and test ~200,000 RfxCas13d guide RNAs targeting essential genes in human cells with systematically designed mismatches and insertions and deletions (indels). We find that mismatches and indels have a position- and context-dependent impact on Cas13d activity, and mismatches that result in G-U wobble pairings are better tolerated than other single-base mismatches. Using this large-scale dataset, we train a convolutional neural network that we term targeted inhibition of gene expression via gRNA design (TIGER) to predict efficacy from guide sequence and context. TIGER outperforms the existing models at predicting on-target and off-target activity on our dataset and published datasets. We show that TIGER scoring combined with specific mismatches yields the first general framework to modulate transcript expression, enabling the use of RNA-targeting CRISPRs to precisely control gene dosage.
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Affiliation(s)
- Hans-Hermann Wessels
- New York Genome Center, New York City, NY, USA
- Department of Biology, New York University, New York City, NY, USA
| | - Andrew Stirn
- New York Genome Center, New York City, NY, USA
- Department of Computer Science, Columbia University, New York City, NY, USA
| | - Alejandro Méndez-Mancilla
- New York Genome Center, New York City, NY, USA
- Department of Biology, New York University, New York City, NY, USA
| | - Eric J Kim
- Department of Computer Science, Columbia University, New York City, NY, USA
| | - Sydney K Hart
- New York Genome Center, New York City, NY, USA
- Department of Biology, New York University, New York City, NY, USA
| | - David A Knowles
- New York Genome Center, New York City, NY, USA.
- Department of Computer Science, Columbia University, New York City, NY, USA.
- Data Science Institute, Columbia University, New York City, NY, USA.
- Department of Systems Biology, Columbia University, New York City, NY, USA.
| | - Neville E Sanjana
- New York Genome Center, New York City, NY, USA.
- Department of Biology, New York University, New York City, NY, USA.
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24
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Arriaga JM, Ronaldson-Bouchard K, Picech F, Nunes de Almeida F, Afari S, Chhouri H, Vunjak-Novakovic G, Abate-Shen C. In vivo genome-wide CRISPR screening identifies CITED2 as a driver of prostate cancer bone metastasis. Oncogene 2024; 43:1303-1315. [PMID: 38454137 PMCID: PMC11101692 DOI: 10.1038/s41388-024-02995-5] [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: 08/07/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024]
Abstract
Most cancer deaths are due to metastatic dissemination to distant organs. Bone is the most frequently affected organ in metastatic prostate cancer and a major cause of prostate cancer deaths. Yet, our partial understanding of the molecular factors that drive bone metastasis has been a limiting factor for developing preventative and therapeutic strategies to improve patient survival and well-being. Although recent studies have uncovered molecular alterations that occur in prostate cancer metastasis, their functional relevance for bone metastasis is not well understood. Using genome-wide CRISPR activation and inhibition screens we have identified multiple drivers and suppressors of prostate cancer metastasis. Through functional validation, including an innovative organ-on-a-chip invasion platform for studying bone tropism, our study identifies the transcriptional modulator CITED2 as a novel driver of prostate cancer bone metastasis and uncovers multiple new potential molecular targets for bone metastatic disease.
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Affiliation(s)
- Juan M Arriaga
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Oncological Sciences, Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | | | - Florencia Picech
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Francisca Nunes de Almeida
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Stephanie Afari
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Houssein Chhouri
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, 10032, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Cory Abate-Shen
- Departments of Molecular Pharmacology and Therapeutics, Urology, Medicine, Pathology & Cell Biology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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25
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Hoque ME, Kabir ML, Shiekh S, Balci H, Basu S. Stalling of Transcription by Putative G-quadruplex Sequences and CRISPR-dCas9. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585391. [PMID: 38559215 PMCID: PMC10979993 DOI: 10.1101/2024.03.17.585391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Putative G-quadruplex forming sequences (PQS) have been identified in promoter sequences of prominent genes that are implicated among others in cancer and neurological disorders. We explored mechanistic aspects of CRISPR-dCas9-mediated gene expression regulation, which is transient and sequence specific unlike alternative approaches that lack such specificity or create permanent mutations, using the PQS in tyrosine hydroxylase (TH) and c-Myc promoters as model systems. We performed in vitro ensemble and single molecule investigations to study whether G-quadruplex (GQ) structures or dCas9 impede T7 RNA polymerase (RNAP) elongation process and whether orientation of these factors is significant. Our results demonstrate that dCas9 is more likely to block RNAP progression when the non-template strand is targeted. While the GQ in TH promoter was effectively destabilized when the dCas9 target site partially overlapped with the PQS, the c-Myc GQ remained folded and stalled RNAP elongation. We also determined that a minimum separation between the transcription start site and the dCas9 target site is required for effective stalling of RNAP by dCas9. Our study provides significant insights about the factors that impact dCas9-mediated transcription regulation when dCas9 targets the vicinity of sequences that form secondary structures and provides practical guidelines for designing guide RNA sequences.
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Affiliation(s)
- Mohammed Enamul Hoque
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Mohammad Lutful Kabir
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
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26
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Spisak S, Chen D, Likasitwatanakul P, Doan P, Li Z, Bala P, Vizkeleti L, Tisza V, De Silva P, Giannakis M, Wolpin B, Qi J, Sethi NS. Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system. Nat Commun 2024; 15:2230. [PMID: 38472198 PMCID: PMC10933491 DOI: 10.1038/s41467-024-46285-w] [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: 02/02/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators of these key cellular programs, we engineer a dual endogenous reporter system by genome-editing the SOX9 and KRT20 loci of human CRC cell lines to express fluorescent reporters, broadcasting aberrant stem cell-like and differentiation activity, respectively. By applying a CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs to this platform, we identify factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominate SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency and required for in vivo growth of human CRC models. These studies highlight the utility of biologically designed endogenous reporter platforms to uncover regulators with therapeutic potential.
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Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094, Budapest, Hungary
| | - Viktoria Tisza
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pushpamali De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA.
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA.
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27
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Lee HG, Rone JM, Li Z, Akl CF, Shin SW, Lee JH, Flausino LE, Pernin F, Chao CC, Kleemann KL, Srun L, Illouz T, Giovannoni F, Charabati M, Sanmarco LM, Kenison JE, Piester G, Zandee SEJ, Antel JP, Rothhammer V, Wheeler MA, Prat A, Clark IC, Quintana FJ. Disease-associated astrocyte epigenetic memory promotes CNS pathology. Nature 2024; 627:865-872. [PMID: 38509377 PMCID: PMC11016191 DOI: 10.1038/s41586-024-07187-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024]
Abstract
Disease-associated astrocyte subsets contribute to the pathology of neurologic diseases, including multiple sclerosis and experimental autoimmune encephalomyelitis1-8 (EAE), an experimental model for multiple sclerosis. However, little is known about the stability of these astrocyte subsets and their ability to integrate past stimulation events. Here we report the identification of an epigenetically controlled memory astrocyte subset that exhibits exacerbated pro-inflammatory responses upon rechallenge. Specifically, using a combination of single-cell RNA sequencing, assay for transposase-accessible chromatin with sequencing, chromatin immunoprecipitation with sequencing, focused interrogation of cells by nucleic acid detection and sequencing, and cell-specific in vivo CRISPR-Cas9-based genetic perturbation studies we established that astrocyte memory is controlled by the metabolic enzyme ATP-citrate lyase (ACLY), which produces acetyl coenzyme A (acetyl-CoA) that is used by histone acetyltransferase p300 to control chromatin accessibility. The number of ACLY+p300+ memory astrocytes is increased in acute and chronic EAE models, and their genetic inactivation ameliorated EAE. We also detected the pro-inflammatory memory phenotype in human astrocytes in vitro; single-cell RNA sequencing and immunohistochemistry studies detected increased numbers of ACLY+p300+ astrocytes in chronic multiple sclerosis lesions. In summary, these studies define an epigenetically controlled memory astrocyte subset that promotes CNS pathology in EAE and, potentially, multiple sclerosis. These findings may guide novel therapeutic approaches for multiple sclerosis and other neurologic diseases.
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Affiliation(s)
- Hong-Gyun Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph M Rone
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Camilo Faust Akl
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seung Won Shin
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences, QB3, University of California Berkeley, Berkeley, CA, USA
| | - Joon-Hyuk Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lucas E Flausino
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Florian Pernin
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Chun-Cheih Chao
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Lena Srun
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tomer Illouz
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Federico Giovannoni
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc Charabati
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jessica E Kenison
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gavin Piester
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Stephanie E J Zandee
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Veit Rothhammer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, University Hospital, Friedrich-Alexander University Erlangen Nuremberg, Erlangen, Germany
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandre Prat
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Iain C Clark
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences, QB3, University of California Berkeley, Berkeley, CA, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Gene Lay Institute of Immunology and Inflammation, Boston, MA, USA.
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28
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Liang J, Bi G, Huang Y, Zhao G, Sui Q, Zhang H, Bian Y, Yin J, Wang Q, Chen Z, Zhan C. MAFF confers vulnerability to cisplatin-based and ionizing radiation treatments by modulating ferroptosis and cell cycle progression in lung adenocarcinoma. Drug Resist Updat 2024; 73:101057. [PMID: 38266355 DOI: 10.1016/j.drup.2024.101057] [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: 06/04/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
AIMS Lung cancer is the leading cause of cancer mortality and lung adenocarcinoma (LUAD) accounts for more than half of all lung cancer cases. Tumor elimination is mostly hindered by drug resistance and the mechanisms remain to be explored in LUAD. METHODS CRISPR screens in cell and murine models and single-cell RNA sequencing were conducted, which identified MAF bZIP transcription factor F (MAFF) as a critical factor regulating tumor growth and treatment resistance in LUAD. RNA and ChIP sequencing analyses were performed for transcriptional target expression and specific binding sites of MAFF. Functions of MAFF in inhibiting tumor growth and promoting cisplatin or irradiation efficacy were investigated using cellular and xenograft models. RESULTS Patients with lung adenocarcinoma and reduced MAFF expression had worse clinical outcomes. MAFF inhibited tumor cell proliferation by regulating the expression of SLC7A11, CDK6, and CDKN2C, promoting ferroptosis and preventing cell cycle progression from G1 to S. MAFF also conferred tumor cells vulnerable to cisplatin-based or ionizing radiation treatments. MAFF reduction was a final event in the acquisition of cisplatin resistance of LUAD cells. The intracellular cAMP/PKA/CREB1 pathway upregulated MAFF in response to cisplatin-based or ionizing radiation treatments. CONCLUSIONS MAFF suppresses tumor growth, and pharmacological agonists targeting MAFF may improve cisplatin or irradiation therapies for lung adenocarcinoma patients.
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Affiliation(s)
- Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Guangyin Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Qihai Sui
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Huan Zhang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Yunyi Bian
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Jiacheng Yin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China.
| | - Zhencong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China.
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China.
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29
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Gliech CR, Yeow ZY, Tapias-Gomez D, Yang Y, Huang Z, Tijhuis AE, Spierings DC, Foijer F, Chung G, Tamayo N, Bahrami-Nejad Z, Collins P, Nguyen TT, Plata Stapper A, Hughes PE, Payton M, Holland AJ. Weakened APC/C activity at mitotic exit drives cancer vulnerability to KIF18A inhibition. EMBO J 2024; 43:666-694. [PMID: 38279026 PMCID: PMC10907621 DOI: 10.1038/s44318-024-00031-6] [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: 05/01/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/28/2024] Open
Abstract
The efficacy of current antimitotic cancer drugs is limited by toxicity in highly proliferative healthy tissues. A cancer-specific dependency on the microtubule motor protein KIF18A therefore makes it an attractive therapeutic target. Not all cancers require KIF18A, however, and the determinants underlying this distinction remain unclear. Here, we show that KIF18A inhibition drives a modest and widespread increase in spindle assembly checkpoint (SAC) signaling from kinetochores which can result in lethal mitotic delays. Whether cells arrest in mitosis depends on the robustness of the metaphase-to-anaphase transition, and cells predisposed with weak basal anaphase-promoting complex/cyclosome (APC/C) activity and/or persistent SAC signaling through metaphase are uniquely sensitive to KIF18A inhibition. KIF18A-dependent cancer cells exhibit hallmarks of this SAC:APC/C imbalance, including a long metaphase-to-anaphase transition, and slow mitosis overall. Together, our data reveal vulnerabilities in the cell division apparatus of cancer cells that can be exploited for therapeutic benefit.
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Affiliation(s)
- Colin R Gliech
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Zhong Y Yeow
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Daniel Tapias-Gomez
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yuchen Yang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Zhaoyu Huang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Andréa E Tijhuis
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, AV, 9713, The Netherlands
| | - Diana Cj Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, AV, 9713, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, AV, 9713, The Netherlands
| | - Grace Chung
- Oncology Research, Amgen Research, Thousand Oaks, CA, 91320, USA
| | - Nuria Tamayo
- Medicinal Chemistry, Amgen Research, Thousand Oaks, CA, 91320, USA
| | | | - Patrick Collins
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, 94084, USA
| | - Thong T Nguyen
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, 94084, USA
| | - Andres Plata Stapper
- Center for Research Acceleration by Digital Innovation, Amgen Research, South San Francisco, CA, 94084, USA
| | - Paul E Hughes
- Oncology Research, Amgen Research, Thousand Oaks, CA, 91320, USA
| | - Marc Payton
- Oncology Research, Amgen Research, Thousand Oaks, CA, 91320, USA
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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30
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Rogava M, Aprati TJ, Chi WY, Melms JC, Hug C, Davis SH, Earlie EM, Chung C, Deshmukh SK, Wu S, Sledge G, Tang S, Ho P, Amin AD, Caprio L, Gurjao C, Tagore S, Ngo B, Lee MJ, Zanetti G, Wang Y, Chen S, Ge W, Melo LMN, Allies G, Rösler J, Gibney GT, Schmitz OJ, Sykes M, Creusot RJ, Tüting T, Schadendorf D, Röcken M, Eigentler TK, Molotkov A, Mintz A, Bakhoum SF, Beyaz S, Cantley LC, Sorger PK, Meckelmann SW, Tasdogan A, Liu D, Laughney AM, Izar B. Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. NATURE CANCER 2024; 5:433-447. [PMID: 38286827 PMCID: PMC11175596 DOI: 10.1038/s43018-023-00704-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/08/2023] [Indexed: 01/31/2024]
Abstract
Liver metastasis (LM) confers poor survival and therapy resistance across cancer types, but the mechanisms of liver-metastatic organotropism remain unknown. Here, through in vivo CRISPR-Cas9 screens, we found that Pip4k2c loss conferred LM but had no impact on lung metastasis or primary tumor growth. Pip4k2c-deficient cells were hypersensitized to insulin-mediated PI3K/AKT signaling and exploited the insulin-rich liver milieu for organ-specific metastasis. We observed concordant changes in PIP4K2C expression and distinct metabolic changes in 3,511 patient melanomas, including primary tumors, LMs and lung metastases. We found that systemic PI3K inhibition exacerbated LM burden in mice injected with Pip4k2c-deficient cancer cells through host-mediated increase in hepatic insulin levels; however, this circuit could be broken by concurrent administration of an SGLT2 inhibitor or feeding of a ketogenic diet. Thus, this work demonstrates a rare example of metastatic organotropism through co-optation of physiological metabolic cues and proposes therapeutic avenues to counteract these mechanisms.
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Affiliation(s)
- Meri Rogava
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Tyler J Aprati
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wei-Yu Chi
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Johannes C Melms
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Clemens Hug
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Stephanie H Davis
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ethan M Earlie
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charlie Chung
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Sharon Wu
- Caris Life Sciences, Phoenix, AZ, USA
| | | | - Stephen Tang
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Patricia Ho
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Amit Dipak Amin
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lindsay Caprio
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carino Gurjao
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY, USA
| | - Somnath Tagore
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY, USA
| | - Bryan Ngo
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Michael J Lee
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Giorgia Zanetti
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yiping Wang
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY, USA
| | - Sean Chen
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - William Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Luiza Martins Nascentes Melo
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - Gabriele Allies
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - Jonas Rösler
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - Goeffrey T Gibney
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Oliver J Schmitz
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Megan Sykes
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Rémi J Creusot
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Thomas Tüting
- Laboratory for Experimental Dermatology, Department of Dermatology, University of Magdeburg, Magdeburg, Germany
| | - Dirk Schadendorf
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - Martin Röcken
- Department of Dermatology, University Hospital Tuebingen, Tuebingen, Germany
| | - Thomas K Eigentler
- Department of Dermatology, Venerology and Allergology, Charité University Hospital, Berlin, Germany
| | - Andrei Molotkov
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Peter K Sorger
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sven W Meckelmann
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Alpaslan Tasdogan
- Department for Dermatology, Venerology and Allergology, University Hospital Essen, NCT West, Campus Essen, German Cancer Consortium, Partner Site Essen & University Alliance Ruhr, Research Center One Health, Essen, Germany
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashley M Laughney
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin Izar
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos School of Physicians and Surgeons, New York, NY, USA.
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA.
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY, USA.
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31
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Liu X, Shi L, Zhao Z, Shu J, Min W. VIBRANT: spectral profiling for single-cell drug responses. Nat Methods 2024; 21:501-511. [PMID: 38374266 PMCID: PMC11214684 DOI: 10.1038/s41592-024-02185-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
High-content cell profiling has proven invaluable for single-cell phenotyping in response to chemical perturbations. However, methods with improved throughput, information content and affordability are still needed. We present a new high-content spectral profiling method named vibrational painting (VIBRANT), integrating mid-infrared vibrational imaging, multiplexed vibrational probes and an optimized data analysis pipeline for measuring single-cell drug responses. Three infrared-active vibrational probes were designed to measure distinct essential metabolic activities in human cancer cells. More than 20,000 single-cell drug responses were collected, corresponding to 23 drug treatments. The resulting spectral profile is highly sensitive to phenotypic changes under drug perturbation. Using this property, we built a machine learning classifier to accurately predict drug mechanism of action at single-cell level with minimal batch effects. We further designed an algorithm to discover drug candidates with new mechanisms of action and evaluate drug combinations. Overall, VIBRANT has demonstrated great potential across multiple areas of phenotypic screening.
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Affiliation(s)
- Xinwen Liu
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Lixue Shi
- Department of Chemistry, Columbia University, New York, NY, USA
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhilun Zhao
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Jian Shu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA.
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
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32
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Yang A, Chidiac R, Russo E, Steenland H, Pauli Q, Bonin R, Blazer LL, Adams JJ, Sidhu SS, Goeva A, Salahpour A, Angers S. Exploiting spatiotemporal regulation of FZD5 during neural patterning for efficient ventral midbrain specification. Development 2024; 151:dev202545. [PMID: 38358799 PMCID: PMC10946437 DOI: 10.1242/dev.202545] [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: 11/14/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
The Wnt/β-catenin signaling governs anterior-posterior neural patterning during development. Current human pluripotent stem cell (hPSC) differentiation protocols use a GSK3 inhibitor to activate Wnt signaling to promote posterior neural fate specification. However, GSK3 is a pleiotropic kinase involved in multiple signaling pathways and, as GSK3 inhibition occurs downstream in the signaling cascade, it bypasses potential opportunities for achieving specificity or regulation at the receptor level. Additionally, the specific roles of individual FZD receptors in anterior-posterior patterning are poorly understood. Here, we have characterized the cell surface expression of FZD receptors in neural progenitor cells with different regional identity. Our data reveal unique upregulation of FZD5 expression in anterior neural progenitors, and this expression is downregulated as cells adopt a posterior fate. This spatial regulation of FZD expression constitutes a previously unreported regulatory mechanism that adjusts the levels of β-catenin signaling along the anterior-posterior axis and possibly contributes to midbrain-hindbrain boundary formation. Stimulation of Wnt/β-catenin signaling in hPSCs, using a tetravalent antibody that selectively triggers FZD5 and LRP6 clustering, leads to midbrain progenitor differentiation and gives rise to functional dopaminergic neurons in vitro and in vivo.
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Affiliation(s)
- Andy Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Rony Chidiac
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Emma Russo
- Department of Pharmacology and Toxicology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hendrik Steenland
- Department of Pharmacology and Toxicology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- NeuroTek Innovative Technology, Toronto, ON M6C 3A2, Canada
| | - Quinn Pauli
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Robert Bonin
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Levi L. Blazer
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jarrett J. Adams
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aleksandrina Goeva
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Ali Salahpour
- Department of Pharmacology and Toxicology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephane Angers
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
- Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
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33
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Han HV, Efem R, Rosati B, Lu K, Maimouni S, Jiang YP, Montoya V, Van Der Velden A, Zong WX, Lin RZ. Propionyl-CoA carboxylase subunit B regulates anti-tumor T cells in a pancreatic cancer mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.24.550301. [PMID: 37546948 PMCID: PMC10402106 DOI: 10.1101/2023.07.24.550301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Most human pancreatic ductal adenocarcinoma (PDAC) are not infiltrated with cytotoxic T cells and are highly resistant to immunotherapy. Over 90% of PDAC have oncogenic KRAS mutations, and phosphoinositide 3-kinases (PI3Ks) are direct effectors of KRAS. Our previous study demonstrated that ablation of Pik3ca in KPC (KrasG12D; Trp53R172H; Pdx1-Cre) pancreatic cancer cells induced host T cells to infiltrate and completely eliminate the tumors in a syngeneic orthotopic implantation mouse model. Now, we show that implantation of Pik3ca-/- KPC (named αKO) cancer cells induces clonal expansion of cytotoxic T cells infiltrating the pancreatic tumors. To identify potential molecules that can regulate the activity of these anti-tumor T cells, we conducted an in vivo genome-wide gene-deletion screen using αKO cells implanted in the mouse pancreas. The result shows that deletion of propionyl-CoA carboxylase subunit B gene (Pccb) in αKO cells (named p-αKO) leads to immune evasion, tumor progression and death of host mice. Surprisingly, p-αKO tumors are still infiltrated with clonally expanded CD8+ T cells but they are inactive against tumor cells. However, blockade of PD-L1/PD1 interaction reactivated these clonally expanded T cells infiltrating p-αKO tumors, leading to slower tumor progression and improve survival of host mice. These results indicate that Pccb can modulate the activity of cytotoxic T cells infiltrating some pancreatic cancers and this understanding may lead to improvement in immunotherapy for this difficult-to-treat cancer.
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34
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Geller E, Noble MA, Morales M, Gockley J, Emera D, Uebbing S, Cotney JL, Noonan JP. Massively parallel disruption of enhancers active in human neural stem cells. Cell Rep 2024; 43:113693. [PMID: 38271204 PMCID: PMC11078116 DOI: 10.1016/j.celrep.2024.113693] [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: 02/03/2023] [Revised: 11/02/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Changes in gene regulation have been linked to the expansion of the human cerebral cortex and to neurodevelopmental disorders, potentially by altering neural progenitor proliferation. However, the effects of genetic variation within regulatory elements on neural progenitors remain obscure. We use sgRNA-Cas9 screens in human neural stem cells (hNSCs) to disrupt 10,674 genes and 26,385 conserved regions in 2,227 enhancers active in the developing human cortex and determine effects on proliferation. Genes with proliferation phenotypes are associated with neurodevelopmental disorders and show biased expression in specific fetal human brain neural progenitor populations. Although enhancer disruptions overall have weaker effects than gene disruptions, we identify enhancer disruptions that severely alter hNSC self-renewal. Disruptions in human accelerated regions, implicated in human brain evolution, also alter proliferation. Integrating proliferation phenotypes with chromatin interactions reveals regulatory relationships between enhancers and their target genes contributing to neurogenesis and potentially to human cortical evolution.
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Affiliation(s)
- Evan Geller
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mark A Noble
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Matheo Morales
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jake Gockley
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Deena Emera
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Justin L Cotney
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA.
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35
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Mondal P, Alyateem G, Mitchell AV, Gottesman MM. A whole-genome CRISPR screen identifies the spindle accessory checkpoint as a locus of nab-paclitaxel resistance in pancreatic cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580539. [PMID: 38410481 PMCID: PMC10896345 DOI: 10.1101/2024.02.15.580539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Pancreatic adenocarcinoma is one of the most aggressive and lethal forms of cancer. Chemotherapy is the primary treatment for pancreatic cancer, but resistance to the drugs used remains a major challenge. A genome-wide CRISPR interference and knockout screen in the PANC-1 cell line with the drug nab-paclitaxel has identified a group of spindle assembly checkpoint (SAC) genes that enhance survival in nab-paclitaxel. Knockdown of these SAC genes (BUB1B, BUB3, and TTK) attenuates paclitaxel-induced cell death. Cells treated with the small molecule inhibitors BAY 1217389 or MPI 0479605, targeting the threonine tyrosine kinase (TTK), also enhance survival in paclitaxel. Overexpression of these SAC genes does not affect sensitivity to paclitaxel. These discoveries have helped to elucidate the mechanisms behind paclitaxel cytotoxicity. The outcomes of this investigation may pave the way for a deeper comprehension of the diverse responses of pancreatic cancer to therapies including paclitaxel. Additionally, they could facilitate the formulation of novel treatment approaches for pancreatic cancer.
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Affiliation(s)
- Priya Mondal
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - George Alyateem
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Allison V. Mitchell
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Michael M. Gottesman
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
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36
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Gabel AM, Belleville AE, Thomas JD, McKellar SA, Nicholas TR, Banjo T, Crosse EI, Bradley RK. Multiplexed screening reveals how cancer-specific alternative polyadenylation shapes tumor growth in vivo. Nat Commun 2024; 15:959. [PMID: 38302465 PMCID: PMC10834521 DOI: 10.1038/s41467-024-44931-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
Alternative polyadenylation (APA) is strikingly dysregulated in many cancers. Although global APA dysregulation is frequently associated with poor prognosis, the importance of most individual APA events is controversial simply because few have been functionally studied. Here, we address this gap by developing a CRISPR-Cas9-based screen to manipulate endogenous polyadenylation and systematically quantify how APA events contribute to tumor growth in vivo. Our screen reveals individual APA events that control mouse melanoma growth in an immunocompetent host, with concordant associations in clinical human cancer. For example, forced Atg7 3' UTR lengthening in mouse melanoma suppresses ATG7 protein levels, slows tumor growth, and improves host survival; similarly, in clinical human melanoma, a long ATG7 3' UTR is associated with significantly prolonged patient survival. Overall, our study provides an easily adaptable means to functionally dissect APA in physiological systems and directly quantifies the contributions of recurrent APA events to tumorigenic phenotypes.
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Affiliation(s)
- Austin M Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Andrea E Belleville
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Siegen A McKellar
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Taylor R Nicholas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Toshihiro Banjo
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Edie I Crosse
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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37
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Yin HZ, Zhang MC, Wu H. Clinical and Immunological Significance of ANKRD52 in Pan-Cancer. Biochem Genet 2024:10.1007/s10528-023-10645-w. [PMID: 38296907 DOI: 10.1007/s10528-023-10645-w] [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: 02/09/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024]
Abstract
Ankyrin repeat domain 52 (ANKRD52) is a regulatory component of the protein phosphatase 6 (PP6) holoenzyme. Evidence has emerged to suggest involvement of ANKRD52 in tumor metastases and cancer cell escape from T cell-mediated elimination and immunotherapy but there has been no research across different cancer types. The current study explored the biological functions of ANKRD52 by combining data from many databases. The aim was to expose new diagnostic or treatment biomarkers for malignant tumors. The roles of ANKRD52 with respect to immunotherapy in 33 human cancer types were analyzed by combining data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), UCSC Xena, the Tumor Immune Estimation Resource (TIMER), TISIDB and Cellminer. Bioinformatics methods were used to analyze the association between ANKRD52 expression and prognosis, immunological indicators (immune cell infiltration, ESTIMATE scores and tumor microenvironment (TME) signatures), tumor mutational burden (TMB), microsatellite instability (MSI) and drug sensitivity. ANKRD52 expression was generally higher in 24 tumor tissues than in normal tissues and was associated with poor prognosis, especially in kidney chromophobe (KICH). Lower expression was observed in advanced cancer. ANKRD52 expression was strongly linked to major immunological indicators, such as immune cell infiltration, ESTIMATE scores, TME signatures, as well as expression of immune and tumor-related genes. Expression was also associated with indicators of immunotherapy efficacy and outcome, such as TMB in 7 cancer types and MSI in 12. In addition, ANKRD52 expression was linked to sensitivity to a number of anticancer drugs. ANKRD52 had a distinct immune function in breast invasive carcinoma (BRCA) that correlated negatively with most immune indicators. Expression was enriched in proliferation-, differentiation- and metabolism-related pathways and linked to other immune cells and TME signatures. A nomogram to predict 3- or 5-year overall survival (OS) of patients with BRCA was constructed. ANKRD52 may have utility as an oncological and immunological biomarker. New insights into oncogenesis are presented and the development of ANKRD52-targeting to increase the therapeutic efficacy of immunotherapy combined with chemotherapy explored.
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Affiliation(s)
- Hui-Zi Yin
- Department of Breast Radiotherapy, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin, 150081, China
| | - Meng-Chun Zhang
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin, 150081, China
| | - Hao Wu
- Key Laboratory of Tumor Biotherapy, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China.
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin, 150081, China.
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38
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Wang C, Chen L, Fu D, Liu W, Puri A, Kellis M, Yang J. Antigen presenting cells in cancer immunity and mediation of immune checkpoint blockade. Clin Exp Metastasis 2024:10.1007/s10585-023-10257-z. [PMID: 38261139 DOI: 10.1007/s10585-023-10257-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024]
Abstract
Antigen-presenting cells (APCs) are pivotal mediators of immune responses. Their role has increasingly been spotlighted in the realm of cancer immunology, particularly as our understanding of immunotherapy continues to evolve and improve. There is growing evidence that these cells play a non-trivial role in cancer immunity and have roles dependent on surface markers, growth factors, transcription factors, and their surrounding environment. The main dendritic cell (DC) subsets found in cancer are conventional DCs (cDC1 and cDC2), monocyte-derived DCs (moDC), plasmacytoid DCs (pDC), and mature and regulatory DCs (mregDC). The notable subsets of monocytes and macrophages include classical and non-classical monocytes, macrophages, which demonstrate a continuum from a pro-inflammatory (M1) phenotype to an anti-inflammatory (M2) phenotype, and tumor-associated macrophages (TAMs). Despite their classification in the same cell type, each subset may take on an immune-activating or immunosuppressive phenotype, shaped by factors in the tumor microenvironment (TME). In this review, we introduce the role of DCs, monocytes, and macrophages and recent studies investigating them in the cancer immunity context. Additionally, we review how certain characteristics such as abundance, surface markers, and indirect or direct signaling pathways of DCs and macrophages may influence tumor response to immune checkpoint blockade (ICB) therapy. We also highlight existing knowledge gaps regarding the precise contributions of different myeloid cell subsets in influencing the response to ICB therapy. These findings provide a summary of our current understanding of myeloid cells in mediating cancer immunity and ICB and offer insight into alternative or combination therapies that may enhance the success of ICB in cancers.
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Affiliation(s)
- Cassia Wang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lee Chen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Doris Fu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendi Liu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Anusha Puri
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jiekun Yang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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39
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Spisak S, Chen D, Likasitwatanakul P, Doan P, Li Z, Bala P, Vizkeleti L, Tisza V, De Silva P, Giannakis M, Wolpin B, Qi J, Sethi NS. Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545895. [PMID: 38293113 PMCID: PMC10827082 DOI: 10.1101/2023.06.21.545895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation, respectively, and then performed pooled genetic perturbation screens. Constructing a dual reporter system that simultaneously monitored aberrant stem cell-like and differentiation activity in the same CRC cell line improved our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency in CRC and required for in vivo growth of human CRC models. These studies highlight the utility of a biologically designed endogenous reporter system to uncover novel therapeutic targets for drug development.
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Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Bangkok, Thailand
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary
| | - Viktoria Tisza
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pushpamail De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
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40
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Lee HG, Rone JM, Li Z, Akl CF, Shin SW, Lee JH, Flausino LE, Pernin F, Chao CC, Kleemann KL, Srun L, Illouz T, Giovannoni F, Charabati M, Sanmarco LM, Kenison JE, Piester G, Zandee SEJ, Antel J, Rothhammer V, Wheeler MA, Prat A, Clark IC, Quintana FJ. Disease-associated astrocyte epigenetic memory promotes CNS pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574196. [PMID: 38260616 PMCID: PMC10802318 DOI: 10.1101/2024.01.04.574196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Astrocytes play important roles in the central nervous system (CNS) physiology and pathology. Indeed, astrocyte subsets defined by specific transcriptional activation states contribute to the pathology of neurologic diseases, including multiple sclerosis (MS) and its pre-clinical model experimental autoimmune encephalomyelitis (EAE) 1-8 . However, little is known about the stability of these disease-associated astrocyte subsets, their regulation, and whether they integrate past stimulation events to respond to subsequent challenges. Here, we describe the identification of an epigenetically controlled memory astrocyte subset which exhibits exacerbated pro-inflammatory responses upon re-challenge. Specifically, using a combination of single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin with sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing (ChIP-seq), focused interrogation of cells by nucleic acid detection and sequencing (FIND-seq), and cell-specific in vivo CRISPR/Cas9-based genetic perturbation studies we established that astrocyte memory is controlled by the metabolic enzyme ATP citrate lyase (ACLY), which produces acetyl coenzyme A (acetyl-CoA) used by the histone acetyltransferase p300 to control chromatin accessibility. ACLY + p300 + memory astrocytes are increased in acute and chronic EAE models; the genetic targeting of ACLY + p300 + astrocytes using CRISPR/Cas9 ameliorated EAE. We also detected responses consistent with a pro-inflammatory memory phenotype in human astrocytes in vitro ; scRNA-seq and immunohistochemistry studies detected increased ACLY + p300 + astrocytes in chronic MS lesions. In summary, these studies define an epigenetically controlled memory astrocyte subset that promotes CNS pathology in EAE and, potentially, MS. These findings may guide novel therapeutic approaches for MS and other neurologic diseases.
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Yang X, Xu H, Yang X, Wang H, Zou L, Yang Q, Qi X, Li L, Duan H, Yan X, Fu NY, Tan J, Hou Z, Jiao B. Mcam inhibits macrophage-mediated development of mammary gland through non-canonical Wnt signaling. Nat Commun 2024; 15:36. [PMID: 38167296 PMCID: PMC10761817 DOI: 10.1038/s41467-023-44338-0] [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: 12/23/2022] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
While canonical Wnt signaling is well recognized for its crucial regulatory functions in cell fate decisions, the role of non-canonical Wnt signaling in adult stem cells remains elusive and contradictory. Here, we identified Mcam, a potential member of the non-canonical Wnt signaling, as an important negative regulator of mammary gland epithelial cells (MECs) by genome-scale CRISPR-Cas9 knockout (GeCKO) library screening. Loss of Mcam increases the clonogenicity and regenerative capacity of MECs, and promotes the proliferation, differentiation, and ductal morphogenesis of mammary epithelial in knockout mice. Mechanically, Mcam knockout recruits and polarizes macrophages through the Il4-Stat6 axis, thereby promoting secretion of the non-canonical Wnt ligand Wnt5a and its binding to the non-canonical Wnt signaling receptor Ryk to induce the above phenotypes. These findings reveal Mcam roles in mammary gland development by orchestrating communications between MECs and macrophages via a Wnt5a/Ryk axis, providing evidences for non-canonical Wnt signaling in mammary development.
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Affiliation(s)
- Xing Yang
- Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, Yunnan, 650051, China
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Haibo Xu
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xu Yang
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hui Wang
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Li Zou
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Qin Yang
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xiaopeng Qi
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Li Li
- Research Center of Stem cells and Ageing, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Hongxia Duan
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100000, China
| | - Xiyun Yan
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100000, China
| | - Nai Yang Fu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Jing Tan
- Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China.
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, Yunnan, 650051, China.
| | - Zongliu Hou
- Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, 650051, China.
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, Yunnan, 650051, China.
| | - Baowei Jiao
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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42
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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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43
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Patange S, Maragh S. Fire Burn and Cauldron Bubble: What Is in Your Genome Editing Brew? Biochemistry 2023; 62:3500-3511. [PMID: 36306429 PMCID: PMC10734218 DOI: 10.1021/acs.biochem.2c00431] [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: 07/19/2022] [Revised: 09/28/2022] [Indexed: 11/28/2022]
Abstract
Genome editing is a rapidly evolving biotechnology with the potential to transform many sectors of industry such as agriculture, biomanufacturing, and medicine. This technology is enabled by an ever-growing portfolio of biomolecular reagents that span the central dogma, from DNA to RNA to protein. In this paper, we draw from our unique perspective as the National Metrology Institute of the United States to bring attention to the importance of understanding and reporting genome editing formulations accurately and promoting concepts to verify successful delivery into cells. Achieving the correct understanding may be hindered by the way units, quantities, and stoichiometries are reported in the field. We highlight the variability in how editing formulations are reported in the literature and examine how a reference molecule could be used to verify the delivery of a reagent into cells. We provide recommendations on how more accurate reporting of editing formulations and more careful verification of the steps in an editing experiment can help set baseline expectations of reagent performance, toward the aim of enabling genome editing studies to be more reproducible. We conclude with a future outlook on technologies that can further our control and enable our understanding of genome editing outcomes at the single-cell level.
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Affiliation(s)
- Simona Patange
- Biosystems and Biomaterials
Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Samantha Maragh
- Biosystems and Biomaterials
Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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44
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Lu C, Garipler G, Dai C, Roush T, Salome-Correa J, Martin A, Liscovitch-Brauer N, Mazzoni EO, Sanjana NE. Essential transcription factors for induced neuron differentiation. Nat Commun 2023; 14:8362. [PMID: 38102126 PMCID: PMC10724217 DOI: 10.1038/s41467-023-43602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
Neurogenins are proneural transcription factors required to specify neuronal identity. Their overexpression in human pluripotent stem cells rapidly produces cortical-like neurons with spiking activity and, because of this, they have been widely adopted for human neuron disease models. However, we do not fully understand the key downstream regulatory effectors responsible for driving neural differentiation. Here, using inducible expression of NEUROG1 and NEUROG2, we identify transcription factors (TFs) required for directed neuronal differentiation by combining expression and chromatin accessibility analyses with a pooled in vitro CRISPR-Cas9 screen targeting all ~1900 TFs in the human genome. The loss of one of these essential TFs (ZBTB18) yields few MAP2-positive neurons. Differentiated ZBTB18-null cells have radically altered gene expression, leading to cytoskeletal defects and stunted neurites and spines. In addition to identifying key downstream TFs for neuronal differentiation, our work develops an integrative multi-omics and TFome-wide perturbation platform to rapidly characterize essential TFs for the differentiation of any human cell type.
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Affiliation(s)
- Congyi Lu
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Görkem Garipler
- Department of Biology, New York University, New York, NY, USA
| | - Chao Dai
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Timothy Roush
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Jose Salome-Correa
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Alex Martin
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Noa Liscovitch-Brauer
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY, USA.
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY, USA.
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA.
- Department of Biology, New York University, New York, NY, USA.
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Binan L, Danquah S, Valakh V, Simonton B, Bezney J, Nehme R, Cleary B, Farhi SL. Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569494. [PMID: 38076932 PMCID: PMC10705493 DOI: 10.1101/2023.11.30.569494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but have not yet leveraged the power of highly-plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present Perturb-FISH, which bridges these approaches by combining imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs. We show that Perturb-FISH recovers intracellular effects that are consistent with Perturb-seq results in a screen of lipopolysaccharide response in cultured monocytes, and uncover new intercellular and density-dependent regulation of the innate immune response. We further pair Perturb-FISH with a functional readout in a screen of autism spectrum disorder risk genes, showing common calcium activity phenotypes in induced pluripotent stem cell derived astrocytes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a generally applicable method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.
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Affiliation(s)
- Loϊc Binan
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Serwah Danquah
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vera Valakh
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brooke Simonton
- Present address: The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Jon Bezney
- Present address: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Ralda Nehme
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian Cleary
- Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Program in Bioinformatics, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
| | - Samouil L Farhi
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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46
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Lee TW, Hunter FW, Tsai P, Print CG, Wilson WR, Jamieson SMF. Clonal dynamics limits detection of selection in tumour xenograft CRISPR/Cas9 screens. Cancer Gene Ther 2023; 30:1610-1623. [PMID: 37684549 PMCID: PMC10721547 DOI: 10.1038/s41417-023-00664-5] [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: 05/31/2023] [Revised: 08/08/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Transplantable in vivo CRISPR/Cas9 knockout screens, in which cells are edited in vitro and inoculated into mice to form tumours, allow evaluation of gene function in a cancer model that incorporates the multicellular interactions of the tumour microenvironment. To improve our understanding of the key parameters for success with this method, we investigated the choice of cell line, mouse host, tumour harvesting timepoint and guide RNA (gRNA) library size. We found that high gRNA (80-95%) representation was maintained in a HCT116 subline transduced with the GeCKOv2 whole-genome gRNA library and transplanted into NSG mice when tumours were harvested at early (14 d) but not late time points (38-43 d). The decreased representation in older tumours was accompanied by large increases in variance in gRNA read counts, with notable expansion of a small number of random clones in each sample. The variable clonal dynamics resulted in a high level of 'noise' that limited the detection of gRNA-based selection. Using simulated datasets derived from our experimental data, we show that considerable reductions in count variance would be achieved with smaller library sizes. Based on our findings, we suggest a pathway to rationally design adequately powered in vivo CRISPR screens for successful evaluation of gene function.
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Affiliation(s)
- Tet Woo Lee
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | - Francis W Hunter
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
- Oncology Therapeutic Area, Janssen Research and Development, Spring House, PA, USA
| | - Peter Tsai
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Cristin G Print
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - William R Wilson
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Stephen M F Jamieson
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand.
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47
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Du Y, Li T, Yi M. Is MG53 a potential therapeutic target for cancer? Front Endocrinol (Lausanne) 2023; 14:1295349. [PMID: 38033997 PMCID: PMC10684902 DOI: 10.3389/fendo.2023.1295349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Cancer treatment still encounters challenges, such as side effects and drug resistance. The tripartite-motif (TRIM) protein family is widely involved in regulation of the occurrence, development, and drug resistance of tumors. MG53, a member of the TRIM protein family, shows strong potential in cancer therapy, primarily due to its E3 ubiquitin ligase properties. The classic membrane repair function and anti-inflammatory capacity of MG53 may also be beneficial for cancer prevention and treatment. However, MG53 appears to be a key regulatory factor in impaired glucose metabolism and a negative regulatory mechanism in muscle regeneration that may have a negative effect on cancer treatment. Developing MG53 mutants that balance the pros and cons may be the key to solving the problem. This article aims to summarize the role and mechanism of MG53 in the occurrence, progression, and invasion of cancer, focusing on the potential impact of the biological function of MG53 on cancer therapy.
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Affiliation(s)
- Yunyu Du
- School of Sports Science, Beijing Sport University, Beijing, China
- National Institute of Sports Medicine, Beijing, China
| | - Tieying Li
- National Institute of Sports Medicine, Beijing, China
| | - Muqing Yi
- National Institute of Sports Medicine, Beijing, China
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48
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Zhou X, Renauer PA, Zhou L, Fang SY, Chen S. Applications of CRISPR technology in cellular immunotherapy. Immunol Rev 2023; 320:199-216. [PMID: 37449673 PMCID: PMC10787818 DOI: 10.1111/imr.13241] [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: 05/17/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023]
Abstract
CRISPR technology has transformed multiple fields, including cancer and immunology. CRISPR-based gene editing and screening empowers direct genomic manipulation of immune cells, opening doors to unbiased functional genetic screens. These screens aid in the discovery of novel factors that regulate and reprogram immune responses, offering novel drug targets. The engineering of immune cells using CRISPR has sparked a transformation in the cellular immunotherapy field, resulting in a multitude of ongoing clinical trials. In this review, we discuss the development and applications of CRISPR and related gene editing technologies in immune cells, focusing on functional genomics screening, gene editing-based cell therapies, as well as future directions in this rapidly advancing field.
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Affiliation(s)
- Xiaoyu Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Paul A. Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Liqun Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
| | - Shao-Yu Fang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
- Department of Immunobiology, Yale University, New Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
- Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
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49
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Tao S, Hou Y, Diao L, Hu Y, Xu W, Xie S, Xiao Z. Long noncoding RNA study: Genome-wide approaches. Genes Dis 2023; 10:2491-2510. [PMID: 37554208 PMCID: PMC10404890 DOI: 10.1016/j.gendis.2022.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/09/2022] [Accepted: 10/23/2022] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been confirmed to play a crucial role in various biological processes across several species. Though many efforts have been devoted to the expansion of the lncRNAs landscape, much about lncRNAs is still unknown due to their great complexity. The development of high-throughput technologies and the constantly improved bioinformatic methods have resulted in a rapid expansion of lncRNA research and relevant databases. In this review, we introduced genome-wide research of lncRNAs in three parts: (i) novel lncRNA identification by high-throughput sequencing and computational pipelines; (ii) functional characterization of lncRNAs by expression atlas profiling, genome-scale screening, and the research of cancer-related lncRNAs; (iii) mechanism research by large-scale experimental technologies and computational analysis. Besides, primary experimental methods and bioinformatic pipelines related to these three parts are summarized. This review aimed to provide a comprehensive and systemic overview of lncRNA genome-wide research strategies and indicate a genome-wide lncRNA research system.
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Affiliation(s)
- Shuang Tao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yarui Hou
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Liting Diao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yanxia Hu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Wanyi Xu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Shujuan Xie
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
- Institute of Vaccine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Zhendong Xiao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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50
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Zhang H, Li X, Wang Y, Liu X, Guo J, Wang Z, Zhang L, Xiong S, Dong C. Genome-Wide CRISPR/Cas9 Screening Identifies That Mitochondrial Solute Carrier SLC25A23 Attenuates Type I IFN Antiviral Immunity via Interfering with MAVS Aggregation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1406-1417. [PMID: 37695673 DOI: 10.4049/jimmunol.2300187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/24/2023] [Indexed: 09/12/2023]
Abstract
Activation of the mitochondrial antiviral signaling (MAVS) adaptor, also known as IPS-1, VISA, or Cardif, is crucial for antiviral immunity in retinoic acid-inducible gene I (RIG-I)-like receptor signaling. Upon interacting with RIG-I, MAVS undergoes K63-linked polyubiquitination by the E3 ligase Trim31, and subsequently aggregates to activate downstream signaling effectors. However, the molecular mechanisms that modulate MAVS activation are not yet fully understood. In this study, the mitochondrial solute carrier SLC25A23 was found to attenuate type I IFN antiviral immunity using genome-wide CRISPR/Cas9 screening. SLC25A23 interacts with Trim31, interfering with its binding of Trim31 to MAVS. Indeed, SLC25A23 downregulation was found to increase K63-linked polyubiquitination and subsequent aggregation of MAVS, which promoted type I IFN production upon RNA virus infection. Consistently, mice with SLC25A23 knockdown were more resistant to RNA virus infection in vivo. These findings establish SLC25A23 as a novel regulator of MAVS posttranslational modifications and of type I antiviral immunity.
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Affiliation(s)
- Hongguang Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Xin Li
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Yiwei Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Xianxian Liu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jing Guo
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Zheng Wang
- Department of Reproductive Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Lulu Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Chunsheng Dong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
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