1
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Lang F, Cornwell JA, Kaur K, Elmogazy O, Zhang W, Zhang M, Song H, Sun Z, Wu X, Aladjem MI, Aregger M, Cappell SD, Yang C. Abrogation of the G2/M checkpoint as a chemosensitization approach for alkylating agents. Neuro Oncol 2024; 26:1083-1096. [PMID: 38134889 PMCID: PMC11145461 DOI: 10.1093/neuonc/noad252] [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: 08/17/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND The cell cycle is tightly regulated by checkpoints, which play a vital role in controlling its progression and timing. Cancer cells exploit the G2/M checkpoint, which serves as a resistance mechanism against genotoxic anticancer treatments, allowing for DNA repair prior to cell division. Manipulating cell cycle timing has emerged as a potential strategy to augment the effectiveness of DNA damage-based therapies. METHODS In this study, we conducted a forward genome-wide CRISPR/Cas9 screening with repeated exposure to the alkylating agent temozolomide (TMZ) to investigate the mechanisms underlying tumor cell survival under genotoxic stress. RESULTS Our findings revealed that canonical DNA repair pathways, including the Ataxia-telangiectasia mutated (ATM)/Fanconi and mismatch repair, determine cell fate under genotoxic stress. Notably, we identified the critical role of PKMYT1, in ensuring cell survival. Depletion of PKMYT1 led to overwhelming TMZ-induced cytotoxicity in cancer cells. Isobologram analysis demonstrated potent drug synergy between alkylating agents and a Myt1 kinase inhibitor, RP-6306. Mechanistically, inhibiting Myt1 forced G2/M-arrested cells into an unscheduled transition to the mitotic phase without complete resolution of DNA damage. This forced entry into mitosis, along with persistent DNA damage, resulted in severe mitotic abnormalities. Ultimately, these aberrations led to mitotic exit with substantial apoptosis. Preclinical animal studies demonstrated that the combination regimen involving TMZ and RP-6306 prolonged the overall survival of glioma-bearing mice. CONCLUSIONS Collectively, our findings highlight the potential of targeting cell cycle timing through Myt1 inhibition as an effective strategy to enhance the efficacy of current standard cancer therapies, potentially leading to improved disease outcomes.
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Affiliation(s)
- Fengchao Lang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - James A Cornwell
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Karambir Kaur
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Omar Elmogazy
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Wei Zhang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Meili Zhang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Hua Song
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Zhonghe Sun
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Michael Aregger
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Steven D Cappell
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Chunzhang Yang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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2
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Dhaliwal NK, Weng OY, Dong X, Bhattacharya A, Ahmed M, Nishimura H, Choi WWY, Aggarwal A, Luikart BW, Shu Q, Li X, Wilson MD, Moffat J, Wang LY, Muffat J, Li Y. Synergistic hyperactivation of both mTORC1 and mTORC2 underlies the neural abnormalities of PTEN-deficient human neurons and cortical organoids. Cell Rep 2024; 43:114173. [PMID: 38700984 DOI: 10.1016/j.celrep.2024.114173] [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: 09/22/2023] [Revised: 03/20/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
Mutations in the phosphatase and tensin homolog (PTEN) gene are associated with severe neurodevelopmental disorders. Loss of PTEN leads to hyperactivation of the mechanistic target of rapamycin (mTOR), which functions in two distinct protein complexes, mTORC1 and mTORC2. The downstream signaling mechanisms that contribute to PTEN mutant phenotypes are not well delineated. Here, we show that pluripotent stem cell-derived PTEN mutant human neurons, neural precursors, and cortical organoids recapitulate disease-relevant phenotypes, including hypertrophy, electrical hyperactivity, enhanced proliferation, and structural overgrowth. PTEN loss leads to simultaneous hyperactivation of mTORC1 and mTORC2. We dissect the contribution of mTORC1 and mTORC2 by generating double mutants of PTEN and RPTOR or RICTOR, respectively. Our results reveal that the synergistic hyperactivation of both mTORC1 and mTORC2 is essential for the PTEN mutant human neural phenotypes. Together, our findings provide insights into the molecular mechanisms that underlie PTEN-related neural disorders and highlight novel therapeutic targets.
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Affiliation(s)
- Navroop K Dhaliwal
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Octavia Yifang Weng
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program in Neurosciences and Mental Health, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Physiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Xiaoxue Dong
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; The Children's Hospital, National Clinical Research Center for Child Health, School of Medicine, Zhejiang University, Hangzhou 310052, China; The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Afrin Bhattacharya
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Mai Ahmed
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Haruka Nishimura
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Wendy W Y Choi
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Aditi Aggarwal
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Bryan W Luikart
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Qiang Shu
- The Children's Hospital, National Clinical Research Center for Child Health, School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Xuekun Li
- The Children's Hospital, National Clinical Research Center for Child Health, School of Medicine, Zhejiang University, Hangzhou 310052, China; The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Michael D Wilson
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Lu-Yang Wang
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Physiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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3
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Wang Z, Wang H, Lin S, Angers S, Sargent EH, Kelley SO. Phenotypic targeting using magnetic nanoparticles for rapid characterization of cellular proliferation regulators. SCIENCE ADVANCES 2024; 10:eadj1468. [PMID: 38718125 PMCID: PMC11078187 DOI: 10.1126/sciadv.adj1468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/03/2024] [Indexed: 05/12/2024]
Abstract
Genome-wide CRISPR screens have provided a systematic way to identify essential genetic regulators of a phenotype of interest with single-cell resolution. However, most screens use live/dead readout of viability to identify factors of interest. Here, we describe an approach that converts cell proliferation into the degree of magnetization, enabling downstream microfluidic magnetic sorting to be performed. We performed a head-to-head comparison and verified that the magnetic workflow can identify the same hits from a traditional screen while reducing the screening period from 4 weeks to 1 week. Taking advantage of parallelization and performance, we screened multiple mesenchymal cancer cell lines for their dependency on cell proliferation. We found and validated pan- and cell-specific potential therapeutic targets. The method presented provides a nanoparticle-enabled approach means to increase the breadth of data collected in CRISPR screens, enabling the rapid discovery of drug targets for treatment.
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Affiliation(s)
- Zongjie Wang
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Hansen Wang
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Sichun Lin
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Edward H. Sargent
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada
- Department of Chemistry, Weinberg College of Arts and Science, Northwestern University, Evanston, IL 60208, USA
- Department of Electrical and Computer Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
| | - Shana O. Kelley
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada
- Department of Chemistry, Weinberg College of Arts and Science, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Chan Zuckerberg Biohub Chicago, Chicago, IL 60607, USA
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4
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Papakyriacou I, Kutkaite G, Rúbies Bedós M, Nagarajan D, Alford LP, Menden MP, Mao Y. Loss of NEDD8 in cancer cells causes vulnerability to immune checkpoint blockade in triple-negative breast cancer. Nat Commun 2024; 15:3581. [PMID: 38678024 PMCID: PMC11055868 DOI: 10.1038/s41467-024-47987-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
Immune checkpoint blockade therapy aims to activate the immune system to eliminate cancer cells. However, clinical benefits are only recorded in a subset of patients. Here, we leverage genome-wide CRISPR/Cas9 screens in a Tumor-Immune co-Culture System focusing on triple-negative breast cancer (TNBC). We reveal that NEDD8 loss in cancer cells causes a vulnerability to nivolumab (anti-PD-1). Genetic deletion of NEDD8 only delays cell division initially but cell proliferation is unaffected after recovery. Since the NEDD8 gene is commonly essential, we validate this observation with additional CRISPR screens and uncover enhanced immunogenicity in NEDD8 deficient cells using proteomics. In female immunocompetent mice, PD-1 blockade lacks efficacy against established EO771 breast cancer tumors. In contrast, we observe tumor regression mediated by CD8+ T cells against Nedd8 deficient EO771 tumors after PD-1 blockade. In essence, we provide evidence that NEDD8 is conditionally essential in TNBC and presents as a synergistic drug target for PD-1/L1 blockade therapy.
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Affiliation(s)
- Irineos Papakyriacou
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ginte Kutkaite
- Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, Martinsried, Germany
| | - Marta Rúbies Bedós
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Divya Nagarajan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Liam P Alford
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Michael P Menden
- Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Yumeng Mao
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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5
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Cacheiro P, Lawson S, Van den Veyver IB, Marengo G, Zocche D, Murray SA, Duyzend M, Robinson PN, Smedley D. Lethal phenotypes in Mendelian disorders. Genet Med 2024; 26:101141. [PMID: 38629401 DOI: 10.1016/j.gim.2024.101141] [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: 02/05/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
PURPOSE Existing resources that characterize the essentiality status of genes are based on either proliferation assessment in human cell lines, viability evaluation in mouse knockouts, or constraint metrics derived from human population sequencing studies. Several repositories document phenotypic annotations for rare disorders; however, there is a lack of comprehensive reporting on lethal phenotypes. METHODS We queried Online Mendelian Inheritance in Man for terms related to lethality and classified all Mendelian genes according to the earliest age of death recorded for the associated disorders, from prenatal death to no reports of premature death. We characterized the genes across these lethality categories, examined the evidence on viability from mouse models and explored how this information could be used for novel gene discovery. RESULTS We developed the Lethal Phenotypes Portal to showcase this curated catalog of human essential genes. Differences in the mode of inheritance, physiological systems affected, and disease class were found for genes in different lethality categories, as well as discrepancies between the lethal phenotypes observed in mouse and human. CONCLUSION We anticipate that this resource will aid clinicians in the diagnosis of early lethal conditions and assist researchers in investigating the properties that make these genes essential for human development.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Samantha Lawson
- ITS Research, Queen Mary University of London, London, United Kingdom
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | - Gabriel Marengo
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park and St Mark's Hospitals, London, United Kingdom
| | | | - Michael Duyzend
- Massachusetts General Hospital, Boston, MA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Peter N Robinson
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom.
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6
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Cacheiro P, Lawson S, Van den Veyver IB, Marengo G, Zocche D, Murray SA, Duyzend M, Robinson PN, Smedley D. Lethal phenotypes in Mendelian disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.12.24301168. [PMID: 38260283 PMCID: PMC10802756 DOI: 10.1101/2024.01.12.24301168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Essential genes are those whose function is required for cell proliferation and/or organism survival. A gene's intolerance to loss-of-function can be allocated within a spectrum, as opposed to being considered a binary feature, since this function might be essential at different stages of development, genetic backgrounds or other contexts. Existing resources that collect and characterise the essentiality status of genes are based on either proliferation assessment in human cell lines, embryonic and postnatal viability evaluation in different model organisms, and gene metrics such as intolerance to variation scores derived from human population sequencing studies. There are also several repositories available that document phenotypic annotations for rare disorders in humans such as the Online Mendelian Inheritance in Man (OMIM) and the Human Phenotype Ontology (HPO) knowledgebases. This raises the prospect of being able to use clinical data, including lethality as the most severe phenotypic manifestation, to further our characterisation of gene essentiality. Here we queried OMIM for terms related to lethality and classified all Mendelian genes into categories, according to the earliest age of death recorded for the associated disorders, from prenatal death to no reports of premature death. To showcase this curated catalogue of human essential genes, we developed the Lethal Phenotypes Portal (https://lethalphenotypes.research.its.qmul.ac.uk), where we also explore the relationships between these lethality categories, constraint metrics and viability in cell lines and mouse. Further analysis of the genes in these categories reveals differences in the mode of inheritance of the associated disorders, physiological systems affected and disease class. We highlight how the phenotypic similarity between genes in the same lethality category combined with gene family/group information can be used for novel disease gene discovery. Finally, we explore the overlaps and discrepancies between the lethal phenotypes observed in mouse and human and discuss potential explanations that include differences in transcriptional regulation, functional compensation and molecular disease mechanisms. We anticipate that this resource will aid clinicians in the diagnosis of early lethal conditions and assist researchers in investigating the properties that make these genes essential for human development.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Ignatia B. Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Gabriel Marengo
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park & St Mark’s Hospitals, London, UK
| | | | | | - Peter N. Robinson
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK
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7
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Giordano M, Falbo E, Maddalena L, Piccirillo M, Granata I. Untangling the Context-Specificity of Essential Genes by Means of Machine Learning: A Constructive Experience. Biomolecules 2023; 14:18. [PMID: 38254618 PMCID: PMC10813179 DOI: 10.3390/biom14010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Gene essentiality is a genetic concept crucial for a comprehensive understanding of life and evolution. In the last decade, many essential genes (EGs) have been determined using different experimental and computational approaches, and this information has been used to reduce the genomes of model organisms. A growing amount of evidence highlights that essentiality is a property that depends on the context. Because of their importance in vital biological processes, recognising context-specific EGs (csEGs) could help for identifying new potential pharmacological targets and to improve precision therapeutics. Since most of the computational procedures proposed to identify and predict EGs neglect their context-specificity, we focused on this aspect, providing a theoretical and experimental overview of the literature, data and computational methods dedicated to recognising csEGs. To this end, we adapted existing computational methods to exploit a specific context (the kidney tissue) and experimented with four different prediction methods using the labels provided by four different identification approaches. The considerations derived from the analysis of the obtained results, confirmed and validated also by further experiments for a different tissue context, provide the reader with guidance on exploiting existing tools for achieving csEGs identification and prediction.
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Affiliation(s)
- Maurizio Giordano
- Institute for High-Performance Computing and Networking (ICAR), National Research Council (CNR), V. Pietro Castellino 111, 80131 Naples, Italy; (E.F.); (L.M.); (M.P.); (I.G.)
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8
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Mukhopadhyay S, Huang HY, Lin Z, Ranieri M, Li S, Sahu S, Liu Y, Ban Y, Guidry K, Hu H, Lopez A, Sherman F, Tan YJ, Lee YT, Armstrong AP, Dolgalev I, Sahu P, Zhang T, Lu W, Gray NS, Christensen JG, Tang TT, Velcheti V, Khodadadi-Jamayran A, Wong KK, Neel BG. Genome-Wide CRISPR Screens Identify Multiple Synthetic Lethal Targets That Enhance KRASG12C Inhibitor Efficacy. Cancer Res 2023; 83:4095-4111. [PMID: 37729426 PMCID: PMC10841254 DOI: 10.1158/0008-5472.can-23-2729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/22/2023]
Abstract
Non-small lung cancers (NSCLC) frequently (∼30%) harbor KRAS driver mutations, half of which are KRASG12C. KRAS-mutant NSCLC with comutated STK11 and/or KEAP1 is particularly refractory to conventional, targeted, and immune therapy. Development of KRASG12C inhibitors (G12Ci) provided a major therapeutic advance, but resistance still limits their efficacy. To identify genes whose deletion augments efficacy of the G12Cis adagrasib (MRTX-849) or adagrasib plus TNO155 (SHP2i), we performed genome-wide CRISPR/Cas9 screens on KRAS/STK11-mutant NSCLC lines. Recurrent, potentially targetable, synthetic lethal (SL) genes were identified, including serine-threonine kinases, tRNA-modifying and proteoglycan synthesis enzymes, and YAP/TAZ/TEAD pathway components. Several SL genes were confirmed by siRNA/shRNA experiments, and the YAP/TAZ/TEAD pathway was extensively validated in vitro and in mice. Mechanistic studies showed that G12Ci treatment induced gene expression of RHO paralogs and activators, increased RHOA activation, and evoked ROCK-dependent nuclear translocation of YAP. Mice and patients with acquired G12Ci- or G12Ci/SHP2i-resistant tumors showed strong overlap with SL pathways, arguing for the relevance of the screen results. These findings provide a landscape of potential targets for future combination strategies, some of which can be tested rapidly in the clinic. SIGNIFICANCE Identification of synthetic lethal genes with KRASG12C using genome-wide CRISPR/Cas9 screening and credentialing of the ability of TEAD inhibition to enhance KRASG12C efficacy provides a roadmap for combination strategies. See related commentary by Johnson and Haigis, p. 4005.
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Affiliation(s)
- Suman Mukhopadhyay
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Hsin-Yi Huang
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Ziyan Lin
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University Grossman School of Medicine, New York, United States
| | - Michela Ranieri
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Shuai Li
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Soumyadip Sahu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yingzhuo Liu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yi Ban
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Kayla Guidry
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Hai Hu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Alfonso Lopez
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Fiona Sherman
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yi Jer Tan
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yeuan Ting Lee
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Amanda P. Armstrong
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Igor Dolgalev
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Priyanka Sahu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, California, United States
| | - Wenchao Lu
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, California, United States
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, California, United States
| | | | - Tracy T. Tang
- Vivace Therapeutics, Inc., San Mateo, California, United States
| | - Vamsidhar Velcheti
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University Grossman School of Medicine, New York, United States
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
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9
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van Schie JJM, de Lint K, Molenaar TM, Moronta Gines M, Balk J, Rooimans M, Roohollahi K, Pai G, Borghuis L, Ramadhin A, Corazza F, Dorsman J, Wendt K, Wolthuis RF, de Lange J. CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin. Nucleic Acids Res 2023; 51:9594-9609. [PMID: 37702151 PMCID: PMC10570055 DOI: 10.1093/nar/gkad756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
The cohesin complex regulates higher order chromosome architecture through maintaining sister chromatid cohesion and folding chromatin by DNA loop extrusion. Impaired cohesin function underlies a heterogeneous group of genetic syndromes and is associated with cancer. Here, we mapped the genetic dependencies of human cell lines defective of cohesion regulators DDX11 and ESCO2. The obtained synthetic lethality networks are strongly enriched for genes involved in DNA replication and mitosis and support the existence of parallel sister chromatid cohesion establishment pathways. Among the hits, we identify the chromatin binding, BRCT-domain containing protein PAXIP1 as a novel cohesin regulator. Depletion of PAXIP1 severely aggravates cohesion defects in ESCO2 mutant cells, leading to mitotic cell death. PAXIP1 promotes global chromatin association of cohesin, independent of DNA replication, a function that cannot be explained by indirect effects of PAXIP1 on transcription or DNA repair. Cohesin regulation by PAXIP1 requires its binding partner PAGR1 and a conserved FDF motif in PAGR1. PAXIP1 co-localizes with cohesin on multiple genomic loci, including active gene promoters and enhancers. Possibly, this newly identified role of PAXIP1-PAGR1 in regulating cohesin occupancy on chromatin is also relevant for previously described functions of PAXIP1 in transcription, immune cell maturation and DNA repair.
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Affiliation(s)
- Janne J M van Schie
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Klaas de Lint
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Thom M Molenaar
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | | | - Jesper A Balk
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Martin A Rooimans
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Khashayar Roohollahi
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Govind M Pai
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Lauri Borghuis
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Anisha R Ramadhin
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Francesco Corazza
- Erasmus Medical Centre, Department of Cell Biology, Rotterdam, The Netherlands
| | - Josephine C Dorsman
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Kerstin S Wendt
- Erasmus Medical Centre, Department of Cell Biology, Rotterdam, The Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Job de Lange
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
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10
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [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: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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11
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Hertz EPT, Vega IAD, Kruse T, Wang Y, Hendriks IA, Bizard AH, Eugui-Anta A, Hay RT, Nielsen ML, Nilsson J, Hickson ID, Mailand N. The SUMO-NIP45 pathway processes toxic DNA catenanes to prevent mitotic failure. Nat Struct Mol Biol 2023; 30:1303-1313. [PMID: 37474739 PMCID: PMC10497417 DOI: 10.1038/s41594-023-01045-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 06/26/2023] [Indexed: 07/22/2023]
Abstract
SUMOylation regulates numerous cellular processes, but what represents the essential functions of this protein modification remains unclear. To address this, we performed genome-scale CRISPR-Cas9-based screens, revealing that the BLM-TOP3A-RMI1-RMI2 (BTRR)-PICH pathway, which resolves ultrafine anaphase DNA bridges (UFBs) arising from catenated DNA structures, and the poorly characterized protein NIP45/NFATC2IP become indispensable for cell proliferation when SUMOylation is inhibited. We demonstrate that NIP45 and SUMOylation orchestrate an interphase pathway for converting DNA catenanes into double-strand breaks (DSBs) that activate the G2 DNA-damage checkpoint, thereby preventing cytokinesis failure and binucleation when BTRR-PICH-dependent UFB resolution is defective. NIP45 mediates this new TOP2-independent DNA catenane resolution process via its SUMO-like domains, promoting SUMOylation of specific factors including the SLX4 multi-nuclease complex, which contributes to catenane conversion into DSBs. Our findings establish that SUMOylation exerts its essential role in cell proliferation by enabling resolution of toxic DNA catenanes via nonepistatic NIP45- and BTRR-PICH-dependent pathways to prevent mitotic failure.
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Affiliation(s)
- Emil P T Hertz
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Ignacio Alonso-de Vega
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Kruse
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Yiqing Wang
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Anna H Bizard
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ania Eugui-Anta
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Nilsson
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark.
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12
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Dickson AS, Pauzaite T, Arnaiz E, Ortmann BM, West JA, Volkmar N, Martinelli AW, Li Z, Wit N, Vitkup D, Kaser A, Lehner PJ, Nathan JA. A HIF independent oxygen-sensitive pathway for controlling cholesterol synthesis. Nat Commun 2023; 14:4816. [PMID: 37558666 PMCID: PMC10412576 DOI: 10.1038/s41467-023-40541-1] [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: 02/16/2023] [Accepted: 07/30/2023] [Indexed: 08/11/2023] Open
Abstract
Cholesterol biosynthesis is a highly regulated, oxygen-dependent pathway, vital for cell membrane integrity and growth. In fungi, the dependency on oxygen for sterol production has resulted in a shared transcriptional response, resembling prolyl hydroxylation of Hypoxia Inducible Factors (HIFs) in metazoans. Whether an analogous metazoan pathway exists is unknown. Here, we identify Sterol Regulatory Element Binding Protein 2 (SREBP2), the key transcription factor driving sterol production in mammals, as an oxygen-sensitive regulator of cholesterol synthesis. SREBP2 degradation in hypoxia overrides the normal sterol-sensing response, and is HIF independent. We identify MARCHF6, through its NADPH-mediated activation in hypoxia, as the main ubiquitin ligase controlling SREBP2 stability. Hypoxia-mediated degradation of SREBP2 protects cells from statin-induced cell death by forcing cells to rely on exogenous cholesterol uptake, explaining why many solid organ tumours become auxotrophic for cholesterol. Our findings therefore uncover an oxygen-sensitive pathway for governing cholesterol synthesis through regulated SREBP2-dependent protein degradation.
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Affiliation(s)
- Anna S Dickson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Tekle Pauzaite
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Esther Arnaiz
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
- Ochre-Bio Ltd, Hayakawa Building, Oxford Science Park, Edmund Halley Road, Oxford, OX4 4GB, UK
| | - Brian M Ortmann
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
- Biosciences Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU, UK
| | - James A West
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Norbert Volkmar
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
- Institute for Molecular Systems Biology (IMSB), ETH Zürich, Zürich, Switzerland
- DISCO Pharmaceuticals Swiss GmbH, ETH Zürich, Zürich, Switzerland
| | - Anthony W Martinelli
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Zhaoqi Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Tango Therapeutics, 201 Brookline Ave Suite 901, Boston, MA, USA
| | - Niek Wit
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Dennis Vitkup
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Arthur Kaser
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK.
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13
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Park M, Kim D, Kim I, Im SH, Kim S. Drug approval prediction based on the discrepancy in gene perturbation effects between cells and humans. EBioMedicine 2023; 94:104705. [PMID: 37453362 PMCID: PMC10366401 DOI: 10.1016/j.ebiom.2023.104705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 06/15/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Poor translation between in vitro and clinical studies due to the cells/humans discrepancy in drug target perturbation effects leads to safety failures in clinical trials, thus increasing drug development costs and reducing patients' life quality. Therefore, developing a predictive model for drug approval considering the cells/humans discrepancy is needed to reduce drug attrition rates in clinical trials. METHODS Our machine learning framework predicts drug approval in clinical trials based on the cells/humans discrepancy in drug target perturbation effects. To evaluate the discrepancy to predict drug approval (1404 approved and 1070 unapproved drugs), we analysed CRISPR-Cas9 knockout and loss-of-function mutation rate-based gene perturbation effects on cells and humans, respectively. To validate the risk of drug targets with the cells/humans discrepancy, we examined the targets of failed and withdrawn drugs due to safety problems. FINDINGS Drug approvals in clinical trials were correlated with the cells/humans discrepancy in gene perturbation effects. Genes tolerant to perturbation effects on cells but intolerant to those on humans were associated with failed drug targets. Furthermore, genes with the cells/humans discrepancy were related to drugs withdrawn due to severe side effects. Motivated by previous studies assessing drug safety through chemical properties, we improved drug approval prediction by integrating chemical information with the cells/humans discrepancy. INTERPRETATION The cells/humans discrepancy in gene perturbation effects facilitates drug approval prediction and explains drug safety failures in clinical trials. FUNDING S.K. received grants from the Korean National Research Foundation (2021R1A2B5B01001903 and 2020R1A6A1A03047902) and IITP (2019-0-01906, Artificial Intelligence Graduate School Program, POSTECH).
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Affiliation(s)
- Minhyuk Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Inhae Kim
- ImmunoBiome Inc., Pohang, South Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea; ImmunoBiome Inc., Pohang, South Korea
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea.
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14
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Singh AK, Amar I, Ramadasan H, Kappagantula KS, Chavali S. Proteins with amino acid repeats constitute a rapidly evolvable and human-specific essentialome. Cell Rep 2023; 42:112811. [PMID: 37453061 DOI: 10.1016/j.celrep.2023.112811] [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: 01/11/2023] [Revised: 05/30/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Protein products of essential genes, indispensable for organismal survival, are highly conserved and bring about fundamental functions. Interestingly, proteins that contain amino acid homorepeats that tend to evolve rapidly are enriched in eukaryotic essentialomes. Why are proteins with hypermutable homorepeats enriched in conserved and functionally vital essential proteins? We solve this functional versus evolutionary paradox by demonstrating that human essential proteins with homorepeats bring about crosstalk across biological processes through high interactability and have distinct regulatory functions affecting expansive global regulation. Importantly, essential proteins with homorepeats rapidly diverge with the amino acid substitutions frequently affecting functional sites, likely facilitating rapid adaptability. Strikingly, essential proteins with homorepeats influence human-specific embryonic and brain development, implying that the presence of homorepeats could contribute to the emergence of human-specific processes. Thus, we propose that homorepeat-containing essential proteins affecting species-specific traits can be potential intervention targets across pathologies, including cancers and neurological disorders.
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Affiliation(s)
- Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Ishita Amar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Harikrishnan Ramadasan
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Keertana S Kappagantula
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India.
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15
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Zhang H, Yan J, Lu Z, Zhou Y, Zhang Q, Cui T, Li Y, Chen H, Ma L. Deep sampling of gRNA in the human genome and deep-learning-informed prediction of gRNA activities. Cell Discov 2023; 9:48. [PMID: 37193681 DOI: 10.1038/s41421-023-00549-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/21/2023] [Indexed: 05/18/2023] Open
Abstract
Life science studies involving clustered regularly interspaced short palindromic repeat (CRISPR) editing generally apply the best-performing guide RNA (gRNA) for a gene of interest. Computational models are combined with massive experimental quantification on synthetic gRNA-target libraries to accurately predict gRNA activity and mutational patterns. However, the measurements are inconsistent between studies due to differences in the designs of the gRNA-target pair constructs, and there has not yet been an integrated investigation that concurrently focuses on multiple facets of gRNA capacity. In this study, we analyzed the DNA double-strand break (DSB)-induced repair outcomes and measured SpCas9/gRNA activities at both matched and mismatched locations using 926,476 gRNAs covering 19,111 protein-coding genes and 20,268 non-coding genes. We developed machine learning models to forecast the on-target cleavage efficiency (AIdit_ON), off-target cleavage specificity (AIdit_OFF), and mutational profiles (AIdit_DSB) of SpCas9/gRNA from a uniformly collected and processed dataset by deep sampling and massively quantifying gRNA capabilities in K562 cells. Each of these models exhibited superlative performance in predicting SpCas9/gRNA activities on independent datasets when benchmarked with previous models. A previous unknown parameter was also empirically determined regarding the "sweet spot" in the size of datasets used to establish an effective model to predict gRNA capabilities at a manageable experimental scale. In addition, we observed cell type-specific mutational profiles and were able to link nucleotidylexotransferase as the key factor driving these outcomes. These massive datasets and deep learning algorithms have been implemented into the user-friendly web service http://crispr-aidit.com to evaluate and rank gRNAs for life science studies.
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Affiliation(s)
- Heng Zhang
- Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- AIdit Therapeutics, Hangzhou, Zhejiang, China
| | - Jianfeng Yan
- Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- AIdit Therapeutics, Hangzhou, Zhejiang, China
| | - Zhike Lu
- Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yangfan Zhou
- Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | | | | | - Yini Li
- Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Hui Chen
- AIdit Therapeutics, Hangzhou, Zhejiang, China
| | - Lijia Ma
- Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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16
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Rosen BP, Li QV, Cho H, Liu D, Yang D, Graff S, Yan J, Luo R, Verma N, Damodaran JR, Beer MA, Sidoli S, Huangfu D. Parallel genome-scale CRISPR screens distinguish pluripotency and self-renewal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539283. [PMID: 37205540 PMCID: PMC10187244 DOI: 10.1101/2023.05.03.539283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Pluripotent stem cells are defined by both the ability to unlimitedly self-renew and differentiate to any somatic cell lineage, but understanding the mechanisms that control stem cell fitness versus the pluripotent cell identity is challenging. We performed four parallel genome-scale CRISPR-Cas9 screens to investigate the interplay between these two aspects of pluripotency. Our comparative analyses led to the discovery of genes with distinct roles in pluripotency regulation, including many mitochondrial and metabolism regulators crucial for stem cell fitness, and chromatin regulators that control stem cell identity. We further discovered a core set of factors that control both stem cell fitness and pluripotency identity, including an interconnected network of chromatin factors that safeguard pluripotency. Our unbiased and systematic screening and comparative analyses disentangle two interconnected aspects of pluripotency, provide rich datasets for exploring pluripotent cell identity versus self-renewal, and offer a valuable model for categorizing gene function in broad biological contexts.
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17
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Wei W, Geer MJ, Guo X, Dolgalev I, Sanjana NE, Neel BG. Genome-wide CRISPR/Cas9 screens reveal shared and cell-specific mechanisms of resistance to SHP2 inhibition. J Exp Med 2023; 220:e20221563. [PMID: 36820830 PMCID: PMC9998968 DOI: 10.1084/jem.20221563] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/14/2022] [Accepted: 01/20/2023] [Indexed: 02/24/2023] Open
Abstract
SHP2 (PTPN11) acts upstream of SOS1/2 to enable RAS activation. Allosteric SHP2 inhibitors (SHP2i) in the clinic prevent SHP2 activation, block proliferation of RTK- or cycling RAS mutant-driven cancers, and overcome "adaptive resistance." To identify SHP2i resistance mechanisms, we performed genome-wide CRISPR/Cas9 knockout screens on two SHP2i-sensitive cell lines, recovering genes expected to cause resistance (NF1, PTEN, CDKN1B, LZTR1, and RASA2) and novel targets (INPPL1, MAP4K5, epigenetic modifiers). We screened 14 additional lines with a focused CRISPR library targeting common "hits" from the genome-wide screens. LZTR1 deletion conferred resistance in 12/14 lines, followed by MAP4K5 (8/14), SPRED2/STK40 (6/14), and INPPL1 (5/14). INPPL1, MAP4K5, or LZTR1 deletion reactivated ERK signaling. INPPL1-mediated sensitization to SHP2i required its NPXY motif but not lipid phosphatase activity. MAP4K5 acted upstream of MEK through a kinase-dependent target(s); LZTR1 had cell-dependent effects on RIT and RAS stability. INPPL1, MAP4K5, or LZTR1 deletion also conferred SHP2i resistance in vivo. Defining the SHP2i resistance landscape could suggest effective combination approaches.
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Affiliation(s)
- Wei Wei
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Mitchell J. Geer
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Xinyi Guo
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Igor Dolgalev
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Neville E. Sanjana
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
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18
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Usluer S, Hallast P, Crepaldi L, Zhou Y, Urgo K, Dincer C, Su J, Noell G, Alasoo K, El Garwany O, Gerety SS, Newman B, Dovey OM, Parts L. Optimized whole-genome CRISPR interference screens identify ARID1A-dependent growth regulators in human induced pluripotent stem cells. Stem Cell Reports 2023; 18:1061-1074. [PMID: 37028423 DOI: 10.1016/j.stemcr.2023.03.008] [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: 09/17/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 04/09/2023] Open
Abstract
Perturbing expression is a powerful way to understand the role of individual genes, but can be challenging in important models. CRISPR-Cas screens in human induced pluripotent stem cells (iPSCs) are of limited efficiency due to DNA break-induced stress, while the less stressful silencing with an inactive Cas9 has been considered less effective so far. Here, we developed the dCas9-KRAB-MeCP2 fusion protein for screening in iPSCs from multiple donors. We found silencing in a 200 bp window around the transcription start site in polyclonal pools to be as effective as using wild-type Cas9 for identifying essential genes, but with much reduced cell numbers. Whole-genome screens to identify ARID1A-dependent dosage sensitivity revealed the PSMB2 gene, and enrichment of proteasome genes among the hits. This selective dependency was replicated with a proteasome inhibitor, indicating a targetable drug-gene interaction. Many more plausible targets in challenging cell models can be efficiently identified with our approach.
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Affiliation(s)
| | | | | | - Yan Zhou
- Wellcome Sanger Institute, Cambridge, UK
| | - Katie Urgo
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Jing Su
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Kaur Alasoo
- Department of Computer Science, University of Tartu, Tartu, Estonia
| | | | | | - Ben Newman
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Leopold Parts
- Wellcome Sanger Institute, Cambridge, UK; Department of Computer Science, University of Tartu, Tartu, Estonia.
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19
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Wells MF, Nemesh J, Ghosh S, Mitchell JM, Salick MR, Mello CJ, Meyer D, Pietilainen O, Piccioni F, Guss EJ, Raghunathan K, Tegtmeyer M, Hawes D, Neumann A, Worringer KA, Ho D, Kommineni S, Chan K, Peterson BK, Raymond JJ, Gold JT, Siekmann MT, Zuccaro E, Nehme R, Kaykas A, Eggan K, McCarroll SA. Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages. Cell Stem Cell 2023; 30:312-332.e13. [PMID: 36796362 PMCID: PMC10581885 DOI: 10.1016/j.stem.2023.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023]
Abstract
Human genome variation contributes to diversity in neurodevelopmental outcomes and vulnerabilities; recognizing the underlying molecular and cellular mechanisms will require scalable approaches. Here, we describe a "cell village" experimental platform we used to analyze genetic, molecular, and phenotypic heterogeneity across neural progenitor cells from 44 human donors cultured in a shared in vitro environment using algorithms (Dropulation and Census-seq) to assign cells and phenotypes to individual donors. Through rapid induction of human stem cell-derived neural progenitor cells, measurements of natural genetic variation, and CRISPR-Cas9 genetic perturbations, we identified a common variant that regulates antiviral IFITM3 expression and explains most inter-individual variation in susceptibility to the Zika virus. We also detected expression QTLs corresponding to GWAS loci for brain traits and discovered novel disease-relevant regulators of progenitor proliferation and differentiation such as CACHD1. This approach provides scalable ways to elucidate the effects of genes and genetic variation on cellular phenotypes.
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Affiliation(s)
- Michael F Wells
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jana M Mitchell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Insitro, South San Francisco, CA 94080, USA
| | | | - Curtis J Mello
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Olli Pietilainen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Ellen J Guss
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kavya Raghunathan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Derek Hawes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Kathleen A Worringer
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel Ho
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Sravya Kommineni
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Karrie Chan
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Brant K Peterson
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Joseph J Raymond
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - John T Gold
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Biology, Davidson College, Davidson, NC 28035, USA
| | - Marco T Siekmann
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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20
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Ahmed M, Muffat J, Li Y. Understanding neural development and diseases using CRISPR screens in human pluripotent stem cell-derived cultures. Front Cell Dev Biol 2023; 11:1158373. [PMID: 37101616 PMCID: PMC10123288 DOI: 10.3389/fcell.2023.1158373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
The brain is arguably the most complex part of the human body in form and function. Much remains unclear about the molecular mechanisms that regulate its normal and pathological physiology. This lack of knowledge largely stems from the inaccessible nature of the human brain, and the limitation of animal models. As a result, brain disorders are difficult to understand and even more difficult to treat. Recent advances in generating human pluripotent stem cells (hPSCs)-derived 2-dimensional (2D) and 3-dimensional (3D) neural cultures have provided an accessible system to model the human brain. Breakthroughs in gene editing technologies such as CRISPR/Cas9 further elevate the hPSCs into a genetically tractable experimental system. Powerful genetic screens, previously reserved for model organisms and transformed cell lines, can now be performed in human neural cells. Combined with the rapidly expanding single-cell genomics toolkit, these technological advances culminate to create an unprecedented opportunity to study the human brain using functional genomics. This review will summarize the current progress of applying CRISPR-based genetic screens in hPSCs-derived 2D neural cultures and 3D brain organoids. We will also evaluate the key technologies involved and discuss their related experimental considerations and future applications.
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Affiliation(s)
- Mai Ahmed
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Yun Li,
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21
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Tang S, Wu X, Liu J, Zhang Q, Wang X, Shao S, Gokbag B, Fan K, Liu X, Li F, Cheng L, Li L. Generation of dual-gRNA library for combinatorial CRISPR screening of synthetic lethal gene pairs. STAR Protoc 2022; 3:101556. [PMID: 36060092 PMCID: PMC9428847 DOI: 10.1016/j.xpro.2022.101556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Combinatorial CRISPR screening is useful for investigating synthetic lethality (SL) gene pairs. Here, we detail the steps for dual-gRNA library construction, with the introduction of two backbones, LentiGuide_DKO and LentiCRISPR_DKO. We describe steps for in vitro screening with 22Rv1-Cas9 and SaOS2-Cas9 cells followed by sequencing and data analysis. By introducing two backbones, we optimized the library construction process, facilitated standard pair-end sequencing, and provided options of screening on cells with or without modification of Cas9 expression.
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Affiliation(s)
- Shan Tang
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA.
| | - Xue Wu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Jinghui Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Qiongsi Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Xinyi Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Shuai Shao
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Birkan Gokbag
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kunjie Fan
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Fuhai Li
- Institute for Informatics and Department of Pediatrics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Lijun Cheng
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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22
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Paeniclostridium sordellii hemorrhagic toxin targets TMPRSS2 to induce colonic epithelial lesions. Nat Commun 2022; 13:4331. [PMID: 35882856 PMCID: PMC9321280 DOI: 10.1038/s41467-022-31994-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/12/2022] [Indexed: 12/21/2022] Open
Abstract
Hemorrhagic toxin (TcsH) is an important exotoxin produced by Paeniclostridium sordellii, but the exact role of TcsH in the pathogenesis remains unclear, partly due to the lack of knowledge of host receptor(s). Here, we carried out two genome-wide CRISPR/Cas9 screens parallelly with TcsH and identified cell surface fucosylation and TMPRSS2 as host factors contributing to the binding and entry of TcsH. Genetic deletion of either fucosylation biosynthesis enzymes or TMPRSS2 in the cells confers resistance to TcsH intoxication. Interestingly, TMPRSS2 and fucosylated glycans can mediate the binding/entry of TcsH independently, thus serving as redundant receptors. Both TMPRSS2 and fucosylation recognize TcsH through its CROPs domain. By using Tmprss2‒/‒ mice, we show that Tmprss2 is important for TcsH-induced systematic toxicity and colonic epithelial lesions. These findings reveal the importance of TMPRSS2 and surface fucosylation in TcsH actions and further provide insights into host recognition mechanisms for large clostridial toxins. Paeniclostridium sordellii is an opportunistic pathogen that can occur and be fatal in women undergoing abortion or childbirth. The pathogenesis of a hemorrhagic toxin, TcsH, produced by this bacteria, remains unknown. Here, authors carry out genome-wide screens to identify pathologically relevant host factors of TcsH.
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23
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Ancos-Pintado R, Bragado-García I, Morales ML, García-Vicente R, Arroyo-Barea A, Rodríguez-García A, Martínez-López J, Linares M, Hernández-Sánchez M. High-Throughput CRISPR Screening in Hematological Neoplasms. Cancers (Basel) 2022; 14:3612. [PMID: 35892871 PMCID: PMC9329962 DOI: 10.3390/cancers14153612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
CRISPR is becoming an indispensable tool in biological research, revolutionizing diverse fields of medical research and biotechnology. In the last few years, several CRISPR-based genome-targeting tools have been translated for the study of hematological neoplasms. However, there is a lack of reviews focused on the wide uses of this technology in hematology. Therefore, in this review, we summarize the main CRISPR-based approaches of high throughput screenings applied to this field. Here we explain several libraries and algorithms for analysis of CRISPR screens used in hematology, accompanied by the most relevant databases. Moreover, we focus on (1) the identification of novel modulator genes of drug resistance and efficacy, which could anticipate relapses in patients and (2) new therapeutic targets and synthetic lethal interactions. We also discuss the approaches to uncover novel biomarkers of malignant transformations and immune evasion mechanisms. We explain the current literature in the most common lymphoid and myeloid neoplasms using this tool. Then, we conclude with future directions, highlighting the importance of further gene candidate validation and the integration and harmonization of the data from CRISPR screening approaches.
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Affiliation(s)
- Raquel Ancos-Pintado
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Irene Bragado-García
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Luz Morales
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Roberto García-Vicente
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Andrés Arroyo-Barea
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Alba Rodríguez-García
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Joaquín Martínez-López
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain
| | - María Linares
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
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24
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Lorenzo-Martín LF, Menacho-Márquez M, Fernández-Parejo N, Rodríguez-Fdez S, Pascual G, Abad A, Crespo P, Dosil M, Benitah SA, Bustelo XR. The Rho guanosine nucleotide exchange factors Vav2 and Vav3 modulate epidermal stem cell function. Oncogene 2022; 41:3341-3354. [PMID: 35534539 PMCID: PMC9187518 DOI: 10.1038/s41388-022-02341-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/21/2022]
Abstract
It is known that Rho GTPases control different aspects of the biology of skin stem cells (SSCs). However, little information is available on the role of their upstream regulators under normal and tumorigenic conditions in this process. To address this issue, we have used here mouse models in which the activity of guanosine nucleotide exchange factors of the Vav subfamily has been manipulated using both gain- and loss-of-function strategies. These experiments indicate that Vav2 and Vav3 regulate the number, functional status, and responsiveness of hair follicle bulge stem cells. This is linked to gene expression programs related to the reinforcement of the identity and the quiescent state of normal SSCs. By contrast, in the case of cancer stem cells, they promote transcriptomal programs associated with the identity, activation state, and cytoskeletal remodeling. These results underscore the role of these Rho exchange factors in the regulation of normal and tumor epidermal stem cells.
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Affiliation(s)
- L Francisco Lorenzo-Martín
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 37007, Salamanca, Spain
| | - Mauricio Menacho-Márquez
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 37007, Salamanca, Spain
| | - Natalia Fernández-Parejo
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain
| | - Sonia Rodríguez-Fdez
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain
| | | | - Antonio Abad
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 37007, Salamanca, Spain
| | - Piero Crespo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 37007, Salamanca, Spain.,Instituto de Biomedicina y Biotecnología de Cantabria, CSIC-University of Cantabria, 39011, Santander, Spain
| | - Mercedes Dosil
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 37007, Salamanca, Spain
| | | | - Xosé R Bustelo
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain. .,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007, Salamanca, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 37007, Salamanca, Spain.
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25
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Dong C, Fu S, Karvas RM, Chew B, Fischer LA, Xing X, Harrison JK, Popli P, Kommagani R, Wang T, Zhang B, Theunissen TW. A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells. Nat Commun 2022; 13:2548. [PMID: 35538076 PMCID: PMC9090837 DOI: 10.1038/s41467-022-30207-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/21/2022] [Indexed: 12/26/2022] Open
Abstract
The recent derivation of human trophoblast stem cells (hTSCs) provides a scalable in vitro model system of human placental development, but the molecular regulators of hTSC identity have not been systematically explored thus far. Here, we utilize a genome-wide CRISPR-Cas9 knockout screen to comprehensively identify essential and growth-restricting genes in hTSCs. By cross-referencing our data to those from similar genetic screens performed in other cell types, as well as gene expression data from early human embryos, we define hTSC-specific and -enriched regulators. These include both well-established and previously uncharacterized trophoblast regulators, such as ARID3A, GATA2, and TEAD1 (essential), and GCM1, PTPN14, and TET2 (growth-restricting). Integrated analysis of chromatin accessibility, gene expression, and genome-wide location data reveals that the transcription factor TEAD1 regulates the expression of many trophoblast regulators in hTSCs. In the absence of TEAD1, hTSCs fail to complete faithful differentiation into extravillous trophoblast (EVT) cells and instead show a bias towards syncytiotrophoblast (STB) differentiation, thus indicating that this transcription factor safeguards the bipotent lineage potential of hTSCs. Overall, our study provides a valuable resource for dissecting the molecular regulation of human placental development and diseases.
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Affiliation(s)
- Chen Dong
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Shuhua Fu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rowan M Karvas
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Brian Chew
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laura A Fischer
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xiaoyun Xing
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jessica K Harrison
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Pooja Popli
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ramakrishna Kommagani
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ting Wang
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Thorold W Theunissen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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26
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Genome-wide screens identify specific drivers of mutant hTERT promoters. Proc Natl Acad Sci U S A 2022; 119:2105171119. [PMID: 35027447 PMCID: PMC8784157 DOI: 10.1073/pnas.2105171119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/31/2022] Open
Abstract
Mutations in hTERT promoter are seen in over 19% of human cancers, irrespective of the cancer type. Understanding the molecular players that regulate Mut-hTERT promoters may help the design of effective targeting strategies to inhibit telomerase reactivation specifically in cancer cells. Our work uses genome-wide functional screens to identify 30 specific regulators of Mut-hTERT promoters. These candidates identified from the screening serve as an excellent resource to understand how telomerase is reactivated and as targets for making inhibitors to telomerase, a key driver of cancer. Cancer-specific hTERT promoter mutations reported in 19% of cancers result in enhanced telomerase activity. Understanding the distinctions between transcriptional regulation of wild-type (WT) and mutant (Mut) hTERT promoters may open up avenues for development of inhibitors which specially block hTERT expression in cancer cells. To comprehensively identify physiological regulators of WT- or Mut-hTERT promoters, we generated several isogenic reporter cells driven by endogenous hTERT loci. Genome-wide CRISPR-Cas9 and small interfering RNA screens using these isogenic reporter lines identified specific regulators of Mut-hTERT promoters. We validate and characterize one of these hits, namely, MED12, a kinase subunit of mediator complex. We demonstrate that MED12 specifically drives expression of hTERT from the Mut-hTERT promoter by mediating long-range chromatin interaction between the proximal Mut-hTERT promoter and T-INT1 distal regulatory region 260 kb upstream. Several hits identified in our screens could serve as potential therapeutic targets, inhibition of which may specifically block Mut-hTERT promoter driven telomerase reactivation in cancers.
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27
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Zhang HL, Hu BX, Li ZL, Du T, Shan JL, Ye ZP, Peng XD, Li X, Huang Y, Zhu XY, Chen YH, Feng GK, Yang D, Deng R, Zhu XF. PKCβII phosphorylates ACSL4 to amplify lipid peroxidation to induce ferroptosis. Nat Cell Biol 2022; 24:88-98. [PMID: 35027735 DOI: 10.1038/s41556-021-00818-3] [Citation(s) in RCA: 184] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022]
Abstract
The accumulation of lipid peroxides is recognized as a determinant of the occurrence of ferroptosis. However, the sensors and amplifying process of lipid peroxidation linked to ferroptosis remain obscure. Here we identify PKCβII as a critical contributor of ferroptosis through independent genome-wide CRISPR-Cas9 and kinase inhibitor library screening. Our results show that PKCβII senses the initial lipid peroxides and amplifies lipid peroxidation linked to ferroptosis through phosphorylation and activation of ACSL4. Lipidomics analysis shows that activated ACSL4 catalyses polyunsaturated fatty acid-containing lipid biosynthesis and promotes the accumulation of lipid peroxidation products, leading to ferroptosis. Attenuation of the PKCβII-ACSL4 pathway effectively blocks ferroptosis in vitro and impairs ferroptosis-associated cancer immunotherapy in vivo. Our results identify PKCβII as a sensor of lipid peroxidation, and the lipid peroxidation-PKCβII-ACSL4 positive-feedback axis may provide potential targets for ferroptosis-associated disease treatment.
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Affiliation(s)
- Hai-Liang Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Bing-Xin Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhi-Ling Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tian Du
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Lu Shan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhi-Peng Ye
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Dan Peng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xuan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yun Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xian-Ying Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu-Hong Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Gong-Kan Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dajun Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rong Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Xiao-Feng Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.
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28
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Chen Y, Li L, Lan J, Cui Y, Rao X, Zhao J, Xing T, Ju G, Song G, Lou J, Liang J. CRISPR screens uncover protective effect of PSTK as a regulator of chemotherapy-induced ferroptosis in hepatocellular carcinoma. Mol Cancer 2022; 21:11. [PMID: 34983546 PMCID: PMC8725338 DOI: 10.1186/s12943-021-01466-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is among the most common forms of cancer and is associated with poor patient outcomes. The emergence of therapeutic resistance has hampered the efficacy of targeted treatments employed to treat HCC patients to date. In this study, we conducted a series of CRISPR/Cas9 screens to identify genes associated with synthetic lethality capable of improving HCC patient clinical responses. METHODS CRISPR-based loss-of-function genetic screens were used to target 18,053 protein-coding genes in HCC cells to identify chemotherapy-related synthetic lethal genes in these cells. Synergistic effects were analyzed through in vitro and in vivo analyses, while related mechanisms were explored through RNA-seq and metabolomics analyses. Potential inhibitors of identified genetic targets were selected through high-throughput virtual screening. RESULTS The inhibition of phosphoseryl-tRNA kinase (PSTK) was found to increase HCC cell sensitivity to chemotherapeutic treatment. PSTK was associated with the suppression of chemotherapy-induced ferroptosis in HCC cells, and the depletion of PSTK resulted in the inactivation of glutathione peroxidative 4 (GPX4) and the disruption of glutathione (GSH) metabolism owing to the inhibition of selenocysteine and cysteine synthesis, thus enhancing the induction of ferroptosis upon targeted chemotherapeutic treatment. Punicalin, an agent used to treat hepatitis B virus (HBV), was identified as a possible PSTK inhibitor that exhibited synergistic efficacy when applied together with Sorafenib to treat HCC in vitro and in vivo. CONCLUSIONS These results highlight a key role for PSTK as a mediator of resistance to targeted therapeutic treatment in HCC cells that functions by suppressing ferroptotic induction. PSTK inhibitors may thus represent ideal candidates for overcoming drug resistance in HCC.
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Affiliation(s)
- Yiran Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Oncology, Peking University Cancer Hospital and Institute, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, P.R. China
| | - Li Li
- Department of Oncology, Peking University International Hospital, Beijing, 102206, China
| | - Jie Lan
- Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Cui
- Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaosong Rao
- Department of Pathology, Boao Evergrande International Hospital, Qionghai, 571400, Hainan, China.,Department of Pathology, Peking University International Hospital, Beijing, 102206, China
| | - Jing Zhao
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, China
| | - Tao Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Oncology, Peking University Cancer Hospital and Institute, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, P.R. China
| | - Gaoda Ju
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Oncology, Peking University Cancer Hospital and Institute, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, P.R. China
| | - Guangtao Song
- Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
| | - Jizhong Lou
- Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jun Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Oncology, Peking University Cancer Hospital and Institute, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, P.R. China. .,Department of Oncology, Peking University International Hospital, Beijing, 102206, China.
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29
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The application of genome-wide CRISPR-Cas9 screens to dissect the molecular mechanisms of toxins. Comput Struct Biotechnol J 2022; 20:5076-5084. [PMID: 36187925 PMCID: PMC9489804 DOI: 10.1016/j.csbj.2022.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Many toxins are life-threatening to both animals and humans. However, specific antidotes are not available for most of those toxins. The molecular mechanisms underlying the toxicology of well-known toxins are not yet fully characterized. Recently, the advance in CRISPR-Cas9 technologies has greatly accelerated the process of revealing the toxic mechanisms of some common toxins on hosts from a genome-wide perspective. The high-throughput CRISPR screen has made it feasible to untangle complicated interactions between a particular toxin and its corresponding targeting tissue(s). In this review, we present an overview of recent advances in molecular dissection of toxins’ cytotoxicity by using genome-wide CRISPR screens, summarize the components essential for toxin-specific CRISPR screens, and propose new strategies for future research.
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30
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Zhang S, Wu J, Zhu X, Song H, Ren L, Tang Q, Xu X, Liu C, Zhang J, Hu W, Liu Z, Shi S. A novel approach to identify the mechanism of miR-145-5p toxicity to podocytes based on the essential genes targeting analysis. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:749-759. [PMID: 34729245 PMCID: PMC8526908 DOI: 10.1016/j.omtn.2021.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 11/03/2022]
Abstract
MicroRNAs (miRNAs) are emerging as effective therapeutic agents. When testing whether miR-145-5p could alleviate kidney injury, we unexpectedly found that extracellular vesicles loaded with miR-145-5p induced proteinuria and podocyte foot process effacement in normal control mice. To explore the mechanism of miR-145-5p’s toxicity to podocytes, we hypothesized that miR-145-5p could enter podocytes and inhibit genes essential for podocytes. We demonstrated that systemically administered miRNA can enter podocytes. Next, we predicted 611 podocyte essential genes based on single-cell RNA sequencing (RNA-seq) and found that 32 of them are predicted to be targeted by miR-145-5p. Functional annotation of the 32 podocyte essential genes revealed small GTPase-mediated signal transduction as the top pathway. We experimentally validated that miR-145-5p targeted Arhgap24 and Srgap1, the essential regulators of the Rho family of small GTPases, increased the activity of Rac1 and Cdc42, and reduced RhoA activity, accompanied by cellular injury, in podocytes. These results explain how miR-145-5p has deleterious effect on podocytes. Most importantly, our study provides a novel approach to investigate how a miRNA affects a given cell type, allowing not only identification of the molecular mechanism underlying an observed side effect of a miRNA drug but also prediction of miRNA drug toxicity on various cell types.
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Affiliation(s)
- Sipan Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Junnan Wu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Xiaodong Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Hui Song
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Lu Ren
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Qiaoli Tang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Xiaodong Xu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Chunbei Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Jiong Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Weixin Hu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
| | - Shaolin Shi
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 21002, China
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31
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Qiu X, Lin J, Chen Y, Liang B, Li L. Identification of Hub Genes Associated with Abnormal Endothelial Function in Early Coronary Atherosclerosis. Biochem Genet 2021; 60:1189-1204. [PMID: 34800203 DOI: 10.1007/s10528-021-10139-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022]
Abstract
Abnormal coronary endothelial function is an important step in the development of atherosclerosis. Coronary atherosclerosis is one of the main causes of death worldwide. We constructed a co-expression network to identify hub genes associated with abnormal coronary endothelial function in early coronary atherosclerosis. In brief, we used the GSE132651 dataset from the gene expression omnibus database. The top 5000 genes with greatest variances were used for weighted gene co-expression network analysis, and the module most strongly correlated with abnormal coronary endothelial function was chosen as key module. Functional enrichment analysis was performed for genes in the key module, a protein-protein interaction network was constructed to find hub genes, and gene set enrichment analysis (GSEA) was also performed. Genes were classified into 7 modules, with the midnightblue module being the one that was most related to abnormal coronary endothelial function and containing genes enriched in DNA replication, cell cycle, nucleotide excision repair, and Human T-cell leukemia virus 1 infection. We identified nine hub genes (HOXC5, PRND, PADI3, RC3H1, DAPP1, SIT1, DRICH1, GPRIN2, and RHO), which differently expressed in abnormal and normal coronary endothelial function samples. GSEA suggested that samples associated with abnormal coronary endothelial function and highly expressed hub genes were linked with immune, coagulation, hypoxia, and angiogenesis processes. These hub genes, their expression pattern, and pathways may be involved in the development of abnormal coronary endothelial function and promotion of early coronary atherosclerosis.
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Affiliation(s)
- Xue Qiu
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Jinyan Lin
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Yanbing Chen
- The First Clinical Medical School, Guangxi Medical University, Nanning, 530021, Guangxi Province, People's Republic of China
| | - Bixiao Liang
- The First Clinical Medical School, Guangxi Medical University, Nanning, 530021, Guangxi Province, People's Republic of China
| | - Lang Li
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China.
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32
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A Method to Map Gene Essentiality of Human Pluripotent Stem Cells by Genome-Scale CRISPR Screens with Inducible Cas9. Methods Mol Biol 2021. [PMID: 34709608 DOI: 10.1007/978-1-0716-1720-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Human pluripotent stem cells (hPSCs) have the capacity for self-renewal and differentiation into most cell types and, in contrast to widely used cell lines, are karyotypically normal and non-transformed. Hence, hPSCs are considered the gold-standard system for modelling diseases, especially in the field of regenerative medicine. Despite widespread research use of hPSCs and induced pluripotent stem cells (iPSCs), the systematic understanding of pluripotency and lineage differentiation mechanisms are still incomplete. Before tackling the complexities of lineage differentiation with genetic screens, it is critical to catalogue the general genetic requirements for cell fitness and proliferation in the pluripotent state and assess their plasticity under commonly used culture conditions.We describe a method to map essential genetic determinants of hPSC fitness and pluripotency, herein defined as cell reproduction, by genome-scale loss-of-function CRISPR screens in an inducible S. pyogenes Cas9 H1 hPSC line. To address questions of context-dependent gene essentiality, we include protocols for screening hPSCs cultured on feeder cells and laminin, two commonly used growth substrates. This method establishes parameters for genome-wide screens in hPSCs, making human stem cells amenable for functional genomics approaches to facilitate investigation of hPSC biology.
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33
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Application of CHyMErA Cas9-Cas12a combinatorial genome-editing platform for genetic interaction mapping and gene fragment deletion screening. Nat Protoc 2021; 16:4722-4765. [PMID: 34508260 DOI: 10.1038/s41596-021-00595-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 06/17/2021] [Indexed: 02/08/2023]
Abstract
CRISPR-based forward genetic screening represents a powerful approach for the systematic characterization of gene function. Recent efforts have been directed toward establishing CRISPR-based tools for the programmable delivery of combinatorial genetic perturbations, most of which are mediated by a single nuclease and the expression of structurally identical guide backbones from two promoters. In contrast, we have developed CHyMErA (Cas hybrid for multiplexed editing and screening applications), which is based on the co-expression of Cas9 and Cas12a nucleases in conjunction with a hybrid guide RNA (hgRNA) engineered by the fusion of Cas9 and Cas12a guides and expressed from a single U6 promoter. CHyMErA is suitable for the high-throughput deletion of genetic segments including the excision of individual exons. Furthermore, CHyMErA enables the concomitant targeting of two or more genes and can thus be used for the systematic mapping of genetic interactions in mammalian cells. CHyMErA can also be applied for the perturbation of paralogous gene pairs, thereby allowing the capturing of phenotypic roles that would otherwise be masked because of genetic redundancy. Here, we provide instructions for the cloning of hgRNA screening libraries and individual hgRNA constructs and offer guidelines for designing and performing combinatorial pooled genetic screens using CHyMErA. Starting with the generation of Cas9- and Cas12a-expressing cell lines, CHyMErA screening can be implemented within 15-20 weeks.
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34
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Abstract
The past 25 years of genomics research first revealed which genes are encoded by the human genome and then a detailed catalogue of human genome variation associated with many diseases. Despite this, the function of many genes and gene regulatory elements remains poorly characterized, which limits our ability to apply these insights to human disease. The advent of new CRISPR functional genomics tools allows for scalable and multiplexable characterization of genes and gene regulatory elements encoded by the human genome. These approaches promise to reveal mechanisms of gene function and regulation, and to enable exploration of how genes work together to modulate complex phenotypes.
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35
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Tian R, Abarientos A, Hong J, Hashemi SH, Yan R, Dräger N, Leng K, Nalls MA, Singleton AB, Xu K, Faghri F, Kampmann M. Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis. Nat Neurosci 2021; 24:1020-1034. [PMID: 34031600 PMCID: PMC8254803 DOI: 10.1038/s41593-021-00862-0] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Single-cell transcriptomics provide a systematic map of gene expression in different human cell types. The next challenge is to systematically understand cell-type-specific gene function. The integration of CRISPR-based functional genomics and stem cell technology enables the scalable interrogation of gene function in differentiated human cells. Here we present the first genome-wide CRISPR interference and CRISPR activation screens in human neurons. We uncover pathways controlling neuronal response to chronic oxidative stress, which is implicated in neurodegenerative diseases. Unexpectedly, knockdown of the lysosomal protein prosaposin strongly sensitizes neurons, but not other cell types, to oxidative stress by triggering the formation of lipofuscin, a hallmark of aging, which traps iron, generating reactive oxygen species and triggering ferroptosis. We also determine transcriptomic changes in neurons after perturbation of genes linked to neurodegenerative diseases. To enable the systematic comparison of gene function across different human cell types, we establish a data commons named CRISPRbrain.
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Affiliation(s)
- Ruilin Tian
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Anthony Abarientos
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Jason Hong
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Sayed Hadi Hashemi
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Nina Dräger
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Kun Leng
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, LLC, Glen Echo, MD, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Faraz Faghri
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, LLC, Glen Echo, MD, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Jarrige M, Polvèche H, Carteron A, Janczarski S, Peschanski M, Auboeuf D, Martinat C. SISTEMA: A large and standardized collection of transcriptome data sets for human pluripotent stem cell research. iScience 2021; 24:102767. [PMID: 34278269 PMCID: PMC8271161 DOI: 10.1016/j.isci.2021.102767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/29/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
Human pluripotent stem cells have ushered in an exciting new era for disease modeling, drug discovery, and cell therapy development. Continued progress toward realizing the potential of human pluripotent stem cells will be facilitated by robust data sets and complementary resources that are easily accessed and interrogated by the stem cell community. In this context, we present SISTEMA, a quality-controlled curated gene expression database, built on a valuable catalog of human pluripotent stem cell lines, and their derivatives for which transcriptomic analyses have been generated using a single experimental pipeline. SISTEMA functions as a one-step resource that will assist the stem cell community to easily evaluate the expression level for genes of interest, while comparing them across different hPSC lines, cell types, pathological conditions, or after pharmacological treatments. SISTEMA is a curated gene expression database using human pluripotent stem cell lines A single experimental and analytical pipeline are used for the transcriptomic analyses SISTEMA is a user friendly Web portal designed for the stem cell community
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Affiliation(s)
| | | | | | - Stéphane Janczarski
- LBMC, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, 69007 Lyon, France
| | | | - Didier Auboeuf
- LBMC, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, 69007 Lyon, France
| | - Cécile Martinat
- INSERM/UEVE UMR 861, Paris Saclay Univ I-STEM, 91100 Corbeil-Essonnes, France
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ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation. Nat Cell Biol 2021; 23:595-607. [PMID: 34108663 PMCID: PMC8890769 DOI: 10.1038/s41556-021-00688-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. DNA damage-induced binding of the TCR-specific repair factor CSB to RNA polymerase II (RNAPII) triggers RNAPII ubiquitylation of a single lysine (K1268) by the CRL4CSA ubiquitin ligase. How CRL4CSA is specifically directed towards K1268 is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to K1268, revealing ELOF1 as a specificity factor that binds and positions CRL4CSA for optimal RNAPII ubiquitylation. Drug-genetic interaction screening also revealed a CSB-independent pathway in which ELOF1 prevents R-loops in active genes and protects cells against DNA replication stress. Our study offers key insights into the molecular mechanisms of TCR and provides a genetic framework of the interplay between transcriptional stress responses and DNA replication.
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Nagel S, Pommerenke C, Meyer C, Drexler HG. NKL Homeobox Gene VENTX Is Part of a Regulatory Network in Human Conventional Dendritic Cells. Int J Mol Sci 2021; 22:ijms22115902. [PMID: 34072771 PMCID: PMC8198381 DOI: 10.3390/ijms22115902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/27/2021] [Indexed: 01/09/2023] Open
Abstract
Recently, we documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in human myelopoiesis including monocytes and their derived dendritic cells (DCs). Here, we enlarge this map to include normal NKL homeobox gene expressions in progenitor-derived DCs. Analysis of public gene expression profiling and RNA-seq datasets containing plasmacytoid and conventional dendritic cells (pDC and cDC) demonstrated HHEX activity in both entities while cDCs additionally expressed VENTX. The consequent aim of our study was to examine regulation and function of VENTX in DCs. We compared profiling data of VENTX-positive cDC and monocytes with VENTX-negative pDC and common myeloid progenitor entities and revealed several differentially expressed genes encoding transcription factors and pathway components, representing potential VENTX regulators. Screening of RNA-seq data for 100 leukemia/lymphoma cell lines identified prominent VENTX expression in an acute myelomonocytic leukemia cell line, MUTZ-3 containing inv(3)(q21q26) and t(12;22)(p13;q11) and representing a model for DC differentiation studies. Furthermore, extended gene analyses indicated that MUTZ-3 is associated with the subtype cDC2. In addition to analysis of public chromatin immune-precipitation data, subsequent knockdown experiments and modulations of signaling pathways in MUTZ-3 and control cell lines confirmed identified candidate transcription factors CEBPB, ETV6, EVI1, GATA2, IRF2, MN1, SPIB, and SPI1 and the CSF-, NOTCH-, and TNFa-pathways as VENTX regulators. Live-cell imaging analyses of MUTZ-3 cells treated for VENTX knockdown excluded impacts on apoptosis or induced alteration of differentiation-associated cell morphology. In contrast, target gene analysis performed by expression profiling of knockdown-treated MUTZ-3 cells revealed VENTX-mediated activation of several cDC-specific genes including CSFR1, EGR2, and MIR10A and inhibition of pDC-specific genes like RUNX2. Taken together, we added NKL homeobox gene activities for progenitor-derived DCs to the NKL-code, showing that VENTX is expressed in cDCs but not in pDCs and forms part of a cDC-specific gene regulatory network operating in DC differentiation and function.
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NKL-Code in Normal and Aberrant Hematopoiesis. Cancers (Basel) 2021; 13:cancers13081961. [PMID: 33921702 PMCID: PMC8073162 DOI: 10.3390/cancers13081961] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Gene codes represent expression patterns of closely related genes in particular tissues, organs or body parts. The NKL-code describes the activity of NKL homeobox genes in the hematopoietic system. NKL homeobox genes encode transcription factors controlling basic developmental processes. Therefore, aberrations of this code may contribute to deregulated hematopoiesis including leukemia and lymphoma. Normal and abnormal activities of NKL homeobox genes are described and mechanisms of (de)regulation, function, and diseases exemplified. Abstract We have recently described physiological expression patterns of NKL homeobox genes in early hematopoiesis and in subsequent lymphopoiesis and myelopoiesis, including terminally differentiated blood cells. We thereby systematized differential expression patterns of eleven such genes which form the so-called NKL-code. Due to the developmental impact of NKL homeobox genes, these data suggest a key role for their activity in normal hematopoietic differentiation processes. On the other hand, the aberrant overexpression of NKL-code-members or the ectopical activation of non-code members have been frequently reported in lymphoid and myeloid leukemia/lymphoma, revealing the oncogenic potential of these genes in the hematopoietic compartment. Here, I provide an overview of the NKL-code in normal hematopoiesis and instance mechanisms of deregulation and oncogenic functions of selected NKL genes in hematologic cancers. As well as published clinical studies, our conclusions are based on experimental work using hematopoietic cell lines which represent useful models to characterize the role of NKL homeobox genes in specific tumor types.
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Chang L, Ruiz P, Ito T, Sellers WR. Targeting pan-essential genes in cancer: Challenges and opportunities. Cancer Cell 2021; 39:466-479. [PMID: 33450197 PMCID: PMC8157671 DOI: 10.1016/j.ccell.2020.12.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
Despite remarkable successes in the clinic, cancer targeted therapy development remains challenging and the failure rate is disappointingly high. This problem is partly due to the misapplication of the targeted therapy paradigm to therapeutics targeting pan-essential genes, which can result in therapeutics whereby efficacy is attenuated by dose-limiting toxicity. Here we summarize the key features of successful chemotherapy and targeted therapy agents, and use case studies to outline recurrent challenges to drug development efforts targeting pan-essential genes. Finally, we suggest strategies to avoid previous pitfalls for ongoing and future development of pan-essential therapeutics.
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Affiliation(s)
- Liang Chang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Ruiz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Takahiro Ito
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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Paraskevopoulos M, McGuigan AP. Application of CRISPR screens to investigate mammalian cell competition. Brief Funct Genomics 2021; 20:135-147. [PMID: 33782689 DOI: 10.1093/bfgp/elab020] [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: 09/17/2020] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 11/14/2022] Open
Abstract
Cell competition is defined as the context-dependent elimination of cells that is mediated by intercellular communication, such as paracrine or contact-dependent cell signaling, and/or mechanical stresses. It is considered to be a quality control mechanism that facilitates the removal of suboptimal cells from both adult and embryonic tissues. Cell competition, however, can also be hijacked by transformed cells to acquire a 'super-competitor' status and outcompete the normal epithelium to establish a precancerous field. To date, many genetic drivers of cell competition have been identified predominately through studies in Drosophila. Especially during the last couple of years, ethylmethanesulfonate-based genetic screens have been instrumental to our understanding of the molecular regulators behind some of the most common competition mechanisms in Drosophila, namely competition due to impaired ribosomal function (or anabolism) and mechanical sensitivity. Despite recent findings in Drosophila and in mammalian models of cell competition, the drivers of mammalian cell competition remain largely elusive. Since the discovery of CRISPR/Cas9, its use in functional genomics has been indispensable to uncover novel cancer vulnerabilities. We envision that CRISPR/Cas9 screens will enable systematic, genome-scale probing of mammalian cell competition to discover novel mutations that not only trigger cell competition but also identify novel molecular components that are essential for the recognition and elimination of less fit cells. In this review, we summarize recent contributions that further our understanding of the molecular mechanisms of cell competition by genetic screening in Drosophila, and provide our perspective on how similar and novel screening strategies made possible by whole-genome CRISPR/Cas9 screening can advance our understanding of mammalian cell competition in the future.
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Luo H, Lin Y, Liu T, Lai FL, Zhang CT, Gao F, Zhang R. DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools. Nucleic Acids Res 2021; 49:D677-D686. [PMID: 33095861 PMCID: PMC7779065 DOI: 10.1093/nar/gkaa917] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/30/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022] Open
Abstract
Essential genes refer to genes that are required by an organism to survive under specific conditions. Studies of the minimal-gene-set for bacteria have elucidated fundamental cellular processes that sustain life. The past five years have seen a significant progress in identifying human essential genes, primarily due to the successful use of CRISPR/Cas9 in various types of human cells. DEG 15, a new release of the Database of Essential Genes (www.essentialgene.org), has provided major advancements, compared to DEG 10. Specifically, the number of eukaryotic essential genes has increased by more than fourfold, and that of prokaryotic ones has more than doubled. Of note, the human essential-gene number has increased by more than tenfold. Moreover, we have developed built-in analysis modules by which users can perform various analyses, such as essential-gene distributions between bacterial leading and lagging strands, sub-cellular localization distribution, enrichment analysis of gene ontology and KEGG pathways, and generation of Venn diagrams to compare and contrast gene sets between experiments. Additionally, the database offers customizable BLAST tools for performing species- and experiment-specific BLAST searches. Therefore, DEG comprehensively harbors updated human-curated essential-gene records among prokaryotes and eukaryotes with built-in tools to enhance essential-gene analysis.
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Affiliation(s)
- Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Yan Lin
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Tao Liu
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Fei-Liao Lai
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Chun-Ting Zhang
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Ren Zhang
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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McKee C, Brown C, Bakshi S, Walker K, Govind CK, Chaudhry GR. Transcriptomic Analysis of Naïve Human Embryonic Stem Cells Cultured in Three-Dimensional PEG Scaffolds. Biomolecules 2020; 11:E21. [PMID: 33379237 PMCID: PMC7824559 DOI: 10.3390/biom11010021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/24/2020] [Indexed: 12/21/2022] Open
Abstract
Naïve human embryonic stem cells (ESCs) are characterized by improved viability, proliferation, and differentiation capacity in comparison to traditionally derived primed human ESCs. However, currently used two-dimensional (2-D) cell culture techniques fail to mimic the three-dimensional (3-D) in vivo microenvironment, altering morphological and molecular characteristics of ESCs. Here, we describe the use of 3-D self-assembling scaffolds that support growth and maintenance of the naïve state characteristics of ESC line, Elf1. Scaffolds were formed via a Michael addition reaction upon the combination of two 8-arm polyethylene glycol (PEG) polymers functionalized with thiol (PEG-8-SH) and acrylate (PEG-8-Acr) end groups. 3-D scaffold environment maintained the naïve state and supported the long-term growth of ESCs. RNA-sequencing demonstrated significant changes in gene expression profiles between 2-D and 3-D grown cells. Gene ontology analysis revealed upregulation of biological processes involved in the regulation of transcription and translation, extracellular matrix organization, and chromatin remodeling in 3-D grown cells. 3-D culture conditions also induced upregulation of genes associated with Wnt and focal adhesion signaling, while p53 signaling pathway associated genes were downregulated. Our findings, for the first time, provide insight into the possible mechanisms of self-renewal of naïve ESCs stimulated by the transduction of mechanical signals from the 3-D microenvironment.
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Affiliation(s)
- Christina McKee
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - Christina Brown
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - Shreeya Bakshi
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - Keegan Walker
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - Chhabi K. Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - G. Rasul Chaudhry
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
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Xu X, Du Y, Ma L, Zhang S, Shi L, Chen Z, Zhou Z, Hui Y, Liu Y, Fang Y, Fan B, Liu Z, Li N, Zhou S, Jiang C, Liu L, Zhang X. Mapping germ-layer specification preventing genes in hPSCs via genome-scale CRISPR screening. iScience 2020; 24:101926. [PMID: 33385119 PMCID: PMC7772566 DOI: 10.1016/j.isci.2020.101926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/17/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological processes that determine the entry of three germ layers of human pluripotent stem cells (hPSCs) is a central question in developmental and stem cell biology. Here, we genetically engineered hPSCs with the germ layer reporter and inducible CRISPR/Cas9 knockout system, and a genome-scale screening was performed to define pathways restricting germ layer specification. Genes clustered in the key biological processes, including embryonic development, mRNA processing, metabolism, and epigenetic regulation, were centered in the governance of pluripotency and lineage development. Other than typical pluripotent transcription factors and signaling molecules, loss of function of mesendodermal specifiers resulted in advanced neuroectodermal differentiation, given their inter-germ layer antagonizing effect. Regarding the epigenetic superfamily, microRNAs enriched in hPSCs showed clear germ layer-targeting specificity. The cholesterol synthesis pathway maintained hPSCs via retardation of neuroectoderm specification. Thus, in this study, we identified a full landscape of genetic wiring and biological processes that control hPSC self-renewal and trilineage specification. Lineage reporter and CRISPR screening are powerful tools for studying cell fates Lineage-specification preventing genes (LPGs) are identified in hPSCs LPGs maintain pluripotency via targeting one or multiple germ layers LPGs are clustered into distinct functional modules
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Affiliation(s)
- Xiangjie Xu
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yanhua Du
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lin Ma
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
- Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Shuwei Zhang
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Lei Shi
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Zhenyu Chen
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Zhongshu Zhou
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yi Hui
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yang Liu
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yujiang Fang
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
- Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Beibei Fan
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Zhongliang Liu
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Nan Li
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Shanshan Zhou
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Cizhong Jiang
- The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ling Liu
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
- Brain and Spinal Cord Clinical Research Center, Tongji University School of Medicine, Shanghai 200092, China
- Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
- Corresponding author
| | - Xiaoqing Zhang
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Reconstruction and Regeneration of Spine and Spinal Cord Injury, Ministry of Education, Shanghai 200065, China
- Key Laboratory of Neuroregeneration of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
- Tsingtao Advanced Research Institute, Tongji University, Qingdao 266071, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
- Brain and Spinal Cord Clinical Research Center, Tongji University School of Medicine, Shanghai 200092, China
- Corresponding author
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Lawson KA, Sousa CM, Zhang X, Kim E, Akthar R, Caumanns JJ, Yao Y, Mikolajewicz N, Ross C, Brown KR, Zid AA, Fan ZP, Hui S, Krall JA, Simons DM, Slater CJ, De Jesus V, Tang L, Singh R, Goldford JE, Martin S, Huang Q, Francis EA, Habsid A, Climie R, Tieu D, Wei J, Li R, Tong AHY, Aregger M, Chan KS, Han H, Wang X, Mero P, Brumell JH, Finelli A, Ailles L, Bader G, Smolen GA, Kingsbury GA, Hart T, Kung C, Moffat J. Functional genomic landscape of cancer-intrinsic evasion of killing by T cells. Nature 2020; 586:120-126. [PMID: 32968282 DOI: 10.1038/s41586-020-2746-2] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 06/30/2020] [Indexed: 01/05/2023]
Abstract
The genetic circuits that allow cancer cells to evade destruction by the host immune system remain poorly understood1-3. Here, to identify a phenotypically robust core set of genes and pathways that enable cancer cells to evade killing mediated by cytotoxic T lymphocytes (CTLs), we performed genome-wide CRISPR screens across a panel of genetically diverse mouse cancer cell lines that were cultured in the presence of CTLs. We identify a core set of 182 genes across these mouse cancer models, the individual perturbation of which increases either the sensitivity or the resistance of cancer cells to CTL-mediated toxicity. Systematic exploration of our dataset using genetic co-similarity reveals the hierarchical and coordinated manner in which genes and pathways act in cancer cells to orchestrate their evasion of CTLs, and shows that discrete functional modules that control the interferon response and tumour necrosis factor (TNF)-induced cytotoxicity are dominant sub-phenotypes. Our data establish a central role for genes that were previously identified as negative regulators of the type-II interferon response (for example, Ptpn2, Socs1 and Adar1) in mediating CTL evasion, and show that the lipid-droplet-related gene Fitm2 is required for maintaining cell fitness after exposure to interferon-γ (IFNγ). In addition, we identify the autophagy pathway as a conserved mediator of the evasion of CTLs by cancer cells, and show that this pathway is required to resist cytotoxicity induced by the cytokines IFNγ and TNF. Through the mapping of cytokine- and CTL-based genetic interactions, together with in vivo CRISPR screens, we show how the pleiotropic effects of autophagy control cancer-cell-intrinsic evasion of killing by CTLs and we highlight the importance of these effects within the tumour microenvironment. Collectively, these data expand our knowledge of the genetic circuits that are involved in the evasion of the immune system by cancer cells, and highlight genetic interactions that contribute to phenotypes associated with escape from killing by CTLs.
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Affiliation(s)
- Keith A Lawson
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Xiaoyu Zhang
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Eiru Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rummy Akthar
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Yuxi Yao
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Catherine Ross
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Abdelrahman Abou Zid
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | | | - Shirley Hui
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | - Lujia Tang
- Agios Pharmaceuticals, Cambridge, MA, USA
| | | | | | | | - Qian Huang
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | | | - Andrea Habsid
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ryan Climie
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - David Tieu
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jiarun Wei
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ren Li
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amy Hin Yan Tong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Michael Aregger
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Katherine S Chan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Hong Han
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Xiaowei Wang
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Mero
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - John H Brumell
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Antonio Finelli
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laurie Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gary Bader
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gromoslaw A Smolen
- Agios Pharmaceuticals, Cambridge, MA, USA.,Celsius Therapeutics, Cambridge, MA, USA
| | | | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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Abstract
Human pluripotent stem cells harbor the capacity to differentiate into cells from the three embryonic germ layers, and this ability grants them a central role in modeling human disorders and in the field of regenerative medicine. Here, we review pluripotency in human cells with respect to four different aspects: (1) embryonic development, (2) transcriptomes of pluripotent cell stages, (3) genes and pathways that reprogram somatic cells into pluripotent stem cells, and finally (4) the recent identification of the human pluripotent stem cell essentialome. These four aspects of pluripotency collectively culminate in a broader understanding of what makes a cell pluripotent.
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47
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Iyer VS, Jiang L, Shen Y, Boddul SV, Panda SK, Kasza Z, Schmierer B, Wermeling F. Designing custom CRISPR libraries for hypothesis-driven drug target discovery. Comput Struct Biotechnol J 2020; 18:2237-2246. [PMID: 32952937 PMCID: PMC7479249 DOI: 10.1016/j.csbj.2020.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/24/2020] [Accepted: 08/09/2020] [Indexed: 12/20/2022] Open
Abstract
Over the last decade Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) has been developed into a potent molecular biology tool used to rapidly modify genes or their expression in a multitude of ways. In parallel, CRISPR-based screening approaches have been developed as powerful discovery platforms for dissecting the genetic basis of cellular behavior, as well as for drug target discovery. CRISPR screens can be designed in numerous ways. Here, we give a brief background to CRISPR screens and discuss the pros and cons of different design approaches, including unbiased genome-wide screens that target all known genes, as well as hypothesis-driven custom screens in which selected subsets of genes are targeted (Fig. 1). We provide several suggestions for how a custom screen can be designed, which could broadly serve as inspiration for any experiment that includes candidate gene selection. Finally, we discuss how results from CRISPR screens could be translated into drug development, as well as future trends we foresee in the rapidly evolving CRISPR screen field.
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Affiliation(s)
- Vaishnavi Srinivasan Iyer
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Long Jiang
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Yunbing Shen
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sanjaykumar V Boddul
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sudeepta Kumar Panda
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Zsolt Kasza
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Bernhard Schmierer
- High Throughput Genome Engineering, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Fredrik Wermeling
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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48
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Yilmaz A, Braverman-Gross C, Bialer-Tsypin A, Peretz M, Benvenisty N. Mapping Gene Circuits Essential for Germ Layer Differentiation via Loss-of-Function Screens in Haploid Human Embryonic Stem Cells. Cell Stem Cell 2020; 27:679-691.e6. [PMID: 32735778 DOI: 10.1016/j.stem.2020.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/19/2020] [Accepted: 06/24/2020] [Indexed: 12/22/2022]
Abstract
Pluripotent stem cells can differentiate into all embryonic germ layers, yet the genes essential for these cell fate transitions in human remain elusive. Here, we mapped the essential genes for the differentiation of human pluripotent stem cells (hPSCs) into the three germ layers by using a genome-wide loss-of-function library established in haploid hPSCs. Strikingly, we observed a high fraction of essential genes associated with plasma membrane, highlighting signaling pathways needed for each lineage differentiation. Interestingly, analysis of all hereditary neurological disorders uncovered high essentiality among microcephaly-causing genes. Furthermore, we demonstrated lineage-specific hierarchies among essential transcription factors and a set of Golgi- and endoplasmic reticulum-related genes needed for the differentiation into all germ layers. Our work sheds light on the gene networks regulating early gastrulation events in human by defining essential drivers of specific embryonic germ layer fates and essential genes for the exit from pluripotency.
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Affiliation(s)
- Atilgan Yilmaz
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Carmel Braverman-Gross
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Anna Bialer-Tsypin
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Mordecai Peretz
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
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49
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Marderstein AR, Uppal M, Verma A, Bhinder B, Tayyebi Z, Mezey J, Clark AG, Elemento O. Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues. Nat Commun 2020; 11:2213. [PMID: 32371927 PMCID: PMC7200670 DOI: 10.1038/s41467-020-16097-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 04/13/2020] [Indexed: 12/12/2022] Open
Abstract
Despite infiltrating immune cells having an essential function in human disease and patients' responses to treatments, mechanisms influencing variability in infiltration patterns remain unclear. Here, using bulk RNA-seq data from 46 tissues in the Genotype-Tissue Expression project, we apply cell-type deconvolution algorithms to evaluate the immune landscape across the healthy human body. We discover that 49 of 189 infiltration-related phenotypes are associated with either age or sex (FDR < 0.1). Genetic analyses further show that 31 infiltration-related phenotypes have genome-wide significant associations (iQTLs) (P < 5.0 × 10-8), with a significant enrichment of same-tissue expression quantitative trait loci in suggested iQTLs (P < 10-5). Furthermore, we find an association between helper T cell content in thyroid tissue and a COMMD3/DNAJC1 regulatory variant (P = 7.5 × 10-10), which is associated with thyroiditis in other cohorts. Together, our results identify key factors influencing inter-individual variability of immune infiltration, to provide insights on potential therapeutic targets.
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Affiliation(s)
- Andrew R Marderstein
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Manik Uppal
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Akanksha Verma
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bhavneet Bhinder
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zakieh Tayyebi
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason Mezey
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Andrew G Clark
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA.
- Department of Computational Biology, Cornell University, Ithaca, NY, USA.
| | - Olivier Elemento
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA.
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
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50
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Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, Ha KCH, Weiss A, Billmann M, Durbic T, Myers CL, Blencowe BJ, Moffat J. Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform. Nat Biotechnol 2020; 38:638-648. [PMID: 32249828 DOI: 10.1038/s41587-020-0437-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Systematic mapping of genetic interactions (GIs) and interrogation of the functions of sizable genomic segments in mammalian cells represent important goals of biomedical research. To advance these goals, we present a CRISPR (clustered regularly interspaced short palindromic repeats)-based screening system for combinatorial genetic manipulation that employs coexpression of CRISPR-associated nucleases 9 and 12a (Cas9 and Cas12a) and machine-learning-optimized libraries of hybrid Cas9-Cas12a guide RNAs. This system, named Cas Hybrid for Multiplexed Editing and screening Applications (CHyMErA), outperforms genetic screens using Cas9 or Cas12a editing alone. Application of CHyMErA to the ablation of mammalian paralog gene pairs reveals extensive GIs and uncovers phenotypes normally masked by functional redundancy. Application of CHyMErA in a chemogenetic interaction screen identifies genes that impact cell growth in response to mTOR pathway inhibition. Moreover, by systematically targeting thousands of alternative splicing events, CHyMErA identifies exons underlying human cell line fitness. CHyMErA thus represents an effective screening approach for GI mapping and the functional analysis of sizable genomic regions, such as alternative exons.
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Affiliation(s)
| | - Michael Aregger
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Tanja Durbic
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Chad L Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Institute for Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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