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Liu LL, Yin YQ, Ma KX, Xing JC, Ren XX, Huang JY, Liao M, Qi WB, Huang LH. Identification critical host factors for Japanese encephalitis virus replication via CRISPR screening of human sgRNA library. Vet Microbiol 2024; 293:110099. [PMID: 38677125 DOI: 10.1016/j.vetmic.2024.110099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 04/29/2024]
Abstract
Japanese encephalitis virus (JEV) is a pathogen with a substantial impact on both livestock and human health. However, the critical host factors in the virus life cycle remain poorly understood. Using a library comprising 123411 small guide RNAs (sgRNAs) targeting 19050 human genes, we conducted a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based screen to identify essential genes for JEV replication. By employing knockout or knockdown techniques on genes, we identified eleven human genes crucial for JEV replication, such as prolactin releasing hormone receptor (PRLHR), activating signal cointegrator 1 complex subunit 3 (ASCC3), acyl-CoA synthetase long chain family member 3 (ACSL3), and others. Notably, we found that PRLHR knockdown blocked the autophagic flux, thereby inhibiting JEV infection. Taken together, these findings provide effective data for studying important host factors of JEV replication and scientific data for selecting antiviral drug targets.
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Affiliation(s)
- Le-le Liu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - You-Qin Yin
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Kai-Xiong Ma
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Jin-Chao Xing
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Xing-Xing Ren
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Jin-Yu Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Ming Liao
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Wen-Bao Qi
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China.
| | - Li-Hong Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China.
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2
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Lampson BL, Ramίrez AS, Baro M, He L, Hegde M, Koduri V, Pfaff JL, Hanna RE, Kowal J, Shirole NH, He Y, Doench JG, Contessa JN, Locher KP, Kaelin WG. Positive selection CRISPR screens reveal a druggable pocket in an oligosaccharyltransferase required for inflammatory signaling to NF-κB. Cell 2024; 187:2209-2223.e16. [PMID: 38670073 DOI: 10.1016/j.cell.2024.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/29/2023] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
Abstract
Nuclear factor κB (NF-κB) plays roles in various diseases. Many inflammatory signals, such as circulating lipopolysaccharides (LPSs), activate NF-κB via specific receptors. Using whole-genome CRISPR-Cas9 screens of LPS-treated cells that express an NF-κB-driven suicide gene, we discovered that the LPS receptor Toll-like receptor 4 (TLR4) is specifically dependent on the oligosaccharyltransferase complex OST-A for N-glycosylation and cell-surface localization. The tool compound NGI-1 inhibits OST complexes in vivo, but the underlying molecular mechanism remained unknown. We did a CRISPR base-editor screen for NGI-1-resistant variants of STT3A, the catalytic subunit of OST-A. These variants, in conjunction with cryoelectron microscopy studies, revealed that NGI-1 binds the catalytic site of STT3A, where it traps a molecule of the donor substrate dolichyl-PP-GlcNAc2-Man9-Glc3, suggesting an uncompetitive inhibition mechanism. Our results provide a rationale for and an initial step toward the development of STT3A-specific inhibitors and illustrate the power of contemporaneous base-editor and structural studies to define drug mechanism of action.
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Affiliation(s)
- Benjamin L Lampson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Ana S Ramίrez
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Marta Baro
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Lixia He
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute, Cambridge, MA 02142, USA
| | - Vidyasagar Koduri
- Division of Hematology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Jamie L Pfaff
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute, Cambridge, MA 02142, USA
| | - Julia Kowal
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Nitin H Shirole
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Yanfeng He
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute, Cambridge, MA 02142, USA
| | - Joseph N Contessa
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA.
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Li X, Sun S, Zhang W, Liang Z, Fang Y, Sun T, Wan Y, Ma X, Zhang S, Xu Y, Tian R. Identification of genetic modifiers enhancing B7-H3-targeting CAR T cell therapy against glioblastoma through large-scale CRISPRi screening. J Exp Clin Cancer Res 2024; 43:95. [PMID: 38561797 PMCID: PMC10986136 DOI: 10.1186/s13046-024-03027-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is a highly aggressive brain tumor with a poor prognosis. Current treatment options are limited and often ineffective. CAR T cell therapy has shown success in treating hematologic malignancies, and there is growing interest in its potential application in solid tumors, including GBM. However, current CAR T therapy lacks clinical efficacy against GBM due to tumor-related resistance mechanisms and CAR T cell deficiencies. Therefore, there is a need to improve CAR T cell therapy efficacy in GBM. METHODS We conducted large-scale CRISPR interference (CRISPRi) screens in GBM cell line U87 MG cells co-cultured with B7-H3 targeting CAR T cells to identify genetic modifiers that can enhance CAR T cell-mediated tumor killing. Flow cytometry-based tumor killing assay and CAR T cell activation assay were performed to validate screening hits. Bioinformatic analyses on bulk and single-cell RNA sequencing data and the TCGA database were employed to elucidate the mechanism underlying enhanced CAR T efficacy upon knocking down the selected screening hits in U87 MG cells. RESULTS We established B7-H3 as a targetable antigen for CAR T therapy in GBM. Through large-scale CRISPRi screening, we discovered genetic modifiers in GBM cells, including ARPC4, PI4KA, ATP6V1A, UBA1, and NDUFV1, that regulated the efficacy of CAR T cell-mediated tumor killing. Furthermore, we discovered that TNFSF15 was upregulated in both ARPC4 and NDUFV1 knockdown GBM cells and revealed an immunostimulatory role of TNFSF15 in modulating tumor-CAR T interaction to enhance CAR T cell efficacy. CONCLUSIONS Our study highlights the power of CRISPR-based genetic screening in investigating tumor-CAR T interaction and identifies potential druggable targets in tumor cells that confer resistance to CAR T cell killing. Furthermore, we devised targeted strategies that synergize with CAR T therapy against GBM. These findings shed light on the development of novel combinatorial strategies for effective immunotherapy of GBM and other solid tumors.
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Affiliation(s)
- Xing Li
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Shiyu Sun
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710004, China
| | - Wansong Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Ziwei Liang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Yitong Fang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Tianhu Sun
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Yong Wan
- Department of Neurosurgery, Shenzhen People's Hospital, Shenzhen, Guangdong, 518020, China
| | - Xingcong Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710004, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710004, China.
| | - Yang Xu
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China.
| | - Ruilin Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China.
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China.
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Noguchi Y, Onodera Y, Miyamoto T, Maruoka M, Kosako H, Suzuki J. In vivo CRISPR screening directly targeting testicular cells. Cell Genom 2024; 4:100510. [PMID: 38447574 PMCID: PMC10943590 DOI: 10.1016/j.xgen.2024.100510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/10/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
CRISPR-Cas9 short guide RNA (sgRNA) library screening is a powerful approach to understand the molecular mechanisms of biological phenomena. However, its in vivo application is currently limited. Here, we developed our previously established in vitro revival screening method into an in vivo one to identify factors involved in spermatogenesis integrity by utilizing sperm capacitation as an indicator. By introducing an sgRNA library into testicular cells, we successfully pinpointed the retinal degeneration 3 (Rd3) gene as a significant factor in spermatogenesis. Single-cell RNA sequencing (scRNA-seq) analysis highlighted the high expression of Rd3 in round spermatids, and proteomics analysis indicated that Rd3 interacts with mitochondria. To search for cell-type-specific signaling pathways based on scRNA-seq and proteomics analyses, we developed a computational tool, Hub-Explorer. Through this, we discovered that Rd3 modulates oxidative stress by regulating mitochondrial distribution upon ciliogenesis induction. Collectively, our screening system provides a valuable in vivo approach to decipher molecular mechanisms in biological processes.
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Affiliation(s)
- Yuki Noguchi
- Graduate School of Biostudies, Kyoto University, Konoe-cho, Yoshida, Sakyoku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan
| | - Yasuhito Onodera
- Global Center for Biomedical Science and Engineering, Faculty of Medicine, Hokkaido University, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Tatsuo Miyamoto
- Department of Molecular and Cellular Physiology, Yamaguchi University, Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
| | - Masahiro Maruoka
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan; Center for Integrated Biosystems, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Jun Suzuki
- Graduate School of Biostudies, Kyoto University, Konoe-cho, Yoshida, Sakyoku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan; Center for Integrated Biosystems, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.
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5
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Hazan JM, Amador R, Ali-Nasser T, Lahav T, Shotan SR, Steinberg M, Cohen Z, Aran D, Meiri D, Assaraf YG, Guigó R, Bester AC. Integration of transcription regulation and functional genomic data reveals lncRNA SNHG6's role in hematopoietic differentiation and leukemia. J Biomed Sci 2024; 31:27. [PMID: 38419051 PMCID: PMC10900714 DOI: 10.1186/s12929-024-01015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are pivotal players in cellular processes, and their unique cell-type specific expression patterns render them attractive biomarkers and therapeutic targets. Yet, the functional roles of most lncRNAs remain enigmatic. To address the need to identify new druggable lncRNAs, we developed a comprehensive approach integrating transcription factor binding data with other genetic features to generate a machine learning model, which we have called INFLAMeR (Identifying Novel Functional LncRNAs with Advanced Machine Learning Resources). METHODS INFLAMeR was trained on high-throughput CRISPR interference (CRISPRi) screens across seven cell lines, and the algorithm was based on 71 genetic features. To validate the predictions, we selected candidate lncRNAs in the human K562 leukemia cell line and determined the impact of their knockdown (KD) on cell proliferation and chemotherapeutic drug response. We further performed transcriptomic analysis for candidate genes. Based on these findings, we assessed the lncRNA small nucleolar RNA host gene 6 (SNHG6) for its role in myeloid differentiation. Finally, we established a mouse K562 leukemia xenograft model to determine whether SNHG6 KD attenuates tumor growth in vivo. RESULTS The INFLAMeR model successfully reconstituted CRISPRi screening data and predicted functional lncRNAs that were previously overlooked. Intensive cell-based and transcriptomic validation of nearly fifty genes in K562 revealed cell type-specific functionality for 85% of the predicted lncRNAs. In this respect, our cell-based and transcriptomic analyses predicted a role for SNHG6 in hematopoiesis and leukemia. Consistent with its predicted role in hematopoietic differentiation, SNHG6 transcription is regulated by hematopoiesis-associated transcription factors. SNHG6 KD reduced the proliferation of leukemia cells and sensitized them to differentiation. Treatment of K562 leukemic cells with hemin and PMA, respectively, demonstrated that SNHG6 inhibits red blood cell differentiation but strongly promotes megakaryocyte differentiation. Using a xenograft mouse model, we demonstrate that SNHG6 KD attenuated tumor growth in vivo. CONCLUSIONS Our approach not only improved the identification and characterization of functional lncRNAs through genomic approaches in a cell type-specific manner, but also identified new lncRNAs with roles in hematopoiesis and leukemia. Such approaches can be readily applied to identify novel targets for precision medicine.
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Affiliation(s)
- Joshua M Hazan
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Raziel Amador
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Tahleel Ali-Nasser
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Tamar Lahav
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Stav Roni Shotan
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Miryam Steinberg
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Ziv Cohen
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
- The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Dvir Aran
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
- The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - David Meiri
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Assaf C Bester
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel.
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6
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Zhang B, Chen Y, Chen X, Ren Z, Xiang H, Mao L, Zhu G. Genome-wide CRISPR screen identifies ESPL1 limits the response of gastric cancer cells to apatinib. Cancer Cell Int 2024; 24:83. [PMID: 38402402 PMCID: PMC10893712 DOI: 10.1186/s12935-024-03233-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/19/2024] [Indexed: 02/26/2024] Open
Abstract
Apatinib was the first anti-angiogenic agent approved for treatment of metastatic gastric cancer (GC). However, the emergence of resistance was inevitable. Thus investigating new and valuable off-target effect of apatinib directly against cancer cells is of great significance. Here, we identified extra spindle pole bodies-like 1 (ESPL1) was responsible for apatinib resistance in GC cells through CRISPR genome-wide gain-of-function screening. Loss of function studies further showed that ESPL1 inhibition suppressed cell proliferation, migration and promoted apoptosis in vitro, and accordingly ESPL1 knockdown sensitized GC cells to apatinib. In addition, we found ESPL1 interacted with mouse double minute 2 (MDM2), a E3 ubiquitin protein ligase, and the combination of MDM2 siRNA with apatinib synergistically ameliorated the resistance induced by ESPL1 overexpression. In summary, our study indicated that ESPL1 played a critical role in apatinib resistance in GC cells. Inhibition of MDM2 could rescue the sensitivity of GC cells to apatinib and reverse ESPL1-mediated resistance.
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Affiliation(s)
- Bei Zhang
- Institute of Gerontology, Guangzhou Geriatric Hospital, Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Geriatric Hospital, Guangzhou Medical University, Guangzhou, China
- Collaborative Innovation Center for Civil Affairs of Guangzhou, Guangzhou, China
| | - Yan Chen
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinqi Chen
- Department of Oncology, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Zhiyao Ren
- Institute of Gerontology, Guangzhou Geriatric Hospital, Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Geriatric Hospital, Guangzhou Medical University, Guangzhou, China
- Collaborative Innovation Center for Civil Affairs of Guangzhou, Guangzhou, China
| | - Hong Xiang
- Departments of Oncology, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Lipeng Mao
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
| | - Guodong Zhu
- Institute of Gerontology, Guangzhou Geriatric Hospital, Guangzhou Medical University, Guangzhou, China.
- State Key Laboratory of Respiratory Disease, Guangzhou Geriatric Hospital, Guangzhou Medical University, Guangzhou, China.
- Collaborative Innovation Center for Civil Affairs of Guangzhou, Guangzhou, China.
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7
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Heo SJ, Enriquez LD, Federman S, Chang AY, Mace R, Shevade K, Nguyen P, Litterman AJ, Shafer S, Przybyla L, Chow ED. Compact CRISPR genetic screens enabled by improved guide RNA library cloning. Genome Biol 2024; 25:25. [PMID: 38243310 PMCID: PMC10797759 DOI: 10.1186/s13059-023-03132-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/29/2023] [Indexed: 01/21/2024] Open
Abstract
CRISPR genome editing approaches theoretically enable researchers to define the function of each human gene in specific cell types, but challenges remain to efficiently perform genetic perturbations in relevant models. In this work, we develop a library cloning protocol that increases sgRNA uniformity and greatly reduces bias in existing genome-wide libraries. We demonstrate that our libraries can achieve equivalent or better statistical power compared to previously reported screens using an order of magnitude fewer cells. This improved cloning protocol enables genome-scale CRISPR screens in technically challenging cell models and screen formats.
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Affiliation(s)
- Seok-Jin Heo
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Lauren D Enriquez
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Scot Federman
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Amy Y Chang
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Rachel Mace
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Kaivalya Shevade
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Phuong Nguyen
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Adam J Litterman
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Shawn Shafer
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- GSK, San Francisco, CA, 94158, USA
| | - Laralynne Przybyla
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Eric D Chow
- Laboratory for Genomics Research, San Francisco, CA, 94158, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA.
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8
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Li X, Chen Z, Ye W, Yu J, Zhang X, Li Y, Niu Y, Ran S, Wang S, Luo Z, Zhao J, Hao Y, Zong J, Xia C, Xia J, Wu J. High-throughput CRISPR technology: a novel horizon for solid organ transplantation. Front Immunol 2024; 14:1295523. [PMID: 38239344 PMCID: PMC10794540 DOI: 10.3389/fimmu.2023.1295523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024] Open
Abstract
Organ transplantation is the gold standard therapy for end-stage organ failure. However, the shortage of available grafts and long-term graft dysfunction remain the primary barriers to organ transplantation. Exploring approaches to solve these issues is urgent, and CRISPR/Cas9-based transcriptome editing provides one potential solution. Furthermore, combining CRISPR/Cas9-based gene editing with an ex vivo organ perfusion system would enable pre-implantation transcriptome editing of grafts. How to determine effective intervention targets becomes a new problem. Fortunately, the advent of high-throughput CRISPR screening has dramatically accelerated the effective targets. This review summarizes the current advancements, utilization, and workflow of CRISPR screening in various immune and non-immune cells. It also discusses the ongoing applications of CRISPR/Cas-based gene editing in transplantation and the prospective applications of CRISPR screening in solid organ transplantation.
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Affiliation(s)
- Xiaohan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhang Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weicong Ye
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizhang Yu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Zhang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqing Niu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuan Ran
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Song Wang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zilong Luo
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiulu Zhao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanglin Hao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junjie Zong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengkun Xia
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Xia
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Jie Wu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
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9
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Zhao Y, Yuan J, Xiao D, Zhang L, Li C, Hu J, Chen R, Song D, Wen Y, Wu R, Zhao Q, Du S, Yan Q, Han X, Wen X, Cao S, Huang X. HSP90AB1 is a host factor that promotes porcine deltacoronavirus replication. J Biol Chem 2024; 300:105536. [PMID: 38092149 PMCID: PMC10789647 DOI: 10.1016/j.jbc.2023.105536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus. It causes mortality in neonatal piglets and is of growing concern because of its broad host range, including humans. To date, the mechanism of PDCoV infection remains poorly understood. Here, based on a genome-wide CRISPR screen of PDCoV-infected cells, we found that HSP90AB1 (heat shock protein 90 alpha family class B1) promotes PDCoV infection. Knockdown or KO of HSP90AB1 in LLC-PK cells resulted in a significantly suppressed PDCoV infection. Infected cells treated with HSP90 inhibitors 17-AAG and VER-82576 also showed a significantly suppressed PDCoV infection, although KW-2478, which does not affect the ATPase activity of HSP90AB1, had no effect on PDCoV infection. We found that HSP90AB1 interacts with the N, NS7, and NSP10 proteins of PDCoV. We further evaluated the interaction between N and HSP90AB1 and found that the C-tail domain of the N protein is the HSP90AB1-interacting domain. Further studies showed that HSP90AB1 protects N protein from degradation via the proteasome pathway. In summary, our results reveal a key role for HSP90AB1 in the mechanism of PDCoV infection and contribute to provide new host targets for PDCoV antiviral research.
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Affiliation(s)
- Yujia Zhao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China; Laboratory Animal Center, Zunyi Medical University, Zunyi, China
| | - Jianlin Yuan
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dai Xiao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Luwen Zhang
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Cheng Li
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jingfei Hu
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Rui Chen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Daili Song
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yiping Wen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Rui Wu
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qin Zhao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Senyan Du
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qigui Yan
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinfeng Han
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xintian Wen
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sanjie Cao
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China; Sichuan Science-Observation Experiment Station for Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, China; National Animal Experiments Teaching Demonstration Center, Sichuan Agricultural University, Chengdu, China
| | - Xiaobo Huang
- Research Center for Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China; Sichuan Science-Observation Experiment Station for Veterinary Drugs and Veterinary Diagnostic Technology, Ministry of Agriculture, Chengdu, China; National Animal Experiments Teaching Demonstration Center, Sichuan Agricultural University, Chengdu, China.
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10
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Carreras-Sureda A, Zhang X, Laubry L, Brunetti J, Koenig S, Wang X, Castelbou C, Hetz C, Liu Y, Frieden M, Demaurex N. The ER stress sensor IRE1 interacts with STIM1 to promote store-operated calcium entry, T cell activation, and muscular differentiation. Cell Rep 2023; 42:113540. [PMID: 38060449 DOI: 10.1016/j.celrep.2023.113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Store-operated Ca2+ entry (SOCE) mediated by stromal interacting molecule (STIM)-gated ORAI channels at endoplasmic reticulum (ER) and plasma membrane (PM) contact sites maintains adequate levels of Ca2+ within the ER lumen during Ca2+ signaling. Disruption of ER Ca2+ homeostasis activates the unfolded protein response (UPR) to restore proteostasis. Here, we report that the UPR transducer inositol-requiring enzyme 1 (IRE1) interacts with STIM1, promotes ER-PM contact sites, and enhances SOCE. IRE1 deficiency reduces T cell activation and human myoblast differentiation. In turn, STIM1 deficiency reduces IRE1 signaling after store depletion. Using a CaMPARI2-based Ca2+ genome-wide screen, we identify CAMKG2 and slc105a as SOCE enhancers during ER stress. Our findings unveil a direct crosstalk between SOCE and UPR via IRE1, acting as key regulator of ER Ca2+ and proteostasis in T cells and muscles. Under ER stress, this IRE1-STIM1 axis boosts SOCE to preserve immune cell functions, a pathway that could be targeted for cancer immunotherapy.
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Affiliation(s)
- Amado Carreras-Sureda
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.
| | - Xin Zhang
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Loann Laubry
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Jessica Brunetti
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Stéphane Koenig
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Xiaoxia Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Cyril Castelbou
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Claudio Hetz
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP Center for Geroscience (GERO), Brain Health and Metabolism, Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Yong Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Maud Frieden
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Nicolas Demaurex
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
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11
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Shimizu T, Oike A, Kobayashi EH, Sekiya A, Kobayashi N, Shibata S, Hamada H, Saito M, Yaegashi N, Suyama M, Arima T, Okae H. CRISPR screening in human trophoblast stem cells reveals both shared and distinct aspects of human and mouse placental development. Proc Natl Acad Sci U S A 2023; 120:e2311372120. [PMID: 38085778 PMCID: PMC10742386 DOI: 10.1073/pnas.2311372120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
The placenta serves as the interface between the mother and fetus, facilitating the exchange of gases and nutrients between their separate blood circulation systems. Trophoblasts in the placenta play a central role in this process. Our current understanding of mammalian trophoblast development relies largely on mouse models. However, given the diversification of mammalian placentas, findings from the mouse placenta cannot be readily extrapolated to other mammalian species, including humans. To fill this knowledge gap, we performed CRISPR knockout screening in human trophoblast stem cells (hTSCs). We targeted genes essential for mouse placental development and identified more than 100 genes as critical regulators in both human hTSCs and mouse placentas. Among them, we further characterized in detail two transcription factors, DLX3 and GCM1, and revealed their essential roles in hTSC differentiation. Moreover, a gene function-based comparison between human and mouse trophoblast subtypes suggests that their relationship may differ significantly from previous assumptions based on tissue localization or cellular function. Notably, our data reveal that hTSCs may not be analogous to mouse TSCs or the extraembryonic ectoderm (ExE) in which in vivo TSCs reside. Instead, hTSCs may be analogous to progenitor cells in the mouse ectoplacental cone and chorion. This finding is consistent with the absence of ExE-like structures during human placental development. Our data not only deepen our understanding of human trophoblast development but also facilitate cross-species comparison of mammalian placentas.
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Affiliation(s)
- Takanori Shimizu
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
| | - Akira Oike
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto860-0811, Japan
| | - Eri H. Kobayashi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
| | - Asato Sekiya
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto860-0811, Japan
| | - Norio Kobayashi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI48109
| | - Shun Shibata
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
| | - Hirotaka Hamada
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
| | - Masatoshi Saito
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
| | - Nobuo Yaegashi
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka812-8582, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto860-0811, Japan
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12
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Shen W, Hu F, Lei P, Tang Y. Applications of CRISPR screening to lung cancer treatment. Front Cell Dev Biol 2023; 11:1295555. [PMID: 38169973 PMCID: PMC10760454 DOI: 10.3389/fcell.2023.1295555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024] Open
Abstract
Lung cancer is an extremely aggressive and highly prevalent disease worldwide, and it is one of the leading causes of cancer death. Deciphering intrinsic genetic mechanism, finding new targets, and overcoming drug resistance are the key to lung cancer treatment. High-throughput CRISPR screening has been extensively used to obtain the genes related to cancers including lung cancer. This review describes CRISPR/Cas9 or CRISPR/dCas9-based technologies for high-throughput screening. We summarize the applications of CRISPR screening technology in exploring the mechanism of lung cancer development in vivo or in vitro, overcoming drug resistance, improving the effect of immunotherapy, and discovering new therapeutic targets. This review highlights the potential of CRISPR screening in combination with tumor barcoding and high-throughput sequencing (Tuba-seq) to precisely quantify the impact of alterations in many tumor suppressor genes on lung cancer.
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Affiliation(s)
- Wanying Shen
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Fangli Hu
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Pan Lei
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China
- Hubei Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yijun Tang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China
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13
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Dufva O, Gandolfi S, Huuhtanen J, Dashevsky O, Duàn H, Saeed K, Klievink J, Nygren P, Bouhlal J, Lahtela J, Näätänen A, Ghimire BR, Hannunen T, Ellonen P, Lähteenmäki H, Rumm P, Theodoropoulos J, Laajala E, Härkönen J, Pölönen P, Heinäniemi M, Hollmén M, Yamano S, Shirasaki R, Barbie DA, Roth JA, Romee R, Sheffer M, Lähdesmäki H, Lee DA, De Matos Simoes R, Kankainen M, Mitsiades CS, Mustjoki S. Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers. Immunity 2023; 56:2816-2835.e13. [PMID: 38091953 DOI: 10.1016/j.immuni.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/19/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Cancer cells can evade natural killer (NK) cell activity, thereby limiting anti-tumor immunity. To reveal genetic determinants of susceptibility to NK cell activity, we examined interacting NK cells and blood cancer cells using single-cell and genome-scale functional genomics screens. Interaction of NK and cancer cells induced distinct activation and type I interferon (IFN) states in both cell types depending on the cancer cell lineage and molecular phenotype, ranging from more sensitive myeloid to less sensitive B-lymphoid cancers. CRISPR screens in cancer cells uncovered genes regulating sensitivity and resistance to NK cell-mediated killing, including adhesion-related glycoproteins, protein fucosylation genes, and transcriptional regulators, in addition to confirming the importance of antigen presentation and death receptor signaling pathways. CRISPR screens with a single-cell transcriptomic readout provided insight into underlying mechanisms, including regulation of IFN-γ signaling in cancer cells and NK cell activation states. Our findings highlight the diversity of mechanisms influencing NK cell susceptibility across different cancers and provide a resource for NK cell-based therapies.
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Affiliation(s)
- Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Sara Gandolfi
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hanna Duàn
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Khalid Saeed
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Petra Nygren
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jonas Bouhlal
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Anna Näätänen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Bishwa R Ghimire
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Tiina Hannunen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Hanna Lähteenmäki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Pauliina Rumm
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Essi Laajala
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jouni Härkönen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Petri Pölönen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Merja Heinäniemi
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Maija Hollmén
- Medicity Research Laboratory, University of Turku, 20014 Turku, Finland
| | - Shizuka Yamano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Dean A Lee
- Hematology/Oncology/BMT, Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Ricardo De Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Matti Kankainen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusima (HUS), 00290 Helsinki, Finland
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland.
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14
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Ding S, Liu J, Han X, Tang M. CRISPR/Cas9-Mediated Genome Editing in Cancer Therapy. Int J Mol Sci 2023; 24:16325. [PMID: 38003514 PMCID: PMC10671490 DOI: 10.3390/ijms242216325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system, an RNA-based adaptive immune system found in bacteria and archaea, has catalyzed the development and application of a new generation of gene editing tools. Numerous studies have shown that this system can precisely target a wide range of human genes, including those associated with diseases such as cancer. In cancer research, the intricate genetic mutations in tumors have promoted extensive utilization of the CRISPR/Cas9 system due to its efficient and accurate gene editing capabilities. This includes improvements in Chimeric Antigen Receptor (CAR)-T-cell therapy, the establishment of tumor models, and gene and drug target screening. Such progress has propelled the investigation of cancer molecular mechanisms and the advancement of precision medicine. However, the therapeutic potential of genome editing remains underexplored, and lingering challenges could elevate the risk of additional genetic mutations. Here, we elucidate the fundamental principles of CRISPR/Cas9 gene editing and its practical applications in tumor research. We also briefly discuss the primary challenges faced by CRISPR technology and existing solutions, intending to enhance the efficacy of this gene editing therapy and shed light on the underlying mechanisms of tumors.
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Affiliation(s)
- Shuai Ding
- Department of Biochemistry and Molecular Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Jinfeng Liu
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Xin Han
- Department of Biochemistry and Molecular Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Mengfan Tang
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
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15
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Rummel CK, Gagliardi M, Ahmad R, Herholt A, Jimenez-Barron L, Murek V, Weigert L, Hausruckinger A, Maidl S, Hauger B, Raabe FJ, Fürle C, Trastulla L, Turecki G, Eder M, Rossner MJ, Ziller MJ. Massively parallel functional dissection of schizophrenia-associated noncoding genetic variants. Cell 2023; 186:5165-5182.e33. [PMID: 37852259 DOI: 10.1016/j.cell.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 06/12/2023] [Accepted: 09/14/2023] [Indexed: 10/20/2023]
Abstract
Schizophrenia (SCZ) is a highly heritable mental disorder with thousands of associated genetic variants located mostly in the noncoding space of the genome. Translating these associations into insights regarding the underlying pathomechanisms has been challenging because the causal variants, their mechanisms of action, and their target genes remain largely unknown. We implemented a massively parallel variant annotation pipeline (MVAP) to perform SCZ variant-to-function mapping at scale in disease-relevant neural cell types. This approach identified 620 functional variants (1.7%) that operate in a highly developmental context and neuronal-activity-dependent manner. Multimodal integration of epigenomic and CRISPRi screening data enabled us to link these functional variants to target genes, biological processes, and ultimately alterations of neuronal physiology. These results provide a multistage prioritization strategy to map functional single-nucleotide polymorphism (SNP)-to-gene-to-endophenotype relations and offer biological insights into the context-dependent molecular processes modulated by SCZ-associated genetic variation.
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Affiliation(s)
- Christine K Rummel
- Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany
| | - Miriam Gagliardi
- Department of Psychiatry, University of Münster, Münster 48149, Germany
| | - Ruhel Ahmad
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Alexander Herholt
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU, Munich 80336, Germany; Systasy Bioscience GmbH, Munich 81669, Germany
| | - Laura Jimenez-Barron
- Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany
| | - Vanessa Murek
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Liesa Weigert
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | | | - Susanne Maidl
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Barbara Hauger
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Florian J Raabe
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU, Munich 80336, Germany
| | | | - Lucia Trastulla
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich 80804, Germany; Department of Psychiatry, University of Münster, Münster 48149, Germany; Technische Universität München Medical Graduate Center Experimental Medicine, Munich 80333, Germany
| | - Gustavo Turecki
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Matthias Eder
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU, Munich 80336, Germany; Systasy Bioscience GmbH, Munich 81669, Germany
| | - Michael J Ziller
- Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Psychiatry, University of Münster, Münster 48149, Germany; Center for Soft Nanoscience, University of Münster, Münster 48149, Germany.
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16
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Abstract
The CRISPR genome editing technology has revolutionized the way gene function is studied. Genome editing can be achieved in single genes or for thousands of genes simultaneously in sensitive genetic screens. While conventional genetic screens are limited to bulk measurements of cell behavior, recent developments in single-cell technologies make it possible to combine CRISPR screening with single-cell profiling. In this way, cell behavior and gene expression can be monitored simultaneously, with the additional possibility of including data on chromatin accessibility and protein levels. Moreover, the availability of various Cas proteins leading to inactivation, activation, or other effects on gene function further broadens the scope of such screens. The integration of single-cell multi-omics approaches with CRISPR screening open the path to high-content information on the impact of genetic perturbations at single-cell resolution. Current limitations in cell throughput and data density need to be taken into consideration, but new technologies are rapidly evolving and are likely to easily overcome these limitations. In this review, we discuss the use of bulk CRISPR screening in hematology research, as well as the emergence of single-cell CRISPR screening and its added value to the field.
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Affiliation(s)
- Sarah Meyers
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium.
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17
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Ravichandran M, Maddalo D. Applications of CRISPR-Cas9 for advancing precision medicine in oncology: from target discovery to disease modeling. Front Genet 2023; 14:1273994. [PMID: 37908590 PMCID: PMC10613999 DOI: 10.3389/fgene.2023.1273994] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system is a powerful tool that enables precise and efficient gene manipulation. In a relatively short time, CRISPR has risen to become the preferred gene-editing system due to its high efficiency, simplicity, and programmability at low costs. Furthermore, in the recent years, the CRISPR toolkit has been rapidly expanding, and the emerging advancements have shown tremendous potential in uncovering molecular mechanisms and new therapeutic strategies for human diseases. In this review, we provide our perspectives on the recent advancements in CRISPR technology and its impact on precision medicine, ranging from target identification, disease modeling, and diagnostics. We also discuss the impact of novel approaches such as epigenome, base, and prime editing on preclinical cancer drug discovery.
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Affiliation(s)
- Mirunalini Ravichandran
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
| | - Danilo Maddalo
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
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18
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Butterworth S, Kordova K, Chandrasekaran S, Thomas KK, Torelli F, Lockyer EJ, Edwards A, Goldstone R, Koshy AA, Treeck M. High-throughput identification of Toxoplasma gondii effector proteins that target host cell transcription. Cell Host Microbe 2023; 31:1748-1762.e8. [PMID: 37827122 DOI: 10.1016/j.chom.2023.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/04/2023] [Accepted: 09/07/2023] [Indexed: 10/14/2023]
Abstract
Intracellular pathogens and other endosymbionts reprogram host cell transcription to suppress immune responses and recalibrate biosynthetic pathways. This reprogramming is critical in determining the outcome of infection or colonization. We combine pooled CRISPR knockout screening with dual host-microbe single-cell RNA sequencing, a method we term dual perturb-seq, to identify the molecular mediators of these transcriptional interactions. Applying dual perturb-seq to the intracellular pathogen Toxoplasma gondii, we are able to identify previously uncharacterized effector proteins and directly infer their function from the transcriptomic data. We show that TgGRA59 contributes to the export of other effector proteins from the parasite into the host cell and identify an effector, TgSOS1, that is necessary for sustained host STAT6 signaling and thereby contributes to parasite immune evasion and persistence. Together, this work demonstrates a tool that can be broadly adapted to interrogate host-microbe transcriptional interactions and reveal mechanisms of infection and immune evasion.
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Affiliation(s)
- Simon Butterworth
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Kristina Kordova
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | | | - Francesca Torelli
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Eloise J Lockyer
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Amelia Edwards
- Advanced Sequencing Facility, The Francis Crick Institute, London NW1 1AT, UK
| | - Robert Goldstone
- Advanced Sequencing Facility, The Francis Crick Institute, London NW1 1AT, UK
| | - Anita A Koshy
- BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA; Department of Immunobiology, University of Arizona, Tucson, AZ 85719, USA; Department of Neurology, University of Arizona, Tucson, AZ 85719, USA
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Cell Biology of Host-Pathogen Interaction Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal.
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19
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Hafer TL, Felton A, Delgado Y, Srinivasan H, Emerman M. A CRISPR Screen of HIV Dependency Factors Reveals That CCNT1 Is Non-Essential in T Cells but Required for HIV-1 Reactivation from Latency. Viruses 2023; 15:1863. [PMID: 37766271 PMCID: PMC10535513 DOI: 10.3390/v15091863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency reactivation. We identified several HIV-1 dependency factors that play a key role in HIV-1 latency reactivation including ELL, UBE2M, TBL1XR1, HDAC3, AMBRA1, and ALYREF. The knockout of Cyclin T1 (CCNT1), a component of the P-TEFb complex that is important for transcription elongation, was the top hit in the screen and had the largest effect on HIV latency reversal with a wide variety of latency reversal agents. Moreover, CCNT1 knockout prevents latency reactivation in a primary CD4+ T cell model of HIV latency without affecting the activation of these cells. RNA sequencing data showed that CCNT1 regulates HIV-1 proviral genes to a larger extent than any other host gene and had no significant effects on RNA transcripts in primary T cells after activation. We conclude that CCNT1 function is non-essential in T cells but is absolutely required for HIV latency reversal.
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Affiliation(s)
- Terry L. Hafer
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA;
| | - Abby Felton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yennifer Delgado
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Harini Srinivasan
- Bioinformatics Shared Resource, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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20
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Shevade K, Peddada S, Mader K, Przybyla L. Functional genomics in stem cell models: considerations and applications. Front Cell Dev Biol 2023; 11:1236553. [PMID: 37554308 PMCID: PMC10404852 DOI: 10.3389/fcell.2023.1236553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
Protocols to differentiate human pluripotent stem cells have advanced in terms of cell type specificity and tissue-level complexity over the past 2 decades, which has facilitated human disease modeling in the most relevant cell types. The ability to generate induced PSCs (iPSCs) from patients further enables the study of disease mutations in an appropriate cellular context to reveal the mechanisms that underlie disease etiology and progression. As iPSC-derived disease models have improved in robustness and scale, they have also been adopted more widely for use in drug screens to discover new therapies and therapeutic targets. Advancement in genome editing technologies, in particular the discovery of CRISPR-Cas9, has further allowed for rapid development of iPSCs containing disease-causing mutations. CRISPR-Cas9 technologies have now evolved beyond creating single gene edits, aided by the fusion of inhibitory (CRISPRi) or activation (CRISPRa) domains to a catalytically dead Cas9 protein, enabling inhibition or activation of endogenous gene loci. These tools have been used in CRISPR knockout, CRISPRi, or CRISPRa screens to identify genetic modifiers that synergize or antagonize with disease mutations in a systematic and unbiased manner, resulting in identification of disease mechanisms and discovery of new therapeutic targets to accelerate drug discovery research. However, many technical challenges remain when applying large-scale functional genomics approaches to differentiated PSC populations. Here we review current technologies in the field of iPSC disease modeling and CRISPR-based functional genomics screens and practical considerations for implementation across a range of modalities, applications, and disease areas, as well as explore CRISPR screens that have been performed in iPSC models to-date and the insights and therapies these screens have produced.
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Affiliation(s)
- Kaivalya Shevade
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Sailaja Peddada
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Karl Mader
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Laralynne Przybyla
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
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21
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She R, Fair T, Schaefer NK, Saunders RA, Pavlovic BJ, Weissman JS, Pollen AA. Comparative landscape of genetic dependencies in human and chimpanzee stem cells. Cell 2023; 186:2977-2994.e23. [PMID: 37343560 PMCID: PMC10461406 DOI: 10.1016/j.cell.2023.05.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/14/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether human cells exhibit distinct genetic dependencies. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. These genes comprised coherent processes, including cell-cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells. Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells and cerebral organoids, supporting the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion. Our findings demonstrate that evolutionary changes in human cells reshaped the landscape of essential genes and establish a platform for systematically uncovering latent cellular and molecular differences between species.
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Affiliation(s)
- Richard She
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Nathan K Schaefer
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben A Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
| | - Bryan J Pavlovic
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute Technology, Cambridge, MA 02142, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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22
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Billmann M, Ward HN, Aregger M, Costanzo M, Andrews BJ, Boone C, Moffat J, Myers CL. Reproducibility metrics for context-specific CRISPR screens. Cell Syst 2023; 14:418-422.e2. [PMID: 37201508 PMCID: PMC10266068 DOI: 10.1016/j.cels.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/17/2022] [Accepted: 04/07/2023] [Indexed: 05/20/2023]
Abstract
CRISPR screens are used extensively to systematically interrogate the phenotype-to-genotype problem. In contrast to early CRISPR screens, which defined core cell fitness genes, most current efforts now aim to identify context-specific phenotypes that differentiate a cell line, genetic background, or condition of interest, such as a drug treatment. While CRISPR-related technologies have shown great promise and a fast pace of innovation, a better understanding of standards and methods for quality assessment of CRISPR screen results is crucial to guide technology development and application. Specifically, many commonly used metrics for quantifying screen quality do not accurately measure the reproducibility of context-specific hits. We highlight the importance of reporting reproducibility statistics that directly relate to the purpose of the screen and suggest the use of metrics that are sensitive to context-specific signal. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany.
| | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Michael Aregger
- National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Brenda J Andrews
- Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Research and Learning Centre, 686 Bay Street, Toronto, ON M5G0A4, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA; Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA.
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23
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Hamilton MC, Fife JD, Akinci E, Yu T, Khowpinitchai B, Cha M, Barkal S, Thi TT, Yeo GH, Ramos Barroso JP, Francoeur MJ, Velimirovic M, Gifford DK, Lettre G, Yu H, Cassa CA, Sherwood RI. Systematic elucidation of genetic mechanisms underlying cholesterol uptake. Cell Genom 2023; 3:100304. [PMID: 37228746 PMCID: PMC10203276 DOI: 10.1016/j.xgen.2023.100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/02/2022] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we substantially improve the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake. We use co-essentiality-based gene module analysis to show that dysfunction of the RAB10 vesicle transport pathway leads to hypercholesterolemia in humans and mice by impairing surface LDL receptor levels. Further, we demonstrate that loss of function of OTX2 leads to robust reduction in serum LDL-C levels in mice and humans by increasing cellular LDL-C uptake. Altogether, we present an integrated approach that improves our understanding of the genetic regulators of LDL-C levels and provides a roadmap for further efforts to dissect complex human disease genetics.
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Affiliation(s)
- Marisa C. Hamilton
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - James D. Fife
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ersin Akinci
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tian Yu
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Benyapa Khowpinitchai
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minsun Cha
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sammy Barkal
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Thi Tun Thi
- Precision Medicine Research Programme, Cardiovascular Disease Research Programme, and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Grace H.T. Yeo
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juan Pablo Ramos Barroso
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Jake Francoeur
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minja Velimirovic
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David K. Gifford
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Haojie Yu
- Precision Medicine Research Programme, Cardiovascular Disease Research Programme, and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christopher A. Cassa
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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24
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Ryan CJ, Mehta I, Kebabci N, Adams DJ. Targeting synthetic lethal paralogs in cancer. Trends Cancer 2023; 9:397-409. [PMID: 36890003 DOI: 10.1016/j.trecan.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023]
Abstract
Synthetic lethal interactions, where mutation of one gene renders cells sensitive to inhibition of another gene, can be exploited for the development of targeted therapeutics in cancer. Pairs of duplicate genes (paralogs) often share common functionality and hence are a potentially rich source of synthetic lethal interactions. Because the majority of human genes have paralogs, exploiting such interactions could be a widely applicable approach for targeting gene loss in cancer. Moreover, existing small-molecule drugs may exploit synthetic lethal interactions by inhibiting multiple paralogs simultaneously. Consequently, the identification of synthetic lethal interactions between paralogs could be extremely informative for drug development. Here we review approaches to identify such interactions and discuss some of the challenges of exploiting them.
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Affiliation(s)
- Colm J Ryan
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland; Systems Biology Ireland, University College Dublin, Dublin, Ireland.
| | - Ishan Mehta
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Narod Kebabci
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland; Science Foundation Ireland (SFI) Centre for Research Training in Genomics Data Science, University College Dublin, Dublin, Ireland
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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25
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Battistello E, Hixon KA, Comstock DE, Collings CK, Chen X, Rodriguez Hernaez J, Lee S, Cervantes KS, Hinkley MM, Ntatsoulis K, Cesarano A, Hockemeyer K, Haining WN, Witkowski MT, Qi J, Tsirigos A, Perna F, Aifantis I, Kadoch C. Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion. Mol Cell 2023; 83:1216-1236.e12. [PMID: 36944333 PMCID: PMC10121856 DOI: 10.1016/j.molcel.2023.02.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/11/2023] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Highly coordinated changes in gene expression underlie T cell activation and exhaustion. However, the mechanisms by which such programs are regulated and how these may be targeted for therapeutic benefit remain poorly understood. Here, we comprehensively profile the genomic occupancy of mSWI/SNF chromatin remodeling complexes throughout acute and chronic T cell stimulation, finding that stepwise changes in localization over transcription factor binding sites direct site-specific chromatin accessibility and gene activation leading to distinct phenotypes. Notably, perturbation of mSWI/SNF complexes using genetic and clinically relevant chemical strategies enhances the persistence of T cells with attenuated exhaustion hallmarks and increased memory features in vitro and in vivo. Finally, pharmacologic mSWI/SNF inhibition improves CAR-T expansion and results in improved anti-tumor control in vivo. These findings reveal the central role of mSWI/SNF complexes in the coordination of T cell activation and exhaustion and nominate small-molecule-based strategies for the improvement of current immunotherapy protocols.
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Affiliation(s)
- Elena Battistello
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kimberlee A Hixon
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Dawn E Comstock
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xufeng Chen
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Javier Rodriguez Hernaez
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Soobeom Lee
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kasey S Cervantes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Madeline M Hinkley
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konstantinos Ntatsoulis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Annamaria Cesarano
- Department of Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kathryn Hockemeyer
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Matthew T Witkowski
- Department of Pediatrics-HemeOnc and Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Cambridge, MA, USA
| | - Aristotelis Tsirigos
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, Office of Science & Research, NYU Grossman School of Medicine, New York, NY, USA
| | - Fabiana Perna
- Department of Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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26
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Liu J, Zhao Y, He D, Jones KM, Tang S, Allison DB, Zhang Y, Chen J, Zhang Q, Wang X, Li C, Wang C, Li L, Liu X. A kinome-wide CRISPR screen identifies CK1α as a target to overcome enzalutamide resistance of prostate cancer. Cell Rep Med 2023; 4:101015. [PMID: 37075701 PMCID: PMC10140619 DOI: 10.1016/j.xcrm.2023.101015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/13/2023] [Accepted: 03/21/2023] [Indexed: 04/21/2023]
Abstract
Enzalutamide (ENZA), a second-generation androgen receptor antagonist, has significantly increased progression-free and overall survival of patients with metastatic prostate cancer (PCa). However, resistance remains a prominent obstacle in treatment. Utilizing a kinome-wide CRISPR-Cas9 knockout screen, we identified casein kinase 1α (CK1α) as a therapeutic target to overcome ENZA resistance. Depletion or pharmacologic inhibition of CK1α enhanced ENZA efficacy in ENZA-resistant cells and patient-derived xenografts. Mechanistically, CK1α phosphorylates the serine residue S1270 and modulates the protein abundance of ataxia telangiectasia mutated (ATM), a primary initiator of DNA double-strand break (DSB)-response signaling, which is compromised in ENZA-resistant cells and patients. Inhibition of CK1α stabilizes ATM, resulting in the restoration of DSB signaling, and thus increases ENZA-induced cell death and growth arrest. Our study details a therapeutic approach for ENZA-resistant PCa and characterizes a particular perspective for the function of CK1α in the regulation of DNA-damage response.
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Affiliation(s)
- Jinghui Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Daheng He
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Katelyn M Jones
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Shan Tang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Derek B Allison
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Yanquan Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, 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
| | - Chaohao Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Chi Wang
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Lang Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
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27
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Carlson RJ, Leiken MD, Guna A, Hacohen N, Blainey PC. A genome-wide optical pooled screen reveals regulators of cellular antiviral responses. Proc Natl Acad Sci U S A 2023; 120:e2210623120. [PMID: 37043539 PMCID: PMC10120039 DOI: 10.1073/pnas.2210623120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/06/2023] [Indexed: 04/13/2023] Open
Abstract
The infection of mammalian cells by viruses and innate immune responses to infection are spatiotemporally organized processes. Cytosolic RNA sensors trigger nuclear translocation of the transcription factor interferon regulatory factor 3 (IRF3) and consequent induction of host immune responses to RNA viruses. Previous genetic screens for factors involved in viral sensing did not resolve changes in the subcellular localization of host or viral proteins. Here, we increased the throughput of our optical pooled screening technology by over fourfold. This allowed us to carry out a genome-wide CRISPR knockout screen using high-resolution multiparameter imaging of cellular responses to Sendai virus infection coupled with in situ cDNA sequencing by synthesis (SBS) to identify 80,408 single guide RNAs (sgRNAs) in 10,366,390 cells-over an order of magnitude more genomic perturbations than demonstrated previously using an in situ SBS readout. By ranking perturbations using human-designed and deep learning image feature scores, we identified regulators of IRF3 translocation, Sendai virus localization, and peroxisomal biogenesis. Among the hits, we found that ATP13A1, an ER-localized P5A-type ATPase, is essential for viral sensing and is required for targeting of mitochondrial antiviral signaling protein (MAVS) to mitochondrial membranes where MAVS must be localized for effective signaling through retinoic acid-inducible gene I (RIG-I). The ability to carry out genome-wide pooled screens with complex high-resolution image-based phenotyping dramatically expands the scope of functional genomics approaches.
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Affiliation(s)
- Rebecca J. Carlson
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA02139
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | - Michael D. Leiken
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | | | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA02114
| | - Paul C. Blainey
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA02139
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28
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Trivedi V, Ramesh A, Wheeldon I. Analyzing CRISPR screens in non-conventional microbes. J Ind Microbiol Biotechnol 2023; 50:7079136. [PMID: 36928506 PMCID: PMC10124124 DOI: 10.1093/jimb/kuad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
The multifaceted nature of CRISPR screens has propelled advancements in the field of functional genomics. Pooled CRISPR screens involve creating programmed genetic perturbations across multiple genomic sites in a pool of host cells subjected to a challenge, empowering researchers to identify genetic causes of desirable phenotypes. These genome-wide screens have been widely used in mammalian cells to discover biological mechanisms of diseases and drive the development of targeted drugs and therapeutics. Their use in non-model organisms, especially in microbes to improve bioprocessing-relevant phenotypes, has been limited. Further compounding this issue is the lack of bioinformatic algorithms for analyzing microbial screening data with high accuracy. Here, we describe the general approach and underlying principles for conducting pooled CRISPR knockout screens in non-conventional yeasts and performing downstream analysis of the screening data, while also reviewing state-of-the-art algorithms for identification of CRISPR screening outcomes. Application of pooled CRISPR screens to non-model yeasts holds considerable potential to uncover novel metabolic engineering targets and improve industrial bioproduction.
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Affiliation(s)
- Varun Trivedi
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.,Center for Industrial Biotechnology, University of California, Riverside, CA 92521, USA.,Integrative Institute for Genome Biology, University of California, Riverside, CA 92521, USA
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29
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Parker J. How has CRISPR transformed therapeutic drug discovery? Biotechniques 2023; 74:119-121. [PMID: 37083429 DOI: 10.2144/btn-2023-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The genome is the blueprint for life, and over the past decade, CRISPR has become a very powerful method for editing our genetic makeup. In this article, we will explore the importance of CRISPR in developing breakthrough therapies for monogenic conditions and neurodegenerative diseases, and for enhancing the effectiveness of immuno-oncology.
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30
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Lee MC, Cai H, Murray CW, Li C, Shue YT, Andrejka L, He AL, Holzem AME, Drainas AP, Ko JH, Coles GL, Kong C, Zhu S, Zhu C, Wang J, van de Rijn M, Petrov DA, Winslow MM, Sage J. A multiplexed in vivo approach to identify driver genes in small cell lung cancer. Cell Rep 2023; 42:111990. [PMID: 36640300 PMCID: PMC9972901 DOI: 10.1016/j.celrep.2023.111990] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/24/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Small cell lung cancer (SCLC) is a lethal form of lung cancer. Here, we develop a quantitative multiplexed approach on the basis of lentiviral barcoding with somatic CRISPR-Cas9-mediated genome editing to functionally investigate candidate regulators of tumor initiation and growth in genetically engineered mouse models of SCLC. We found that naphthalene pre-treatment enhances lentiviral vector-mediated SCLC initiation, enabling high multiplicity of tumor clones for analysis through high-throughput sequencing methods. Candidate drivers of SCLC identified from a meta-analysis across multiple human SCLC genomic datasets were tested using this approach, which defines both positive and detrimental impacts of inactivating 40 genes across candidate pathways on SCLC development. This analysis and subsequent validation in human SCLC cells establish TSC1 in the PI3K-AKT-mTOR pathway as a robust tumor suppressor in SCLC. This approach should illuminate drivers of SCLC, facilitate the development of precision therapies for defined SCLC genotypes, and identify therapeutic targets.
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Affiliation(s)
- Myung Chang Lee
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Hongchen Cai
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Chuan Li
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Yan Ting Shue
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Laura Andrejka
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Andy L He
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alessandra M E Holzem
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julie H Ko
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Garry L Coles
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Christina Kong
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Shirley Zhu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - ChunFang Zhu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Jason Wang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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31
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Krishnamoorthy V, Daly J, Wisnovsky S. Identifying Genetic Regulators of Protein-Glycan Interactions with Genome-Wide CRISPR Screening. Curr Protoc 2023; 3:e646. [PMID: 36695498 DOI: 10.1002/cpz1.646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Glycans are carbohydrate molecules appended to proteins and lipids on the surface of all living cells. Glycans play key roles in a wide array of biological processes, and structural changes in cell-surface glycosylation patterns have been connected to pathogenesis of several diseases. In particular, cancer cells frequently upregulate expression of glycans that bind to inhibitory receptors (lectins) on immune cells. These glycosylated antigens systematically inhibit immune activity and protect cancer cells from immune surveillance. Understanding how cancer cells generate these glycan ligands can thus lead to identification of novel druggable targets for therapeutic intervention. However, glycan ligand biosynthesis is subject to extremely complex genetic regulation, making it difficult to identify the key genes involved in production of immune-regulatory glycan antigens. In a recent publication, we described a CRISPR/Cas9 screening approach to identify genes that drive synthesis of ligands for glycan-binding immune receptors. Here, we outline a detailed, step-by-step protocol for completing this type of genome-wide screen. Our protocol produces a genome-wide atlas of all genes whose expression is required for cell-surface binding of a recombinant immune lectin. This dataset can be used both to identify novel ligands for immune lectins and annotate regulatory genes that drive changes in cancer-associated glycosylation. Our protocol serves as a general resource for researchers interested in the detailed study of cancer glyco-immunology. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generation of a genome-wide CRISPR library using lentiviral transduction Support Protocol: Generation of dCas9KRAB-expressing K-562 cells Basic Protocol 2: Staining of genome-wide CRISPR libraries with Siglec-Fc reagents and fluorescence-activated cell sorting Basic Protocol 3: Library amplification and sequencing Basic Protocol 4: Data analysis and hit identification.
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Affiliation(s)
| | - John Daly
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Simon Wisnovsky
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
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32
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Birkeälv S, Harland M, Matsuyama LSAS, Rashid M, Mehta I, Laye JP, Haase K, Mell T, Iyer V, Robles‐Espinoza CD, McDermott U, van Loo P, Kuijjer ML, Possik PA, Maria Engler SS, Bishop DT, Newton‐Bishop J, Adams DJ. Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma. J Pathol 2023; 259:56-68. [PMID: 36219477 PMCID: PMC10098817 DOI: 10.1002/path.6019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Melanoma is a heterogenous malignancy with an unpredictable clinical course. Most patients who present in the clinic are diagnosed with primary melanoma, yet large-scale sequencing efforts have focused primarily on metastatic disease. In this study we sequence-profiled 524 American Joint Committee on Cancer Stage I-III primary tumours. Our analysis of these data reveals recurrent driver mutations, mutually exclusive genetic interactions, where two genes were never or rarely co-mutated, and an absence of co-occurring genetic events. Further, we intersected copy number calls from our primary melanoma data with whole-genome CRISPR screening data to identify the transcription factor interferon regulatory factor 4 (IRF4) as a melanoma-associated dependency. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sofia Birkeälv
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Mark Harland
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Larissa Satiko Alcantara Sekimoto Matsuyama
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - Mamun Rashid
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Ishan Mehta
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Jonathan P Laye
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | | | - Tracey Mell
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Vivek Iyer
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Carla Daniela Robles‐Espinoza
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de México, Campus JuriquillaSantiago de QuerétaroMexico
| | - Ultan McDermott
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | | | - Marieke L Kuijjer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Pathology and Leiden Center for Computational OncologyLeiden University Medical CenterLeidenthe Netherlands
| | - Patricia A Possik
- Division of Experimental and Translational ResearchBrazilian National Cancer InstituteRio de JaneiroBrazil
| | - Silvya Stuchi Maria Engler
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - D Timothy Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Julia Newton‐Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - David J Adams
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
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33
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Biederstädt A, Manzar GS, Daher M. Multiplexed engineering and precision gene editing in cellular immunotherapy. Front Immunol 2022; 13:1063303. [PMID: 36483551 PMCID: PMC9723254 DOI: 10.3389/fimmu.2022.1063303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
The advent of cellular immunotherapy in the clinic has entirely redrawn the treatment landscape for a growing number of human cancers. Genetically reprogrammed immune cells, including chimeric antigen receptor (CAR)-modified immune effector cells as well as T cell receptor (TCR) therapy, have demonstrated remarkable responses across different hard-to-treat patient populations. While these novel treatment options have had tremendous success in providing long-term remissions for a considerable fraction of treated patients, a number of challenges remain. Limited in vivo persistence and functional exhaustion of infused immune cells as well as tumor immune escape and on-target off-tumor toxicities are just some examples of the challenges which restrain the potency of today's genetically engineered cell products. Multiple engineering strategies are being explored to tackle these challenges.The advent of multiplexed precision genome editing has in recent years provided a flexible and highly modular toolkit to specifically address some of these challenges by targeted genetic interventions. This class of next-generation cellular therapeutics aims to endow engineered immune cells with enhanced functionality and shield them from immunosuppressive cues arising from intrinsic immune checkpoints as well as the hostile tumor microenvironment (TME). Previous efforts to introduce additional genetic modifications into immune cells have in large parts focused on nuclease-based tools like the CRISPR/Cas9 system or TALEN. However, nuclease-inactive platforms including base and prime editors have recently emerged and promise a potentially safer route to rewriting genetic sequences and introducing large segments of transgenic DNA without inducing double-strand breaks (DSBs). In this review, we discuss how these two exciting and emerging fields-cellular immunotherapy and precision genome editing-have co-evolved to enable a dramatic expansion in the possibilities to engineer personalized anti-cancer treatments. We will lay out how various engineering strategies in addition to nuclease-dependent and nuclease-inactive precision genome editing toolkits are increasingly being applied to overcome today's limitations to build more potent cellular therapeutics. We will reflect on how novel information-rich unbiased discovery approaches are continuously deepening our understanding of fundamental mechanisms governing tumor biology. We will conclude with a perspective of how multiplexed-engineered and gene edited cell products may upend today's treatment paradigms as they evolve into the next generation of more potent cellular immunotherapies.
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Affiliation(s)
- Alexander Biederstädt
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Medicine III, Hematology and Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Gohar Shahwar Manzar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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34
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Tatsumi A, Hirakochi H, Inoue S, Tanaka Y, Furuno H, Ikeda M, Ishibashi S, Taguchi T, Yamamoto K, Onishi I, Sachs Z, Largaespada DA, Kitagawa M, Kurata M. Identification of NRAS Downstream Genes with CRISPR Activation Screening. Biology (Basel) 2022; 11:1551. [PMID: 36358254 PMCID: PMC9687188 DOI: 10.3390/biology11111551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/15/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Mutations in NRAS constitutively activate cell proliferation signaling in malignant neoplasms, such as leukemia and melanoma, and the clarification of comprehensive downstream genes of NRAS might lead to the control of cell-proliferative signals of NRAS-driven cancers. We previously established that NRAS expression and proliferative activity can be controlled with doxycycline and named as THP-1 B11. Using a CRISPR activation library on THP-1 B11 cells with the NRAS-off state, survival clones were harvested, and 21 candidate genes were identified. By inducting each candidate guide RNA with the CRISPR activation system, DOHH, HIST1H2AC, KRT32, and TAF6 showed higher cell-proliferative activity. The expression of DOHH, HIST1H2AC, and TAF6 was definitely upregulated with NRAS expression. Furthermore, MEK inhibitors resulted in the decreased expression of DOHH, HIST1H2AC, and TAF6 proteins in parental THP-1 cells. The knockdown of DOHH, HIST1H2AC, and TAF6 was found to reduce proliferation in THP-1 cells, indicating that they are involved in the downstream proliferation of NRAS. These molecules are expected to be new therapeutic targets for NRAS-mutant leukemia cells.
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Affiliation(s)
- Akiya Tatsumi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
- Department of Molecular Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
- Department of Medical Technology & Sciences, School of Health Sciences at Narita, International University of Health and Welfare, Narita, Chiba 286-8686, Japan
| | - Haruka Hirakochi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Satomi Inoue
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yosuke Tanaka
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hidehiro Furuno
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Masumi Ikeda
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Sachiko Ishibashi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Towako Taguchi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kouhei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Iichiroh Onishi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Zohar Sachs
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Morito Kurata
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
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Zhang J, Hu S, Zhao C, Zhou Y, Zhang L, Liu H, Zhou P, Li S, Fu L, Zheng Z, Xiang Y, Xu X, Ruan J, Li X, Sun L, Cao G, Zhao S, Wang X, Xie S. Genome-Scale CRISPR Knockout Screening Identifies BACH1 as a Key Regulator of Aflatoxin B 1-Induced Oxidative Damage. Antioxidants (Basel) 2022; 11:antiox11091787. [PMID: 36139865 PMCID: PMC9495794 DOI: 10.3390/antiox11091787] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Aflatoxin B1 (AFB1) is amongst the mycotoxins commonly affecting human and animal health, raising global food safety and control concerns. The mechanisms underlying AFB1 toxicity are poorly understood. Moreover, antidotes against AFB1 are lacking. Genome-wide CRISPR/Cas9 knockout screening in porcine kidney cells identified the transcription factor BTB and CNC homolog 1 (BACH1) as a gene required for AFB1 toxicity. The inhibition of BACH1 expression in porcine kidney cells and human hepatoma cells resulted in increased resistance to AFB1. BACH1 depletion attenuates AFB1-induced oxidative damage via the upregulation of antioxidant genes. Subsequently, virtual structural screening identified the small molecule 1-Piperazineethanol, α-[(1,3-benzodioxol-5-yloxy)methyl] -4-(2-methoxyphenyl) (M2) as an inhibitor of BACH1. M2 and its analogues inhibited AFB1-induced porcine and human cell death in vitro, while M2 administration significantly improved AFB1-induced symptoms of weight loss and liver injury in vivo. These findings demonstrate that BACH1 plays a central role in AFB1-induced oxidative damage by regulating antioxidant gene expression. We also present a potent candidate small-molecule inhibitor in developing novel treatments for AFB1 toxicity.
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Affiliation(s)
- Jinfu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Siyi Hu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China;
| | - Changzhi Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Yuan Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Lu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Hailong Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Peng Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Sheng Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Liangliang Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Zhuqing Zheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Yue Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jinxue Ruan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (L.S.); (G.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Lvhui Sun
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (L.S.); (G.C.)
| | - Gang Cao
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (L.S.); (G.C.)
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (L.S.); (G.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (S.Z.); (X.W.); (S.X.)
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China;
- Correspondence: (S.Z.); (X.W.); (S.X.)
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; (J.Z.); (C.Z.); (Y.Z.); (L.Z.); (H.L.); (P.Z.); (S.L.); (L.F.); (Z.Z.); (Y.X.); (X.X.); (J.R.); (X.L.)
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (L.S.); (G.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (S.Z.); (X.W.); (S.X.)
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Berlak M, Tucker E, Dorel M, Winkler A, McGearey A, Rodriguez-Fos E, da Costa BM, Barker K, Fyle E, Calton E, Eising S, Ober K, Hughes D, Koutroumanidou E, Carter P, Stankunaite R, Proszek P, Jain N, Rosswog C, Dorado-Garcia H, Molenaar JJ, Hubank M, Barone G, Anderson J, Lang P, Deubzer HE, Künkele A, Fischer M, Eggert A, Kloft C, Henssen AG, Boettcher M, Hertwig F, Blüthgen N, Chesler L, Schulte JH. Mutations in ALK signaling pathways conferring resistance to ALK inhibitor treatment lead to collateral vulnerabilities in neuroblastoma cells. Mol Cancer 2022; 21:126. [PMID: 35689207 PMCID: PMC9185889 DOI: 10.1186/s12943-022-01583-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/22/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Development of resistance to targeted therapies has tempered initial optimism that precision oncology would improve poor outcomes for cancer patients. Resistance mechanisms, however, can also confer new resistance-specific vulnerabilities, termed collateral sensitivities. Here we investigated anaplastic lymphoma kinase (ALK) inhibitor resistance in neuroblastoma, a childhood cancer frequently affected by activating ALK alterations. METHODS Genome-wide forward genetic CRISPR-Cas9 based screens were performed to identify genes associated with ALK inhibitor resistance in neuroblastoma cell lines. Furthermore, the neuroblastoma cell line NBLW-R was rendered resistant by continuous exposure to ALK inhibitors. Genes identified to be associated with ALK inhibitor resistance were further investigated by generating suitable cell line models. In addition, tumor and liquid biopsy samples of four patients with ALK-mutated neuroblastomas before ALK inhibitor treatment and during tumor progression under treatment were genomically profiled. RESULTS Both genome-wide CRISPR-Cas9-based screens and preclinical spontaneous ALKi resistance models identified NF1 loss and activating NRASQ61K mutations to confer resistance to chemically diverse ALKi. Moreover, human neuroblastomas recurrently developed de novo loss of NF1 and activating RAS mutations after ALKi treatment, leading to therapy resistance. Pathway-specific perturbations confirmed that NF1 loss and activating RAS mutations lead to RAS-MAPK signaling even in the presence of ALKi. Intriguingly, NF1 loss rendered neuroblastoma cells hypersensitive to MEK inhibition. CONCLUSIONS Our results provide a clinically relevant mechanistic model of ALKi resistance in neuroblastoma and highlight new clinically actionable collateral sensitivities in resistant cells.
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Affiliation(s)
- Mareike Berlak
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin School of Integrative Oncology (BSIO), Augustenburger Platz 1, 13353, Berlin, Germany
- Department of Clinical Pharmacy and Biochemistry, Institute of Pharmacy, Freie Universität Berlin, Kelchstr.31, 12169, Berlin, Germany
| | - Elizabeth Tucker
- Paediatric Solid Tumour Biology and Therapeutics Team, Clinical Division and Cancer Therapeutics Division, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Mathurin Dorel
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
- IRI Life Sciences, Humboldt University Berlin, 10115, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Aleixandria McGearey
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, 13125, Berlin, Germany
| | - Barbara Martins da Costa
- Paediatric Solid Tumour Biology and Therapeutics Team, Clinical Division and Cancer Therapeutics Division, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Karen Barker
- Paediatric Solid Tumour Biology and Therapeutics Team, Clinical Division and Cancer Therapeutics Division, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Elicia Fyle
- Paediatric Solid Tumour Biology and Therapeutics Team, Clinical Division and Cancer Therapeutics Division, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Elizabeth Calton
- Paediatric Solid Tumour Biology and Therapeutics Team, Clinical Division and Cancer Therapeutics Division, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Selma Eising
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Kim Ober
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Deborah Hughes
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Eleni Koutroumanidou
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Paul Carter
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Reda Stankunaite
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Paula Proszek
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Neha Jain
- Cancer Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, Center for Molecular Medicine Cologne, 50931, Cologne, Germany
| | - Heathcliff Dorado-Garcia
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jan Jasper Molenaar
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of pharmaceutical sciences, Utrecht University, Utrecht, The Netherlands
| | - Mike Hubank
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Giuseppe Barone
- Cancer Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - John Anderson
- Cancer Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Peter Lang
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Tübingen, Germany
| | - Hedwig Elisabeth Deubzer
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, 13125, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Annette Künkele
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, Center for Molecular Medicine Cologne, 50931, Cologne, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Charlotte Kloft
- Department of Clinical Pharmacy and Biochemistry, Institute of Pharmacy, Freie Universität Berlin, Kelchstr.31, 12169, Berlin, Germany
| | - Anton George Henssen
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, 13125, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Michael Boettcher
- Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Halle, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
- IRI Life Sciences, Humboldt University Berlin, 10115, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Louis Chesler
- Paediatric Solid Tumour Biology and Therapeutics Team, Clinical Division and Cancer Therapeutics Division, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Johannes Hubertus Schulte
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
- German Cancer Consortium (DKTK), Berlin, Germany.
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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Guo D, Yu X, Wang D, Li Z, Zhou Y, Xu G, Yuan B, Qin Y, Chen M. SLC35B2 Acts in a Dual Role in the Host Sulfation Required for EV71 Infection. J Virol 2022; 96:e0204221. [PMID: 35420441 PMCID: PMC9093107 DOI: 10.1128/jvi.02042-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
As an important neurotropic enterovirus, enterovirus 71 (EV71) is occasionally associated with severe neurological diseases and high mortality rates in infants and young children. Understanding the interaction between host factors and EV71 will play a vital role in developing antivirals and optimizing vaccines. Here, we performed a genome-wide CRISPR-Cas9 knockout screen and revealed that scavenger receptor class B member 2 (SCARB2), solute carrier family 35 member B2 (SLC35B2), and beta-1,3-glucuronyltransferase 3 (B3GAT3) are essential in facilitating EV71 replication. Subsequently, the exploration of molecular mechanisms suggested that the knockout of SLC35B2 or B3GAT3, not SCARB2, led to a remarkable decrease in the binding of EV71 to cells and internalization into cells. Furthermore, we found that the infection efficiency for EV71 was positively correlated with the level of host cell sulfation, not simply with the amount of heparan sulfate, suggesting that an unidentified sulfated protein(s) must contribute to EV71 infection. In support of this idea, we screened possible sulfated proteins among the proteinous receptors for EV71 and confirmed that SCARB2 could uniquely interact with both tyrosyl protein sulfotransferases in humans. We then performed mass spectrometric analysis of SCARB2, identifying five sites with tyrosine sulfation. The function verification test indicated that there were more than five tyrosine-sulfated sites on SCARB2. Finally, we constructed a model for EV71 entry in which both heparan sulfate and SCARB2 are regulated by SLC35B2 and act cooperatively to support viral binding, internalization, and uncoating. Taken together, this is the first time that we performed the pooled CRISPR-Cas9 genetic screening to investigate the interplay of host cells and EV71. Furthermore, we found that a novel host factor, SLC35B2, played a dual role in regulating the overall sulfation comprising heparan sulfate sulfation and protein tyrosine sulfation, which are critical for EV71 entry. IMPORTANCE As the most important nonpolio neurotropic enterovirus lacking specific treatments, EV71 can transmit to the central nervous system, leading to severe and fatal neurological complications in infants and young children. The identification of new factors that facilitate or inhibit EV71 replication is crucial to uncover the mechanisms of viral infection and pathogenesis. To date, only a few host factors involved in EV71 infection have been characterized. Herein, we conducted a genome-wide CRISPR-Cas9 functional knockout (GeCKO) screen for the first time to study EV71 in HeLa cells. The screening results are presented as a ranked list of candidates, including 518 hits in the positive selection that facilitate EV71 replication and 1,044 hits in the negative selection that may be essential for cell growth and survival or for suppressing EV71 infection. We subsequently concentrated on the top three hits in the positive selection: SCARB2, SLC35B2, and B3GAT3. The knockout of any of these three genes confers strong resistance against EV71 infection. We confirmed that EV71 infection is codependent on two receptors, heparan sulfate and SCARB2. We also identified a host entry factor, SLC35B2, indirectly facilitating EV71 infection through regulation of the host cell sulfation, and determined a novel posttranslational modification, protein tyrosine sulfation existing in SCARB2. This study revealed that EV71 infectivity exhibits a significant positive correlation with the level of cellular sulfation regulated by SLC35B2. Due to the sulfation pathway being required for many distinct viruses, including but not limited to EV71 and respiratory syncytial virus (RSV), which were tested in this study, SLC35B2 represents a target of broad-spectrum antiviral therapy.
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Affiliation(s)
- Dong Guo
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xinghai Yu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan Wang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhifei Li
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guodong Xu
- Wuhan Canvest Biotechnology Co., Ltd., Wuhan, Hubei, China
| | - Bing Yuan
- Wuhan Canvest Biotechnology Co., Ltd., Wuhan, Hubei, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
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Elmas E, Saljoughian N, de Souza Fernandes Pereira M, Tullius BP, Sorathia K, Nakkula RJ, Lee DA, Naeimi Kararoudi M. CRISPR Gene Editing of Human Primary NK and T Cells for Cancer Immunotherapy. Front Oncol 2022; 12:834002. [PMID: 35449580 PMCID: PMC9016158 DOI: 10.3389/fonc.2022.834002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Antitumor activity of immune cells such as T cells and NK cells has made them auspicious therapeutic regimens for adaptive cancer immunotherapy. Enhancing their cytotoxic effects against malignancies and overcoming their suppression in tumor microenvironment (TME) may improve their efficacy to treat cancers. Clustered, regularly interspaced short palindromic repeats (CRISPR) genome editing has become one of the most popular tools to enhance immune cell antitumor activity. In this review we highlight applications and practicability of CRISPR/Cas9 gene editing and engineering strategies for cancer immunotherapy. In addition, we have reviewed several approaches to study CRISPR off-target effects.
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Affiliation(s)
- Ezgi Elmas
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, United States
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Noushin Saljoughian
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- CRISPR/Gene Editing Core, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Marcelo de Souza Fernandes Pereira
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Brian P. Tullius
- Pediatric Cellular Therapy, AdventHealth for Children, Orlando, FL, United States
| | - Kinnari Sorathia
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Robin J. Nakkula
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Dean A. Lee
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
| | - Meisam Naeimi Kararoudi
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- CRISPR/Gene Editing Core, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
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Abstract
The CRISPR/Cas technology has revolutionized forward genetic screening, and thereby facilitated genetic dissection of cellular processes and pathways. TGF-β signaling is a highly conserved cascade involved in development, regeneration, and diseases such as cancer. Even though many core components of the signaling cascade have already been described, several context-dependent pathway modulators remain unknown. To address this knowledge gap, we have recently developed a CRISPR screening approach for identifying TGF-β pathway regulators in three-dimensional organoid culture systems. Here, we provide a detailed protocol describing this approach in human intestinal organoids. With adaptations, this screening method could also be applied to other organoid types, and to other signaling cascades such as EGF or WNT signaling, thereby uncovering important mechanism in regeneration and disease.
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Affiliation(s)
- Nina Frey
- Department of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Gerald Schwank
- Department of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
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40
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Strybol PP, Larmuseau M, de Schaetzen van Brienen L, Van den Bulcke T, Marchal K. Extracting functional insights from loss-of-function screens using deep link prediction. Cell Rep Methods 2022; 2:100171. [PMID: 35474966 PMCID: PMC9017186 DOI: 10.1016/j.crmeth.2022.100171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/09/2021] [Accepted: 01/25/2022] [Indexed: 11/10/2022]
Abstract
We present deep link prediction (DLP), a method for the interpretation of loss-of-function screens. Our approach uses representation-based link prediction to reprioritize phenotypic readouts by integrating screening experiments with gene-gene interaction networks. We validate on 2 different loss-of-function technologies, RNAi and CRISPR, using datasets obtained from DepMap. Extensive benchmarking shows that DLP-DeepWalk outperforms other methods in recovering cell-specific dependencies, achieving an average precision well above 90% across 7 different cancer types and on both RNAi and CRISPR data. We show that the genes ranked highest by DLP-DeepWalk are appreciably more enriched in drug targets compared to the ranking based on original screening scores. Interestingly, this enrichment is more pronounced on RNAi data compared to CRISPR data, consistent with the greater inherent noise of RNAi screens. Finally, we demonstrate how DLP-DeepWalk can infer the molecular mechanism through which putative targets trigger cell line mortality.
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Affiliation(s)
- Pieter-Paul Strybol
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, 9000 Gent, Belgium
| | - Maarten Larmuseau
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, 9000 Gent, Belgium
| | - Louise de Schaetzen van Brienen
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, 9000 Gent, Belgium
| | | | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, 9000 Gent, Belgium
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41
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Yan J, Kang DD, Turnbull G, Dong Y. Delivery of CRISPR-Cas9 system for screening and editing RNA binding proteins in cancer. Adv Drug Deliv Rev 2022; 180:114042. [PMID: 34767864 PMCID: PMC8724402 DOI: 10.1016/j.addr.2021.114042] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) play an important role in RNA metabolism, regulating the stability, localization, and functional dynamics of RNAs. Alternation in the RBP-RNA network has profound implications in cellular physiology, and is related to the development and spread of cancer in certain cases. To regulate the expression of specific genes and their biological activities, various strategies have been applied to target RBPs for cancer treatments, including small-molecule inhibitors, small-interfering RNA, peptides, and aptamers. Recently, the deployment of the CRISPR-Cas9 technology has provided a new platform for RBP screening and regulation. This review summarizes the delivery systems of the CRISPR-Cas9 system and their role in RBP-based cancer therapeutics, including identification of novel RBPs and regulation of cancer-associated RBPs. The efficient delivery of the CRISPR-Cas9 system is important to the profound understanding and clinical transition of RBPs as cancer therapeutic targets.
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Affiliation(s)
- Jingyue Yan
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Diana D. Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gillian Turnbull
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States,Department of Biomedical Engineering; The Center for Clinical and Translational Science; The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute; Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States
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42
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Bumpus TW, Huang S, Tei R, Baskin JM. Click chemistry-enabled CRISPR screening reveals GSK3 as a regulator of PLD signaling. Proc Natl Acad Sci U S A 2021; 118:e2025265118. [PMID: 34810254 DOI: 10.1073/pnas.2025265118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 12/20/2022] Open
Abstract
Enzymes that produce second messengers are highly regulated. Revealing the mechanisms underlying such regulation is critical to understanding both how cells achieve specific signaling outcomes and return to homeostasis following a particular stimulus. Pooled genome-wide CRISPR screens are powerful unbiased approaches to elucidate regulatory networks, their principal limitation being the choice of phenotype selection. Here, we merge advances in bioorthogonal fluorescent labeling and CRISPR screening technologies to discover regulators of phospholipase D (PLD) signaling, which generates the potent lipid second messenger phosphatidic acid. Our results reveal glycogen synthase kinase 3 as a positive regulator of protein kinase C and PLD signaling. More generally, this work demonstrates how bioorthogonal, activity-based fluorescent tagging can expand the power of CRISPR screening to uncover mechanisms regulating specific enzyme-driven signaling pathways in mammalian cells.
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Onishi I, Yamamoto K, Kinowaki Y, Kitagawa M, Kurata M. To Discover the Efficient and Novel Drug Targets in Human Cancers Using CRISPR/Cas Screening and Databases. Int J Mol Sci 2021; 22:12322. [PMID: 34830205 PMCID: PMC8622676 DOI: 10.3390/ijms222212322] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas has emerged as an excelle nt gene-editing technology and is used worldwide for research. The CRISPR library is an ideal tool for identifying essential genes and synthetic lethality targeted for cancer therapies in human cancers. Synthetic lethality is defined as multiple genetic abnormalities that, when present individually, do not affect function or survival, but when present together, are lethal. Recently, many CRISPR libraries are available, and the latest libraries are more accurate and can be applied to few cells. However, it is easier to efficiently search for cancer targets with their own screenings by effectively using databases of CRISPR screenings, such as Depmap portal, PICKLES (Pooled In-Vitro CRISPR Knockout Library Essentiality Screens), iCSDB, Project Score database, and CRISP-view. This review will suggest recent optimal CRISPR libraries and effective databases for Novel Approaches in the Discovery and Design of Targeted Therapies.
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Affiliation(s)
- Iichiroh Onishi
- Department of Comprehensive Pathology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; (K.Y.); (Y.K.); (M.K.)
| | | | | | | | - Morito Kurata
- Department of Comprehensive Pathology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; (K.Y.); (Y.K.); (M.K.)
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Wang X, Tokheim C, Gu SS, Wang B, Tang Q, Li Y, Traugh N, Zeng Z, Zhang Y, Li Z, Zhang B, Fu J, Xiao T, Li W, Meyer CA, Chu J, Jiang P, Cejas P, Lim K, Long H, Brown M, Liu XS. In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target. Cell 2021; 184:5357-5374.e22. [PMID: 34582788 PMCID: PMC9136996 DOI: 10.1016/j.cell.2021.09.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/14/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022]
Abstract
Despite remarkable clinical efficacy of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits for triple-negative breast cancer (TNBC) remain limited. Through pooled in vivo CRISPR knockout (KO) screens in syngeneic TNBC mouse models, we found that deletion of the E3 ubiquitin ligase Cop1 in cancer cells decreases secretion of macrophage-associated chemokines, reduces tumor macrophage infiltration, enhances anti-tumor immunity, and strengthens ICB response. Transcriptomics, epigenomics, and proteomics analyses revealed that Cop1 functions through proteasomal degradation of the C/ebpδ protein. The Cop1 substrate Trib2 functions as a scaffold linking Cop1 and C/ebpδ, which leads to polyubiquitination of C/ebpδ. In addition, deletion of the E3 ubiquitin ligase Cop1 in cancer cells stabilizes C/ebpδ to suppress expression of macrophage chemoattractant genes. Our integrated approach implicates Cop1 as a target for improving cancer immunotherapy efficacy in TNBC by regulating chemokine secretion and macrophage infiltration in the tumor microenvironment.
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Affiliation(s)
- Xiaoqing Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shengqing Stan Gu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Binbin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Qin Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yihao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicole Traugh
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ziyi Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Boning Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jingxin Fu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tengfei Xiao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wei Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jun Chu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui 230038, China
| | - Peng Jiang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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Einstein JM, Perelis M, Chaim IA, Meena JK, Nussbacher JK, Tankka AT, Yee BA, Li H, Madrigal AA, Neill NJ, Shankar A, Tyagi S, Westbrook TF, Yeo GW. Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer. Mol Cell 2021; 81:3048-3064.e9. [PMID: 34216543 PMCID: PMC8359670 DOI: 10.1016/j.molcel.2021.06.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/11/2021] [Accepted: 06/10/2021] [Indexed: 01/18/2023]
Abstract
RNA-binding proteins (RBPs) are critical regulators of post-transcriptional gene expression, and aberrant RBP-RNA interactions can promote cancer progression. Here, we interrogate the function of RBPs in cancer using pooled CRISPR-Cas9 screening and identify 57 RBP candidates with distinct roles in supporting MYC-driven oncogenic pathways. We find that disrupting YTHDF2-dependent mRNA degradation triggers apoptosis in triple-negative breast cancer (TNBC) cells and tumors. eCLIP and m6A sequencing reveal that YTHDF2 interacts with mRNAs encoding proteins in the MAPK pathway that, when stabilized, induce epithelial-to-mesenchymal transition and increase global translation rates. scRibo-STAMP profiling of translating mRNAs reveals unique alterations in the translatome of single cells within YTHDF2-depleted solid tumors, which selectively contribute to endoplasmic reticulum stress-induced apoptosis in TNBC cells. Thus, our work highlights the therapeutic potential of RBPs by uncovering a critical role for YTHDF2 in counteracting the global increase of mRNA synthesis in MYC-driven breast cancers.
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Affiliation(s)
- Jaclyn M Einstein
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mark Perelis
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Isaac A Chaim
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jitendra K Meena
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julia K Nussbacher
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alexandra T Tankka
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Heyuan Li
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Assael A Madrigal
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas J Neill
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Archana Shankar
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Siddhartha Tyagi
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas F Westbrook
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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Guo S, Chen Y, Liu J, Zhang X, Liu Z, Zhou Z, Wei W. Low-density lipoprotein receptor-related protein 1 is a CROPs-associated receptor for Clostridioides difficile toxin B. Sci China Life Sci 2021; 65:107-118. [PMID: 34279819 DOI: 10.1007/s11427-021-1943-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 04/28/2021] [Indexed: 12/23/2022]
Abstract
As the leading cause of worldwide hospital-acquired infection, Clostridioides difficile (C. difficile) infection has caused heavy economic and hospitalized burden, while its pathogenesis is not fully understood. Toxin B (TcdB) is one of the major virulent factors of C. difficile. Recently, CSPG4 and FZD2 were reported to be the receptors that mediate TcdB cellular entry. However, genetic ablation of genes encoding these receptors failed to completely block TcdB entry, implicating the existence of alternative receptor(s) for this toxin. Here, by employing the CRISPR-Cas9 screen in CSPG4-deficient HeLa cells, we identified LDL receptor-related protein-1 (LRP1) as a novel receptor for TcdB. Knockout of LRP1 in both CSPG4-deficient HeLa cells and colonic epithelium Caco2 cells conferred cells with increased TcdB resistance, while LRP1 overexpression sensitized cells to TcdB at a low concentration. Co-immunoprecipitation assay showed that LRP1 interacts with full-length TcdB. Moreover, CROPs domain, which is dispensable for TcdB's interaction with CSPG4 and FZD2, is sufficient for binding to LRP1. As such, our study provided evidence for a novel mechanism of TcdB entry and suggested potential therapeutic targets for treating C. diff.
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Affiliation(s)
- Shengjie Guo
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yiou Chen
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jingze Liu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xinyi Zhang
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhiheng Liu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
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47
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Cui Y, Wang Z, Köster J, Liao X, Peng S, Tang T, Huang C, Yang C. VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments. BMC Bioinformatics 2021; 22:344. [PMID: 34167459 PMCID: PMC8223366 DOI: 10.1186/s12859-021-04275-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/15/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND VISPR is an interactive visualization and analysis framework for CRISPR screening experiments. However, it only supports the output of MAGeCK, and requires installation and manual configuration. Furthermore, VISPR is designed to run on a single computer, and data sharing between collaborators is challenging. RESULTS To make the tool easily accessible to the community, we present VISPR-online, a web-based general application allowing users to visualize, explore, and share CRISPR screening data online with a few simple steps. VISPR-online provides an exploration of screening results and visualization of read count changes. Apart from MAGeCK, VISPR-online supports two more popular CRISPR screening analysis tools: BAGEL and JACKS. It provides an interactive environment for exploring gene essentiality, viewing guide RNA (gRNA) locations, and allowing users to resume and share screening results. CONCLUSIONS VISPR-online allows users to visualize, explore and share CRISPR screening data online. It is freely available at http://vispr-online.weililab.org , while the source code is available at https://github.com/lemoncyb/VISPR-online .
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Affiliation(s)
- Yingbo Cui
- School of Computer, National University of Defense Technology, Changsha, 410073, China.
| | - Zihang Wang
- College of Information Science and Engineering, Hunan University, Changsha, 410006, China
| | - Johannes Köster
- Algorithms for Reproducible Bioinformatics, Institute of Human Genetics, University of Duisburg-Essen, 45147, Essen, Germany
| | - Xiangke Liao
- School of Computer, National University of Defense Technology, Changsha, 410073, China
| | - Shaoliang Peng
- College of Information Science and Engineering, Hunan University, Changsha, 410006, China
- National Supercomputing Center in Changsha, Changsha, 410082, China
| | - Tao Tang
- School of Computer, National University of Defense Technology, Changsha, 410073, China
| | - Chun Huang
- School of Computer, National University of Defense Technology, Changsha, 410073, China
| | - Canqun Yang
- School of Computer, National University of Defense Technology, Changsha, 410073, China
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Zhang J, Khazalwa EM, Abkallo HM, Zhou Y, Nie X, Ruan J, Zhao C, Wang J, Xu J, Li X, Zhao S, Zuo E, Steinaa L, Xie S. The advancements, challenges, and future implications of the CRISPR/Cas9 system in swine research. J Genet Genomics 2021; 48:347-360. [PMID: 34144928 DOI: 10.1016/j.jgg.2021.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 12/11/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) genome editing technology has dramatically influenced swine research by enabling the production of high-quality disease-resistant pig breeds, thus improving yields. In addition, CRISPR/Cas9 has been used extensively in pigs as one of the tools in biomedical research. In this review, we present the advancements of the CRISPR/Cas9 system in swine research, such as animal breeding, vaccine development, xenotransplantation, and disease modeling. We also highlight the current challenges and some potential applications of the CRISPR/Cas9 technologies.
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Affiliation(s)
- Jinfu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Emmanuel M Khazalwa
- Animal and Human Health Program, Biosciences, International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi 00100, Kenya
| | - Hussein M Abkallo
- Animal and Human Health Program, Biosciences, International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi 00100, Kenya
| | - Yuan Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiongwei Nie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jinxue Ruan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Changzhi Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jieru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, PR China
| | - Jing Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Erwei Zuo
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, PR China.
| | - Lucilla Steinaa
- Animal and Human Health Program, Biosciences, International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi 00100, Kenya.
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China; Animal and Human Health Program, Biosciences, International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi 00100, Kenya; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, PR China.
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Nakamura T, Ogawa M, Kojima K, Takayanagi S, Ishihara S, Hattori K, Naguro I, Ichijo H. The mitochondrial Ca 2+ uptake regulator, MICU1, is involved in cold stress-induced ferroptosis. EMBO Rep 2021; 22:e51532. [PMID: 33822458 PMCID: PMC8097382 DOI: 10.15252/embr.202051532] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
Ferroptosis has recently attracted much interest because of its relevance to human diseases such as cancer and ischemia-reperfusion injury. We have reported that prolonged severe cold stress induces lipid peroxidation-dependent ferroptosis, but the upstream mechanism remains unknown. Here, using genome-wide CRISPR screening, we found that a mitochondrial Ca2+ uptake regulator, mitochondrial calcium uptake 1 (MICU1), is required for generating lipid peroxide and subsequent ferroptosis under cold stress. Furthermore, the gatekeeping activity of MICU1 through mitochondrial calcium uniporter (MCU) is suggested to be indispensable for cold stress-induced ferroptosis. MICU1 is required for mitochondrial Ca2+ increase, hyperpolarization of the mitochondrial membrane potential (MMP), and subsequent lipid peroxidation under cold stress. Collectively, these findings suggest that the MICU1-dependent mitochondrial Ca2+ homeostasis-MMP hyperpolarization axis is involved in cold stress-induced lipid peroxidation and ferroptosis.
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Affiliation(s)
- Toshitaka Nakamura
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Motoyuki Ogawa
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Kazuki Kojima
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Saki Takayanagi
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Shunya Ishihara
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Kazuki Hattori
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Isao Naguro
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Hidenori Ichijo
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
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50
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Abstract
Understanding how genes are expressed in the correct cell types and at the correct level is a key goal of developmental biology research. Gene regulation has traditionally been approached largely through observational methods, whereas perturbational approaches have lacked precision. CRISPR-Cas9 has begun to transform the study of gene regulation, allowing for precise manipulation of genomic sequences, epigenetic functionalization and gene expression. CRISPR-Cas9 technology has already led to the discovery of new paradigms in gene regulation and, as new CRISPR-based tools and methods continue to be developed, promises to transform our knowledge of the gene regulatory code and our ability to manipulate cell fate. Here, we discuss the current and future application of the emerging CRISPR toolbox toward predicting gene regulatory network behavior, improving stem cell disease modeling, dissecting the epigenetic code, reprogramming cell fate and treating diseases of gene dysregulation.
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Affiliation(s)
- Ersin Akinci
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
| | - Marisa C. Hamilton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Benyapa Khowpinitchai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Hubrecht Institute, 3584 CT, Utrecht, The Netherlands
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