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Xu P, Liu Z, Liu Y, Ma H, Xu Y, Bao Y, Zhu S, Cao Z, Wu Z, Zhou Z, Wei W. Genome-wide interrogation of gene functions through base editor screens empowered by barcoded sgRNAs. Nat Biotechnol 2021; 39:1403-1413. [PMID: 34155407 DOI: 10.1038/s41587-021-00944-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 05/06/2021] [Indexed: 12/20/2022]
Abstract
Canonical CRISPR-knockout (KO) screens rely on Cas9-induced DNA double-strand breaks (DSBs) to generate targeted gene KOs. These methodologies may yield distorted results because DSB-associated effects are often falsely assumed to be consequences of gene perturbation itself, especially when high copy-number sites are targeted. In the present study, we report a DSB-independent, genome-wide CRISPR screening method, termed iBARed cytosine base editing-mediated gene KO (BARBEKO). This method leverages CRISPR cytosine base editors for genome-scale KO screens by perturbing gene start codons or splice sites, or by introducing premature termination codons. Furthermore, it is integrated with iBAR, a strategy we devised for improving screening quality and efficiency. By constructing such a cell library through lentiviral infection at a high multiplicity of infection (up to 10), we achieved efficient and accurate screening results with substantially reduced starting cells. More importantly, in comparison with Cas9-mediated fitness screens, BARBEKO screens are no longer affected by DNA cleavage-induced cytotoxicity in HeLa-, K562- or DSB-sensitive retinal pigmented epithelial 1 cells. We anticipate that BARBEKO offers a valuable tool to complement the current CRISPR-KO screens in various settings.
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Affiliation(s)
- Ping Xu
- 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, 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, China
| | - Ying 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, China
| | - Huazheng Ma
- 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, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Peking University, Beijing, China
| | - Yiyuan Xu
- 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, China
| | - Ying Bao
- 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, China
| | - Shiyou Zhu
- 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, China
| | - Zhongzheng Cao
- 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, China
| | - Zeguang Wu
- 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, 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, 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, China.
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102
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Liu J, Hideshima T, Xing L, Wang S, Zhou W, Samur MK, Sewastianik T, Ogiya D, An G, Gao S, Yang L, Ji T, Bianchi G, Wen K, Tai YT, Munshi N, Richardson P, Carrasco R, Cang Y, Anderson KC. ERK signaling mediates resistance to immunomodulatory drugs in the bone marrow microenvironment. SCIENCE ADVANCES 2021; 7:7/23/eabg2697. [PMID: 34088671 PMCID: PMC8177702 DOI: 10.1126/sciadv.abg2697] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/19/2021] [Indexed: 05/05/2023]
Abstract
Immunomodulatory drugs (IMiDs) have markedly improved patient outcome in multiple myeloma (MM); however, resistance to IMiDs commonly underlies relapse of disease. Here, we identify that tumor necrosis factor (TNF) receptor-associated factor 2 (TRAF2) knockdown (KD)/knockout (KO) in MM cells mediates IMiD resistance via activation of noncanonical nuclear factor κB (NF-κB) and extracellular signal-regulated kinase (ERK) signaling. Within MM bone marrow (BM) stromal cell supernatants, TNF-α induces proteasomal degradation of TRAF2, noncanonical NF-κB, and downstream ERK signaling in MM cells, whereas interleukin-6 directly triggers ERK activation. RNA sequencing of MM patient samples shows nearly universal ERK pathway activation at relapse on lenalidomide maintenance therapy, confirming its clinical relevance. Combination MEK inhibitor treatment restores IMiD sensitivity of TRAF2 KO cells both in vitro and in vivo. Our studies provide the framework for clinical trials of MEK inhibitors to overcome IMiD resistance in the BM microenvironment and improve patient outcome in MM.
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Affiliation(s)
- Jiye Liu
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Teru Hideshima
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Lijie Xing
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
| | - Su Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Wenrong Zhou
- Oncology and Immunology Unit, Research Service Division, WuXi AppTec (Shanghai) Co., Ltd., Shanghai 200131, China
| | - Mehmet K Samur
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Department of Biostatistics and Computational Biology, Harvard T.H. Chan School of Public Health, Boston, 02115 MA, USA
| | - Tomasz Sewastianik
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Warsaw 02776, Poland
| | - Daisuke Ogiya
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Gang An
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300020, China
| | - Shaobing Gao
- The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Li Yang
- Multiple Myeloma Treatment Center and Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Tong Ji
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310020, China
| | - Giada Bianchi
- Division of Hematology, Department of Internal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth Wen
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Yu-Tzu Tai
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Nikhil Munshi
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Paul Richardson
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ruben Carrasco
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yong Cang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Kenneth C Anderson
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
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103
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Weiss RJ, Spahn PN, Chiang AW, Liu Q, Li J, Hamill KM, Rother S, Clausen TM, Hoeksema MA, Timm BM, Godula K, Glass CK, Tor Y, Gordts PL, Lewis NE, Esko JD. Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nat Chem Biol 2021; 17:684-692. [PMID: 33846619 PMCID: PMC8159865 DOI: 10.1038/s41589-021-00776-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/18/2021] [Indexed: 02/01/2023]
Abstract
Heparan sulfate (HS) proteoglycans bind extracellular proteins that participate in cell signaling, attachment and endocytosis. These interactions depend on the arrangement of sulfated sugars in the HS chains generated by well-characterized biosynthetic enzymes; however, the regulation of these enzymes is largely unknown. We conducted genome-wide CRISPR-Cas9 screens with a small-molecule ligand that binds to HS. Screening of A375 melanoma cells uncovered additional genes and pathways impacting HS formation. The top hit was the epigenetic factor KDM2B, a histone demethylase. KDM2B inactivation suppressed multiple HS sulfotransferases and upregulated the sulfatase SULF1. These changes differentially affected the interaction of HS-binding proteins. KDM2B-deficient cells displayed decreased growth rates, which was rescued by SULF1 inactivation. In addition, KDM2B deficiency altered the expression of many extracellular matrix genes. Thus, KDM2B controls proliferation of A375 cells through the regulation of HS structure and serves as a master regulator of the extracellular matrix.
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Affiliation(s)
- Ryan J. Weiss
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Philipp N. Spahn
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Austin W.T. Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Qing Liu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Jing Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Kristina M. Hamill
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Sandra Rother
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Thomas M. Clausen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA,Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Marten A. Hoeksema
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Bryce M. Timm
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA,Department of Medicine, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA
| | - Philip L.S.M. Gordts
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA,Department of Medicine, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA,Co-corresponding authors
| | - Jeffrey D. Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA,Co-corresponding authors
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104
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Kaligotla VSA, Jasti T, Kandra P. CRISPR/Cas9 in cancer: An attempt to the present trends and future prospects. Biotechnol Appl Biochem 2021; 69:1238-1251. [PMID: 34033692 DOI: 10.1002/bab.2200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/12/2021] [Indexed: 11/08/2022]
Abstract
Cancer is the second leading cause of death globally. Series of sequential, repeated genetic changes and epigenetic modifications are leading to the formation of tumors. These tumors subsequently causing the infected cells to invade and transform their surrounding cells by metastasis are some hallmarks in cancer. Although tremendous efforts have been extended for structurally characterizing the numerous genomic mutations undergoing in cancer cells, there is a lack of information regarding the functions of many mutated genes. Clustered Regularly Interspaced Short Palindromic repeats/CRISPR-associated nuclease 9 (CRISPR/Cas9) has become a robust method for building changes in genome of many organisms. Recent reports have suggested that modification of CRISPR/Cas9 can provide plot form to probe the mechanisms in tumorigenesis and in cancer therapies. This review focuses on the historical perspectives of CRISPR/Cas9. The study highlights the applications and also role in cancer cell genome editing, which is helpful to understand the dynamics. Intense research in progress on mechanism of action of CRISPR/Cas9 has been reviewed and critically discussed. Further, relevant literature on animal models focusing on various approaches has been highlighted to emphasize the therapeutics of CRISPR/Cas9 with current trends and future challenges.
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Affiliation(s)
| | - Tejaswi Jasti
- Department of Biotechnology, GITAM Institute of Technology, GITAM Deemed to be University, Visakhapatnam, Andhra Pradesh, India
| | - Prameela Kandra
- Department of Biotechnology, GITAM Institute of Technology, GITAM Deemed to be University, Visakhapatnam, Andhra Pradesh, India
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105
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Wenmaekers S, Viergever BJ, Kumar G, Kranenburg O, Black PC, Daugaard M, Meijer RP. A Potential Role for HUWE1 in Modulating Cisplatin Sensitivity. Cells 2021; 10:cells10051262. [PMID: 34065298 PMCID: PMC8160634 DOI: 10.3390/cells10051262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/25/2022] Open
Abstract
Cisplatin is a widely used antineoplastic agent, whose efficacy is limited by primary and acquired therapeutic resistance. Recently, a bladder cancer genome-wide CRISPR/Cas9 knock-out screen correlated cisplatin sensitivity to multiple genetic biomarkers. Among the screen’s top hits was the HECT domain-containing ubiquitin E3 ligase (HUWE1). In this review, HUWE1 is postulated as a therapeutic response modulator, affecting the collision between platinum-DNA adducts and the replication fork, the primary cytotoxic action of platins. HUWE1 can alter the cytotoxic response to platins by targeting essential components of the DNA damage response including BRCA1, p53, and Mcl-1. Deficiency of HUWE1 could lead to enhanced DNA damage repair and a dysfunctional apoptotic apparatus, thereby inducing resistance to platins. Future research on the relationship between HUWE1 and platins could generate new mechanistic insights into therapy resistance. Ultimately, HUWE1 might serve as a clinical biomarker to tailor cancer treatment strategies, thereby improving cancer care and patient outcomes.
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Affiliation(s)
- Stijn Wenmaekers
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Bastiaan J. Viergever
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Gunjan Kumar
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Onno Kranenburg
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
| | - Peter C. Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Mads Daugaard
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
- Correspondence: (M.D.); (R.P.M.)
| | - Richard P. Meijer
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
- Correspondence: (M.D.); (R.P.M.)
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106
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Tian X, Wang X, Cui Z, Liu J, Huang X, Shi C, Zhang M, Liu T, Du X, Li R, Huang L, Gong D, Tian R, Cao C, Jin P, Zeng Z, Pan G, Xia M, Zhang H, Luo B, Xie Y, Li X, Li T, Wu J, Zhang Q, Chen G, Hu Z. A Fifteen-Gene Classifier to Predict Neoadjuvant Chemotherapy Responses in Patients with Stage IB to IIB Squamous Cervical Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2001978. [PMID: 34026427 PMCID: PMC8132153 DOI: 10.1002/advs.202001978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 02/01/2021] [Indexed: 05/09/2023]
Abstract
Neoadjuvant chemotherapy (NACT) remains an attractive alternative for controlling locally advanced cervical cancer. However, approximately 15-34% of women do not respond to induction therapy. To develop a risk stratification tool, 56 patients with stage IB-IIB cervical cancer are included in 2 research centers from the discovery cohort. Patient-specific somatic mutations led to NACT non-responsiveness are identified by whole-exome sequencing. Next, CRISPR/Cas9-based library screenings are performed based on these genes to confirm their biological contribution to drug resistance. A 15-gene classifier is developed by generalized linear regression analysis combined with the logistic regression model. In an independent validation cohort of 102 patients, the classifier showed good predictive ability with an area under the curve of 0.80 (95% confidence interval (CI), 0.69-0.91). Furthermore, the 15-gene classifier is significantly associated with patient responsiveness to NACT in both univariate (odds ratio, 10.8; 95% CI, 3.55-32.86; p = 2.8 × 10-5) and multivariate analysis (odds ratio, 17.34; 95% CI, 4.04-74.40; p = 1.23 × 10-4) in the validation set. In conclusion, the 15-gene classifier can accurately predict the clinical response to NACT before treatment, representing a promising approach for guiding the selection of appropriate treatment strategies for locally advanced cervical cancer.
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Affiliation(s)
- Xun Tian
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Xin Wang
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Zifeng Cui
- Department of Gynecological and OncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityZhongshan 2nd Road, YuexiuGuangzhouGuangdong510080China
| | - Jia Liu
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Xiaoyuan Huang
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Caixia Shi
- Department of Gynecological and OncologyHunan Cancer HospitalThe Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityJiefang Avenue 1095#WuhanHubei430030China
| | - Min Zhang
- NGS Research CenterNovogene Co, LtdBuilding 301, Zone A10 JiuxianqiaoBeijing100015China
| | - Ting Liu
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Xiaofang Du
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Rui Li
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Lei Huang
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Danni Gong
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Rui Tian
- Department of Gynecological and OncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityZhongshan 2nd Road, YuexiuGuangzhouGuangdong510080China
| | - Chen Cao
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Ping Jin
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Zhen Zeng
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Guangxin Pan
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Meng Xia
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Hongfeng Zhang
- Department of PathologyThe Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyShengli Street 26#, Jiang'an DistrictWuhanHubei430030China
| | - Bo Luo
- Department of PathologyThe Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyShengli Street 26#, Jiang'an DistrictWuhanHubei430030China
| | - Yonghui Xie
- Department of PathologyThe Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyShengli Street 26#, Jiang'an DistrictWuhanHubei430030China
| | - Xiaoming Li
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Tianye Li
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Jun Wu
- NGS Research CenterNovogene Co, LtdBuilding 301, Zone A10 JiuxianqiaoBeijing100015China
| | - Qinghua Zhang
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Gang Chen
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Zheng Hu
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
- Department of Gynecological and OncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityZhongshan 2nd Road, YuexiuGuangzhouGuangdong510080China
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107
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Ding R, Long J, Yuan M, Jin Y, Yang H, Chen M, Chen S, Duan G. CRISPR/Cas System: A Potential Technology for the Prevention and Control of COVID-19 and Emerging Infectious Diseases. Front Cell Infect Microbiol 2021; 11:639108. [PMID: 33968799 PMCID: PMC8102830 DOI: 10.3389/fcimb.2021.639108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
The continued global pandemic of coronavirus disease 2019 (COVID-19) poses a serious threat to global public health and social stability and it has become a serious global public health problem. Unfortunately, existing diagnostic and therapeutic approaches for the prevention and control of COVID-19 have many shortcomings. In recent years, the emerging CRISPR/Cas technology can complement the problems of traditional methods. Biological tools based on CRISPR/Cas systems have been widely used in biomedicine. In particular, they are advantageous in pathogen detection, clinical antiviral therapy, drug, and vaccine development. Therefore, CRISPR/Cas technology may have great potential for application in the prevention and control of COVID-19 and emerging infectious diseases in the future. This article summarizes the existing applications of CRISPR/Cas technology in infectious diseases with the aim of providing effective strategies for the prevention and control of COVID-19 and other emerging infectious diseases in the future.
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Affiliation(s)
- Ronghua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jinzhao Long
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Mingzhu Yuan
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yuefei Jin
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Mengshi Chen
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Shuaiyin Chen
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Guangcai Duan
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Key Laboratory of Molecular Medicine in Henan Province, Zhengzhou University, Zhengzhou, China
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108
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Karottki KJLC, Hefzi H, Li S, Pedersen LE, Spahn PN, Joshi C, Ruckerbauer D, Bort JAH, Thomas A, Lee JS, Borth N, Lee GM, Kildegaard HF, Lewis NE. A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes. Metab Eng 2021; 66:114-122. [PMID: 33813034 DOI: 10.1016/j.ymben.2021.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/25/2021] [Accepted: 03/28/2021] [Indexed: 12/20/2022]
Abstract
Media and feed optimization have fueled many-fold improvements in mammalian biopharmaceutical production, but genome editing offers an emerging avenue for further enhancing cell metabolism and bioproduction. However, the complexity of metabolism, involving thousands of genes, makes it unclear which engineering strategies will result in desired traits. Here we present a comprehensive pooled CRISPR screen for CHO cell metabolism, including ~16,000 gRNAs against ~2500 metabolic enzymes and regulators. Using this screen, we identified a glutamine response network in CHO cells. Glutamine is particularly important since it is often over-fed to drive increased TCA cycle flux, but toxic ammonia may accumulate. With the screen we found one orphan glutamine-responsive gene with no clear connection to our network. Knockout of this novel and poorly characterized lipase, Abhd11, substantially increased growth in glutamine-free media by altering the regulation of the TCA cycle. Thus, the screen provides an invaluable targeted platform to comprehensively study genes involved in any metabolic trait, and elucidate novel regulators of metabolism.
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Affiliation(s)
| | - Hooman Hefzi
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA; Department of Pediatrics, University of California, San Diego, USA; Department of Bioengineering, University of California, San Diego, USA
| | - Songyuan Li
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Philipp N Spahn
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA; Department of Pediatrics, University of California, San Diego, USA
| | - Chintan Joshi
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA; Department of Pediatrics, University of California, San Diego, USA
| | - David Ruckerbauer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Alex Thomas
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gyun Min Lee
- Department of Biological Sciences, Kaist, 291 Daehak-Ro, Yuseong-Gu, Daejeon, 305-701, Republic of Korea
| | | | - Nathan E Lewis
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA; Department of Pediatrics, University of California, San Diego, USA; Department of Bioengineering, University of California, San Diego, USA; National Biologics Facility, Technical University of Denmark, Denmark.
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109
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Lawson M, Elf J. Imaging-based screens of pool-synthesized cell libraries. Nat Methods 2021; 18:358-365. [PMID: 33589838 DOI: 10.1038/s41592-020-01053-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Mapping a genetic perturbation to a change in phenotype is at the core of biological research. Advances in microscopy have transformed these studies, but they have largely been confined to examining a few strains or cell lines at a time. In parallel, there has been a revolution in creating synthetic libraries of genetically altered cells with relative ease. Here we describe methods that combine these powerful tools to perform live-cell imaging of pool-generated strain libraries for improved biological discovery.
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Affiliation(s)
- Michael Lawson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Johan Elf
- Department of Cell and Molecular Biology Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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110
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Buquicchio FA, Satpathy AT. Interrogating immune cells and cancer with CRISPR-Cas9. Trends Immunol 2021; 42:432-446. [PMID: 33812776 DOI: 10.1016/j.it.2021.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas9 technologies have transformed the study of genetic pathways governing cellular differentiation and function. Recent advances have adapted these methods to immune cells, which has accelerated the pace of functional genomics in immunology and enabled new avenues for the design of cellular immunotherapies for cancer. In this review, we summarize recent developments in CRISPR-Cas9 technology and discuss how they have been leveraged to discover and manipulate novel genetic regulators of the immune system. We envision that these results will provide a valuable resource to aid in the design, implementation, and interpretation of CRISPR-Cas9-based screens in immunology and immuno-oncology.
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Affiliation(s)
- Frank A Buquicchio
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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111
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Castells-Roca L, Tejero E, Rodríguez-Santiago B, Surrallés J. CRISPR Screens in Synthetic Lethality and Combinatorial Therapies for Cancer. Cancers (Basel) 2021; 13:1591. [PMID: 33808217 PMCID: PMC8037779 DOI: 10.3390/cancers13071591] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
Cancer is a complex disease resulting from the accumulation of genetic dysfunctions. Tumor heterogeneity causes the molecular variety that divergently controls responses to chemotherapy, leading to the recurrent problem of cancer reappearance. For many decades, efforts have focused on identifying essential tumoral genes and cancer driver mutations. More recently, prompted by the clinical success of the synthetic lethality (SL)-based therapy of the PARP inhibitors in homologous recombinant deficient tumors, scientists have centered their novel research on SL interactions (SLI). The state of the art to find new genetic interactions are currently large-scale forward genetic CRISPR screens. CRISPR technology has rapidly evolved to be a common tool in the vast majority of laboratories, as tools to implement CRISPR screen protocols are available to all researchers. Taking advantage of SLI, combinatorial therapies have become the ultimate model to treat cancer with lower toxicity, and therefore better efficiency. This review explores the CRISPR screen methodology, integrates the up-to-date published findings on CRISPR screens in the cancer field and proposes future directions to uncover cancer regulation and individual responses to chemotherapy.
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Affiliation(s)
- Laia Castells-Roca
- Genome Instability and DNA Repair Syndromes Group, Sant Pau Biomedical Research Institute (IIB Sant Pau) and Join Unit UAB-IR Sant Pau on Genomic Medicine, 08041 Barcelona, Spain
- Genetics Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Eudald Tejero
- Sant Pau Biomedical Research Institute (IIB Sant Pau), 08041 Barcelona, Spain;
| | - Benjamín Rodríguez-Santiago
- Genetics Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Center for Biomedical Network Research on Rare Diseases (CIBERER) and Sant Pau Biomedical Research Institute (IIB Sant Pau), 08041 Barcelona, Spain
| | - Jordi Surrallés
- Genome Instability and DNA Repair Syndromes Group, Sant Pau Biomedical Research Institute (IIB Sant Pau) and Join Unit UAB-IR Sant Pau on Genomic Medicine, 08041 Barcelona, Spain
- Genetics Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER) and Sant Pau Biomedical Research Institute (IIB Sant Pau), 08041 Barcelona, Spain
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112
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Alsomali N, Hussein G. CRISPR-Cas9 and He Jiankui's Case: an Islamic Bioethics Review using Maqasid al-Shari'a and Qawaid Fighiyyah. Asian Bioeth Rev 2021; 13:149-165. [PMID: 34394752 DOI: 10.1007/s41649-021-00167-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 01/05/2023] Open
Abstract
The discovery of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-mediated protein 9 (CRISPR-Cas9) immediately revealed numerous potential therapeutic applications. Although CRISPR-Cas9 will most likely be useful for addressing issues such as genetic diseases and related medical issues, use of this modality for germline modification generates complex ethical questions regarding the safety and efficacy, human genetic enhancement, and "designer" babies. In this article, the case of the He Jiankui affair is used as an example of the potential for unregulated use of CRISPR-Cas9 technology. In 2018, Dr He Jiankui reported that he had successfully edited human embryos. This work clearly violates all international principles of bioethics. As such, the purpose of this paper is to explore the ethical challenges inherent in the use of CRISPR-Cas9 for human germline editing from the perspectives of the goals of Islamic law (Maqasid al Shari'a) and the major jurisprudential maxims (Qawaid Fiqhiyyah). We argue that from an Islamic standpoint, the therapeutic application of CRISPR-Cas9 for germline editing may be permissible if the safety and efficacy concerns are resolved and if the principles of Maqasid al-Shari'a are fulfilled.
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Affiliation(s)
- Nimah Alsomali
- Research Center, Neuroscience Department, King Fahad Medical City, Riyadh, Saudi Arabia
- College of Medicine, Prince Sattam Bin Abdulaziz University, Riyadh, Saudi Arabia
| | - Ghaiath Hussein
- College of Public Health & Health Informatics, King Saud bin AbdulAziza University for Health Sciences, Riyadh, Saudi Arabia
- King Abdulla International Medical City, Research Center, Riyadh, Saudi Arabia
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113
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Dubreuil MM, Morgens DW, Okumoto K, Honsho M, Contrepois K, Lee-McMullen B, Traber GM, Sood RS, Dixon SJ, Snyder MP, Fujiki Y, Bassik MC. Systematic Identification of Regulators of Oxidative Stress Reveals Non-canonical Roles for Peroxisomal Import and the Pentose Phosphate Pathway. Cell Rep 2021; 30:1417-1433.e7. [PMID: 32023459 DOI: 10.1016/j.celrep.2020.01.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/07/2019] [Accepted: 01/02/2020] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) play critical roles in metabolism and disease, yet a comprehensive analysis of the cellular response to oxidative stress is lacking. To systematically identify regulators of oxidative stress, we conducted genome-wide Cas9/CRISPR and shRNA screens. This revealed a detailed picture of diverse pathways that control oxidative stress response, ranging from the TCA cycle and DNA repair machineries to iron transport, trafficking, and metabolism. Paradoxically, disrupting the pentose phosphate pathway (PPP) at the level of phosphogluconate dehydrogenase (PGD) protects cells against ROS. This dramatically alters metabolites in the PPP, consistent with rewiring of upper glycolysis to promote antioxidant production. In addition, disruption of peroxisomal import unexpectedly increases resistance to oxidative stress by altering the localization of catalase. Together, these studies provide insights into the roles of peroxisomal matrix import and the PPP in redox biology and represent a rich resource for understanding the cellular response to oxidative stress.
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Affiliation(s)
- Michael M Dubreuil
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - David W Morgens
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Kanji Okumoto
- Department of Biology, Faculty of Sciences, Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masanori Honsho
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | | | | | - Ria S Sood
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Scott J Dixon
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305-5120, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Michael C Bassik
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305-5120, USA.
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114
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Wang C, Fang H, Zhang J, Gu Y. Targeting "undruggable" c-Myc protein by synthetic lethality. Front Med 2021; 15:541-550. [PMID: 33660217 DOI: 10.1007/s11684-020-0780-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
Synthetic lethal screening, which exploits the combination of mutations that result in cell death, is a promising method for identifying novel drug targets. This method provides a new avenue for targeting "undruggable" proteins, such as c-Myc. Here, we revisit current methods used to target c-Myc and discuss the important functional nodes related to c-Myc in non-oncogene addicted network, whose inhibition may cause a catastrophe for tumor cell destiny but not for normal cells. We further discuss strategies to identify these functional nodes in the context of synthetic lethality. We review the progress and shortcomings of this research field and look forward to opportunities offered by synthetic lethal screening to treat tumors potently.
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Affiliation(s)
- Chen Wang
- Division of Genome Medicine and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Hui Fang
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiawei Zhang
- Division of Genome Medicine and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
| | - Ying Gu
- Division of Genome Medicine and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
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115
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Ramadan M, Alariqi M, Ma Y, Li Y, Liu Z, Zhang R, Jin S, Min L, Zhang X. Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton. PLANT METHODS 2021; 17:16. [PMID: 33557889 PMCID: PMC7869495 DOI: 10.1186/s13007-021-00712-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. RESULTS To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. CONCLUSION All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.
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Affiliation(s)
- Mohamed Ramadan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Department of Plant Genetic Resources, Division of Ecology and Dry Land Agriculture, Desert Research Center, Cairo, Egypt
| | - Muna Alariqi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanlong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Rui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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116
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Gene insertion in Saccharomyces cerevisiae using the CRISPR/Cas9 system. 3 Biotech 2021; 11:90. [PMID: 33520576 DOI: 10.1007/s13205-021-02648-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022] Open
Abstract
The aim of this work was to rapidly and efficiently insert target DNA sequences into predetermined genomic sites in Saccharomyces cerevisiae. In this study, we designed two technical routes for gene insertion in the S. cerevisiae genome based on the CRISPR/Cas9 system, and a CRISPR array was inserted into the Amp site and the crRNA site of the pCRCT plasmid, respectively. The CRISPR array consists of a 100 bp donor sequence, the target gene and guide sequence. A 100 bp donor sequence was designed to have two 50 bp homology arms flanking the Cas9 cutting site and incorporate 8 bp or 1000 bp deletions including the PAM sequence, where the target gene was also inserted. The results showed that using only one pCRCTG plasmid and a 100 bp dsDNA mutagenizing homologous recombination donor, we can successfully insert a 2.9 kb gene fragment at the target site of the S. cerevisiae genome. However, inserting the CRISPR array into the crRNA site has a higher recombination efficiency than inserting into the Amp site. This recombination strategy represents a powerful tool for creating yeast strains with target gene inserts.
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117
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Cui Y, Cheng X, Chen Q, Song B, Chiu A, Gao Y, Dawson T, Chao L, Zhang W, Li D, Zeng Z, Yu J, Li Z, Fei T, Peng S, Li W. CRISP-view: a database of functional genetic screens spanning multiple phenotypes. Nucleic Acids Res 2021; 49:D848-D854. [PMID: 33010154 PMCID: PMC7778972 DOI: 10.1093/nar/gkaa809] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022] Open
Abstract
High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides a wealth of knowledge about genotype-to-phenotype relationships and a valuable resource for the systematic analysis of gene functions. Here we present CRISP-view, a comprehensive database of CRISPR/Cas9 and RNAi screening datasets that span multiple phenotypes, including in vitro and in vivo cell proliferation and viability, response to cancer immunotherapy, virus response, protein expression, etc. By 22 September 2020, CRISP-view has collected 10 321 human samples and 825 mouse samples from 167 papers. All the datasets have been curated, annotated, and processed by a standard MAGeCK-VISPR analysis pipeline with quality control (QC) metrics. We also developed a user-friendly webserver to visualize, explore, and search these datasets. The webserver is freely available at http://crispview.weililab.org.
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Affiliation(s)
- Yingbo Cui
- Sanyi Road, Changsha, Hunan Province, People's Republic of China
| | - Xiaolong Cheng
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA
| | - Qing Chen
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA
| | - Bicna Song
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA
| | - Anthony Chiu
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA.,School of Medicine and Health Sciences, George Washington University, 2300 I Street NW, Washington, DC 20037, USA
| | - Yuan Gao
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA.,Department of Biochemistry and Molecular Biology, George Washington University, 2300 I Street NW, Washington, DC 20037, USA
| | - Tyson Dawson
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA.,Institute for Biomedical Sciences, George Washington University, 2300 I Street NW, Washington, DC 20037, USA.,Computational Biology Institute, Milken Institute School of Public Health, George Washington University, 45085 University Drive, Ashburn, VA 20148, USA
| | - Lumen Chao
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA
| | - Wubing Zhang
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health. 450 Brookline Ave., Boston MA 02215, USA
| | - Dian Li
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health. 450 Brookline Ave., Boston MA 02215, USA
| | - Zexiang Zeng
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health. 450 Brookline Ave., Boston MA 02215, USA
| | - Jijun Yu
- Beijing Key Laboratory of Therapeutic Gene Engineering Antibody. Beijing, People's Republic of China
| | - Zexu Li
- College of Life and Health Sciences, Northeastern University. 110819 Shenyang, People's Republic of China
| | - Teng Fei
- College of Life and Health Sciences, Northeastern University. 110819 Shenyang, People's Republic of China
| | - Shaoliang Peng
- Lushan South Road, Changsha, Hunan Province, People's Republic of China
| | - Wei Li
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University. 111 Michigan Ave NW, Washington, DC 20010, USA
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118
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Yadav N, Narang J, Chhillar AK, Rana JS. CRISPR: A new paradigm of theranostics. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 33:102350. [PMID: 33359413 PMCID: PMC7831819 DOI: 10.1016/j.nano.2020.102350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/09/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022]
Abstract
Infectious and hereditary diseases are the primary cause of human mortality globally. Applications of conventional techniques require significant improvement in sensitivity and specificity in therapeutics. However, clustered regularly interspaced short palindromic repeats (CRISPRs) is an innovative genome editing technology which has provided a significant therapeutic tool exhibiting high sensitivity, fast and precise investigation of distinct pathogens in an epidemic. CRISPR technology has also facilitated the understanding of the biology and therapeutic mechanism of cancer and several other hereditary diseases. Researchers have used the CRISPR technology as a theranostic approach for a wide range of diseases causing pathogens including distinct bacteria, viruses, fungi and parasites and genetic mutations as well. In this review article, besides various therapeutic applications of infectious and hereditary diseases we have also explained the structure and mechanism of CRISPR tools and role of CRISPR integrated biosensing technology in provoking diagnostic applications.
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Affiliation(s)
- Neelam Yadav
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonepat; Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana.
| | - Jagriti Narang
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi, India.
| | | | - Jogender Singh Rana
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonepat.
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119
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Recent advance of peptide-based molecules and nonpeptidic small-molecules modulating PD-1/PD-L1 protein-protein interaction or targeting PD-L1 protein degradation. Eur J Med Chem 2021; 213:113170. [PMID: 33454550 DOI: 10.1016/j.ejmech.2021.113170] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 12/13/2022]
Abstract
Tumor immunotherapy has made great progress in recent years. In the tumor microenvironment, the binding of PD-1 and its ligand PD-L1 can promote tumor immune escape and tumor survival. Clinical studies have indicated that antibodies blocking PD-1 and PD-L1 have reliable effects on many advanced malignant tumors. However, no small-molecule inhibitors have been approved so far, indicating that the development of marketable small-molecules PD-1/PD-L1 targeted therapy drugs is a challenging process. Small-molecule inhibitors can overcome the limitations of monoclonal antibodies, including poor oral bioavailability, high cost, poor tissue and tumor penetration and long half-life, which prompt researchers to turn their attention to the development of peptide molecules and small-molecule inhibitors modulating PD-1/PD-L1 to overcome some disadvantages of monoclonal antibodies or targeting PD-L1 protein degradation as potential alternatives or supplements. In this review, we will focus on the peptide-based and nonpeptidic molecules against PD-1/PD-L1 base on the structural classification. More importantly, we also focus on the latest research progress of small-molecules mediated PD-L1 degradation mechanism.
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Kim E, Hart T. Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier. Genome Med 2021; 13:2. [PMID: 33407829 PMCID: PMC7789424 DOI: 10.1186/s13073-020-00809-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023] Open
Abstract
Background Identifying essential genes in genome-wide loss-of-function screens is a critical step in functional genomics and cancer target finding. We previously described the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm for accurate classification of gene essentiality from short hairpin RNA and CRISPR/Cas9 genome-wide genetic screens. Results We introduce an updated version, BAGEL2, which employs an improved model that offers a greater dynamic range of Bayes Factors, enabling detection of tumor suppressor genes; a multi-target correction that reduces false positives from off-target CRISPR guide RNA; and the implementation of a cross-validation strategy that improves performance ~ 10× over the prior bootstrap resampling approach. We also describe a metric for screen quality at the replicate level and demonstrate how different algorithms handle lower quality data in substantially different ways. Conclusions BAGEL2 substantially improves the sensitivity, specificity, and performance over BAGEL and establishes the new state of the art in the analysis of CRISPR knockout fitness screens. BAGEL2 is written in Python 3 and source code, along with all supporting files, are available on github (https://github.com/hart-lab/bagel).
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Affiliation(s)
- Eiru Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Liang Y, Zhang G, Li Q, Han L, Hu X, Guo Y, Tao W, Zhao X, Guo M, Gan T, Tong Y, Xu Y, Zhou Z, Ding Q, Wei W, Zhong J. TRIM26 is a critical host factor for HCV replication and contributes to host tropism. SCIENCE ADVANCES 2021; 7:7/2/eabd9732. [PMID: 33523994 PMCID: PMC7793585 DOI: 10.1126/sciadv.abd9732] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/13/2020] [Indexed: 05/04/2023]
Abstract
Hepatitis C virus (HCV) remains a major human pathogen that requires better understanding of virus-host interactions. In this study, we performed a genome-wide CRISPR-Cas9 screening and identified TRIM26, an E3 ligase, as a critical HCV host factor. Deficiency of TRIM26 specifically impairs HCV genome replication. Mechanistic studies showed that TRIM26 interacts with HCV-encoded NS5B protein and mediates its K27-linked ubiquitination at residue K51, and thus promotes the NS5B-NS5A interaction. Moreover, mouse TRIM26 does not support HCV replication because of its unique six-amino acid insert that prevents its interaction with NS5B. Ectopic expression of human TRIM26 in a mouse hepatoma cell line that has been reconstituted with other essential HCV host factors promotes HCV infection. In conclusion, we identified TRIM26 as a host factor for HCV replication and a new determinant of host tropism. These results shed light on HCV-host interactions and may facilitate the development of an HCV animal model.
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Affiliation(s)
- Yisha Liang
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guigen Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), 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.
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Qiheng Li
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), 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
| | - Lin Han
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyou Hu
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Guo
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), 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
| | - Wanyin Tao
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaomin Zhao
- Center for Infectious Diseases Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Mingzhe Guo
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyu Gan
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimin Tong
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yongfen Xu
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), 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
| | - Qiang Ding
- Center for Infectious Diseases Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), 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.
| | - Jin Zhong
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Bao MHR, Yang C, Tse APW, Wei L, Lee D, Zhang MS, Goh CC, Chiu DKC, Yuen VWH, Law CT, Chin WC, Chui NNQ, Wong BPY, Chan CYK, Ng IOL, Chung CYS, Wong CM, Wong CCL. Genome-wide CRISPR-Cas9 knockout library screening identified PTPMT1 in cardiolipin synthesis is crucial to survival in hypoxia in liver cancer. Cell Rep 2021; 34:108676. [PMID: 33503428 DOI: 10.1016/j.celrep.2020.108676] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 11/11/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Hypoxia, low oxygen (O2), is a key feature of all solid cancers, including hepatocellular carcinoma (HCC). Genome-wide CRISPR-Cas9 knockout library screening is used to identify reliable therapeutic targets responsible for hypoxic survival in HCC. We find that protein-tyrosine phosphatase mitochondrial 1 (PTPMT1), an important enzyme for cardiolipin (CL) synthesis, is the most significant gene and ranks just after hypoxia-inducible factor (HIF)-1α and HIF-1β as crucial to hypoxic survival. CL constitutes the mitochondrial membrane and ensures the proper assembly of electron transport chain (ETC) complexes for efficient electron transfer in respiration. ETC becomes highly unstable during hypoxia. Knockout of PTPMT1 stops the maturation of CL and impairs the assembly of ETC complexes, leading to further electron leakage and ROS accumulation at ETC in hypoxia. Excitingly, HCC cells, especially under hypoxic conditions, show great sensitivity toward PTPMT1 inhibitor alexidine dihydrochloride (AD). This study unravels the protective roles of PTPMT1 in hypoxic survival and cancer development.
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Affiliation(s)
| | - Chunxue Yang
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Aki Pui-Wah Tse
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Lai Wei
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Derek Lee
- Department of Pathology, The University of Hong Kong, Hong Kong
| | | | - Chi Ching Goh
- Department of Pathology, The University of Hong Kong, Hong Kong
| | | | | | - Cheuk-Ting Law
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Wai-Ching Chin
- Department of Pathology, The University of Hong Kong, Hong Kong
| | | | | | | | - Irene Oi-Lin Ng
- Department of Pathology, The University of Hong Kong, Hong Kong; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Clive Yik-Sham Chung
- Department of Pathology, The University of Hong Kong, Hong Kong; School of Biomedical Sciences, The University of Hong Kong, Hong Kong
| | - Chun-Ming Wong
- Department of Pathology, The University of Hong Kong, Hong Kong; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong.
| | - Carmen Chak-Lui Wong
- Department of Pathology, The University of Hong Kong, Hong Kong; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong.
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123
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Janik E, Niemcewicz M, Ceremuga M, Krzowski L, Saluk-Bijak J, Bijak M. Various Aspects of a Gene Editing System-CRISPR-Cas9. Int J Mol Sci 2020; 21:E9604. [PMID: 33339441 PMCID: PMC7767219 DOI: 10.3390/ijms21249604] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
The discovery of clustered, regularly interspaced short palindromic repeats (CRISPR) and their cooperation with CRISPR-associated (Cas) genes is one of the greatest advances of the century and has marked their application as a powerful genome engineering tool. The CRISPR-Cas system was discovered as a part of the adaptive immune system in bacteria and archaea to defend from plasmids and phages. CRISPR has been found to be an advanced alternative to zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) for gene editing and regulation, as the CRISPR-Cas9 protein remains the same for various gene targets and just a short guide RNA sequence needs to be altered to redirect the site-specific cleavage. Due to its high efficiency and precision, the Cas9 protein derived from the type II CRISPR system has been found to have applications in many fields of science. Although CRISPR-Cas9 allows easy genome editing and has a number of benefits, we should not ignore the important ethical and biosafety issues. Moreover, any tool that has great potential and offers significant capabilities carries a level of risk of being used for non-legal purposes. In this review, we present a brief history and mechanism of the CRISPR-Cas9 system. We also describe on the applications of this technology in gene regulation and genome editing; the treatment of cancer and other diseases; and limitations and concerns of the use of CRISPR-Cas9.
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Affiliation(s)
- Edyta Janik
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.)
| | - Marcin Niemcewicz
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.)
| | - Michal Ceremuga
- Military Institute of Armament Technology, Prymasa Stefana Wyszyńskiego 7, 05-220 Zielonka, Poland;
| | - Lukasz Krzowski
- Biodefense Laboratory, Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, gen. Sylwestra Kaliskiego 2, 00-908 Warsaw, Poland;
| | - Joanna Saluk-Bijak
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland;
| | - Michal Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.)
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Hazafa A, Mumtaz M, Farooq MF, Bilal S, Chaudhry SN, Firdous M, Naeem H, Ullah MO, Yameen M, Mukhtiar MS, Zafar F. CRISPR/Cas9: A powerful genome editing technique for the treatment of cancer cells with present challenges and future directions. Life Sci 2020; 263:118525. [PMID: 33031826 PMCID: PMC7533657 DOI: 10.1016/j.lfs.2020.118525] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Cancer is one of the most leading causes of death and a major public health problem, universally. According to accumulated data, annually, approximately 8.5 million people died because of the lethality of cancer. Recently, a novel RNA domain-containing endonuclease-based genome engineering technology, namely the clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-9 (Cas9) have been proved as a powerful technique in the treatment of cancer cells due to its multifunctional properties including high specificity, accuracy, time reducing and cost-effective strategies with minimum off-target effects. The present review investigates the overview of recent studies on the newly developed genome-editing strategy, CRISPR/Cas9, as an excellent pre-clinical therapeutic option in the reduction and identification of new tumor target genes in the solid tumors. Based on accumulated data, we revealed that CRISPR/Cas9 significantly inhibited the robust tumor cell growth (breast, lung, liver, colorectal, and prostate) by targeting the oncogenes, tumor-suppressive genes, genes associated to therapies by inhibitors, genes associated to chemotherapies drug resistance, and suggested that CRISPR/Cas9 could be a potential therapeutic target in inhibiting the tumor cell growth by suppressing the cell-proliferation, metastasis, invasion and inducing the apoptosis during the treatment of malignancies in the near future. The present review also discussed the current challenges and barriers, and proposed future recommendations for a better understanding.
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Affiliation(s)
- Abu Hazafa
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Muhammad Mumtaz
- Department of Chemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Fras Farooq
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Shahid Bilal
- Department of Agronomy, Faculty of Agriculture, University of Agriculture, Faisalabad 38000, Pakistan
| | - Sundas Nasir Chaudhry
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Musfira Firdous
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Huma Naeem
- Department of Computer Science, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Obaid Ullah
- Department of Zoology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Muhammad Yameen
- Department of Biochemistry, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan.
| | - Muhammad Shahid Mukhtiar
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Fatima Zafar
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan
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125
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Pasquer QTL, Tsakoumagkos IA, Hoogendoorn S. From Phenotypic Hit to Chemical Probe: Chemical Biology Approaches to Elucidate Small Molecule Action in Complex Biological Systems. Molecules 2020; 25:E5702. [PMID: 33287212 PMCID: PMC7730769 DOI: 10.3390/molecules25235702] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/22/2023] Open
Abstract
Biologically active small molecules have a central role in drug development, and as chemical probes and tool compounds to perturb and elucidate biological processes. Small molecules can be rationally designed for a given target, or a library of molecules can be screened against a target or phenotype of interest. Especially in the case of phenotypic screening approaches, a major challenge is to translate the compound-induced phenotype into a well-defined cellular target and mode of action of the hit compound. There is no "one size fits all" approach, and recent years have seen an increase in available target deconvolution strategies, rooted in organic chemistry, proteomics, and genetics. This review provides an overview of advances in target identification and mechanism of action studies, describes the strengths and weaknesses of the different approaches, and illustrates the need for chemical biologists to integrate and expand the existing tools to increase the probability of evolving screen hits to robust chemical probes.
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Affiliation(s)
| | | | - Sascha Hoogendoorn
- Department of Organic Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211 Genève, Switzerland; (Q.T.L.P.); (I.A.T.)
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126
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Liu X, Yang Y, Qiu Y, Reyad-Ul-Ferdous M, Ding Q, Wang Y. SeqCor: correct the effect of guide RNA sequences in clustered regularly interspaced short palindromic repeats/Cas9 screening by machine learning algorithm. J Genet Genomics 2020; 47:672-680. [PMID: 33451939 DOI: 10.1016/j.jgg.2020.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 09/07/2020] [Accepted: 10/26/2020] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based screening using various guide RNA (gRNA) libraries has been executed to identify functional components for a wide range of phenotypes with regard to numerous cell types and organisms. Using data from public CRISPR/Cas9-based screening experiments, we found that the sequences of gRNAs in the library influence CRISPR/Cas9-based screening. As building a standard strategy for correcting results of all gRNA libraries is impractical, we developed SeqCor, an open-source programming bundle that enables researchers to address the result bias potentially triggered by the composition of gRNA sequences via the organization of gRNA in the library used in CRISPR/Cas9-based screening. Furthermore, SeqCor completely computerizes the extraction of sequence features that may influence single-guide RNA knockout efficiency using a machine learning approach. Taken together, we have developed a software program bundle that ought to be beneficial to the CRISPR/Cas9-based screening platform.
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Affiliation(s)
- Xiaojian Liu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuanyuan Yang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Qiu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Md Reyad-Ul-Ferdous
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiurong Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China; Human Phenome Institute, Fudan University, Shanghai 200438, China.
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127
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Sreedurgalakshmi K, Srikar R, Rajkumari R. CRISPR-Cas deployment in non-small cell lung cancer for target screening, validations, and discoveries. Cancer Gene Ther 2020; 28:566-580. [PMID: 33191402 DOI: 10.1038/s41417-020-00256-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/14/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022]
Abstract
Continued advancements in CRISPR-Cas systems have accelerated genome research. Use of CRISPR-Cas in cancer research has been of great interest that is resulting in development of orthogonal methods for drug target validations and discovery of new therapeutic targets through genome-wide screens of cancer cells. CRISPR-based screens have also revealed several new cancer drivers through alterations in tumor suppressor genes (TSGs) and oncogenes inducing resistance to targeted therapies via activation of alternate signaling pathways. Given such dynamic status of cancer, we review the application of CRISPR-Cas in non-small cell lung cancer (NSCLC) for development of mutant models, drug screening, target validation, novel target discoveries, and other emerging potential applications. In addition, CRISPR-based approach for development of novel anticancer combination therapies is also discussed in this review.
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Affiliation(s)
- K Sreedurgalakshmi
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India.,Division of Biosimilars and Gene Therapy, R&D, Levim Biotech LLP, Chennai, Tamilnadu, India
| | - R Srikar
- Division of Biosimilars and Gene Therapy, R&D, Levim Biotech LLP, Chennai, Tamilnadu, India.
| | - Reena Rajkumari
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, India.
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128
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Gallegos JE, Rogers MF, Cialek CA, Peccoud J. Rapid, robust plasmid verification by de novo assembly of short sequencing reads. Nucleic Acids Res 2020; 48:e106. [PMID: 32890398 PMCID: PMC7544192 DOI: 10.1093/nar/gkaa727] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/07/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
Plasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and—depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.
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Affiliation(s)
- Jenna E Gallegos
- Department of Chemical & Biological Engineering, Colorado State University, USA
| | | | - Charlotte A Cialek
- GenoFAB, Inc.,Department of Biochemistry and Molecular Biology, Colorado State University, USA
| | - Jean Peccoud
- Department of Chemical & Biological Engineering, Colorado State University, USA.,GenoFAB, Inc
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129
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Azangou-Khyavy M, Ghasemi M, Khanali J, Boroomand-Saboor M, Jamalkhah M, Soleimani M, Kiani J. CRISPR/Cas: From Tumor Gene Editing to T Cell-Based Immunotherapy of Cancer. Front Immunol 2020; 11:2062. [PMID: 33117331 PMCID: PMC7553049 DOI: 10.3389/fimmu.2020.02062] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats system has demonstrated considerable advantages over other nuclease-based genome editing tools due to its high accuracy, efficiency, and strong specificity. Given that cancer is caused by an excessive accumulation of mutations that lead to the activation of oncogenes and inactivation of tumor suppressor genes, the CRISPR/Cas9 system is a therapy of choice for tumor genome editing and treatment. In defining its superior use, we have reviewed the novel applications of the CRISPR genome editing tool in discovering, sorting, and prioritizing targets for subsequent interventions, and passing different hurdles of cancer treatment such as epigenetic alterations and drug resistance. Moreover, we have reviewed the breakthroughs precipitated by the CRISPR system in the field of cancer immunotherapy, such as identification of immune system-tumor interplay, production of universal Chimeric Antigen Receptor T cells, inhibition of immune checkpoint inhibitors, and Oncolytic Virotherapy. The existing challenges and limitations, as well as the prospects of CRISPR based systems, are also discussed.
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Affiliation(s)
| | - Mobina Ghasemi
- Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Khanali
- Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Monire Jamalkhah
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Masoud Soleimani
- Hematology Department, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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130
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Veeneman B, Gao Y, Grant J, Fruhling D, Ahn J, Bosbach B, Bienkowska J, Follettie M, Arndt K, Myers J, Zhong W. PINCER: improved CRISPR/Cas9 screening by efficient cleavage at conserved residues. Nucleic Acids Res 2020; 48:9462-9477. [PMID: 32821942 PMCID: PMC7515706 DOI: 10.1093/nar/gkaa645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 functional genomic screens have emerged as essential tools in drug target discovery. However, the sensitivity of available genome-wide CRISPR libraries is impaired by guides which inefficiently abrogate gene function. While Cas9 cleavage efficiency optimization and essential domain targeting have been developed as independent guide design rationales, no library has yet combined these into a single cohesive strategy to knock out gene function. Here, in a massive reanalysis of CRISPR tiling data using the most comprehensive feature database assembled, we determine which features of guides and their targets best predict activity and how to best combine them into a single guide design algorithm. We present the ProteIN ConsERvation (PINCER) genome-wide CRISPR library, which for the first time combines enzymatic efficiency optimization with conserved length protein region targeting, and also incorporates domains, coding sequence position, U6 termination (TTT), restriction sites, polymorphisms and specificity. Finally, we demonstrate superior performance of the PINCER library compared to alternative genome-wide CRISPR libraries in head-to-head validation. PINCER is available for individual gene knockout and genome-wide screening for both the human and mouse genomes.
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Affiliation(s)
- Brendan Veeneman
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, Pearl River, NY 10965, USA
| | - Ying Gao
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, Pearl River, NY 10965, USA
| | - Joy Grant
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, Pearl River, NY 10965, USA
| | - David Fruhling
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, Pearl River, NY 10965, USA
| | - James Ahn
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, Pearl River, NY 10965, USA
| | - Benedikt Bosbach
- Emerging Sciences & Innovation, Pfizer Worldwide Research, Development and Medical, New York, NY 10016, USA
| | - Jadwiga Bienkowska
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, San Diego, CA 92121, USA
| | - Maximillian Follettie
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, Pearl River, NY 10965, USA
| | - Kim Arndt
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, Pearl River, NY 10965, USA
| | - Jeremy Myers
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, Pearl River, NY 10965, USA
| | - Wenyan Zhong
- Oncology Research and Development, Pfizer Worldwide Research, Development and Medical, Pearl River, NY 10965, USA
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131
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Xu Y, Li Z. CRISPR-Cas systems: Overview, innovations and applications in human disease research and gene therapy. Comput Struct Biotechnol J 2020; 18:2401-2415. [PMID: 33005303 PMCID: PMC7508700 DOI: 10.1016/j.csbj.2020.08.031] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023] Open
Abstract
Genome editing is the modification of genomic DNA at a specific target site in a wide variety of cell types and organisms, including insertion, deletion and replacement of DNA, resulting in inactivation of target genes, acquisition of novel genetic traits and correction of pathogenic gene mutations. Due to the advantages of simple design, low cost, high efficiency, good repeatability and short-cycle, CRISPR-Cas systems have become the most widely used genome editing technology in molecular biology laboratories all around the world. In this review, an overview of the CRISPR-Cas systems will be introduced, including the innovations, the applications in human disease research and gene therapy, as well as the challenges and opportunities that will be faced in the practical application of CRISPR-Cas systems.
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Affiliation(s)
- Yuanyuan Xu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
| | - Zhanjun Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
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132
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Lewis M, Prouzet‐Mauléon V, Lichou F, Richard E, Iggo R, Turcq B, Mahon F. A genome-scale CRISPR knock-out screen in chronic myeloid leukemia identifies novel drug resistance mechanisms along with intrinsic apoptosis and MAPK signaling. Cancer Med 2020; 9:6739-6751. [PMID: 38831555 PMCID: PMC7520295 DOI: 10.1002/cam4.3231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding resistance mechanisms in cancer is of utmost importance for the discovery of novel "druggable" targets. Efficient genetic screening, now even more possible with CRISPR-Cas9 gene-editing technology, next-generation sequencing and bioinformatics, is an important tool for deciphering novel cellular processes, such as resistance to treatment in cancer. Imatinib specifically eliminates chronic myeloid leukemia (CML) cells by targeting and blocking the kinase activity of BCR-ABL1; however, resistance to treatment exists. In order to discover BCR-ABL1 independent mechanisms of imatinib resistance, we utilized the genome-scale CRISPR knock-out library to screen for imatinib-sensitizing genes in vitro on K562 cells. We revealed genes that seem essential for imatinib-induced cell death, such as proapoptotic genes (BIM, BAX) or MAPK inhibitor SPRED2. Specifically, reestablishing apoptosis in BIM knock-out (KO) cells with BH3 mimetics, or inhibiting MAPK signaling in SPRED2 KO cells with MEK inhibitors restores sensitivity to imatinib. In this work, we discovered previously identified pathways and novel pathways that modulate response to imatinib in CML cell lines, such as the implication of the Mediator complex, mRNA processing and protein ubiquitinylation. Targeting these specific genetic lesions with combinational therapy can overcome resistance phenotypes and paves the road for the use of precision oncology.
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Affiliation(s)
- Matthieu Lewis
- Laboratory of Mammary and Leukemic OncogenesisInserm U1218 ACTIONUniversity of BordeauxBergonié Cancer InstituteBordeauxFrance
| | - Valérie Prouzet‐Mauléon
- Laboratory of Mammary and Leukemic OncogenesisInserm U1218 ACTIONUniversity of BordeauxBergonié Cancer InstituteBordeauxFrance
| | - Florence Lichou
- Laboratory of Mammary and Leukemic OncogenesisInserm U1218 ACTIONUniversity of BordeauxBergonié Cancer InstituteBordeauxFrance
| | - Elodie Richard
- Laboratory of Mammary and Leukemic OncogenesisInserm U1218 ACTIONUniversity of BordeauxBergonié Cancer InstituteBordeauxFrance
| | - Richard Iggo
- Laboratory of Mammary and Leukemic OncogenesisInserm U1218 ACTIONUniversity of BordeauxBergonié Cancer InstituteBordeauxFrance
| | - Béatrice Turcq
- Laboratory of Mammary and Leukemic OncogenesisInserm U1218 ACTIONUniversity of BordeauxBergonié Cancer InstituteBordeauxFrance
| | - François‐Xavier Mahon
- Laboratory of Mammary and Leukemic OncogenesisInserm U1218 ACTIONUniversity of BordeauxBergonié Cancer InstituteBordeauxFrance
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133
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Rousset F, Bikard D. CRISPR screens in the era of microbiomes. Curr Opin Microbiol 2020; 57:70-77. [PMID: 32858412 DOI: 10.1016/j.mib.2020.07.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
Recent advances in genomics have uncovered the tremendous diversity and richness of microbial ecosystems. New functional genomics methods are now needed to probe gene function in high-throughput and provide mechanistic insights. Here, we review how the CRISPR toolbox can be used to inactivate, repress or overexpress genes in a sequence-specific manner and how this offers diverse attractive solutions to identify gene function in high-throughput. Developed both in eukaryotes and prokaryotes, CRISPR screening technologies have already provided meaningful insights in microbiology and host-pathogen interactions. In the era of microbiomes, the versatility and the functional diversity of CRISPR-derived tools has the potential to significantly improve our understanding of microbial communities and their interaction with the host.
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Affiliation(s)
- François Rousset
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France; Sorbonne Université, Collège Doctoral, F-75005 Paris, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France.
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134
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Zhu Y, Groth T, Kelkar A, Zhou Y, Neelamegham S. A GlycoGene CRISPR-Cas9 lentiviral library to study lectin binding and human glycan biosynthesis pathways. Glycobiology 2020; 31:173-180. [PMID: 32776087 DOI: 10.1093/glycob/cwaa074] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/25/2022] Open
Abstract
Glycan biosynthesis on cell surface proteins and lipids is orchestrated by different classes of enzymes and proteins including the following: i. glycosyltransferases that add saccharides; ii. glycosidases that trim glycans; iii. conserved oligomeric golgi complex members that regulate intracellular transport; iv. enzymes aiding the biosynthesis of sugar-nucleotides; and v. sulfotransferases. This manuscript describes a pooled "glycoGene CRISPR" lentiviral library that targets 347 human genes involved in the above processes. Approximately 10 single-guide RNA (sgRNA) are included against each glycogene, with the putative editing site spanning the length of the target. A data analysis scheme is presented in order to determine glycosylation pathways regulating biological processes. As proof of principle, forward genetic screen results are presented to identify penetrating glycogenes that regulate the binding of P-/E-selectin, anti-sialyl Lewis-X monoclonal antibody HECA-452 and selected lectins (phaseolus vulgaris leucoagglutinin, vicia villosa lectin, peanut agglutinin) to HL-60 promyelocytic cells. Besides validating previously established biology, the study identifies three enzymes, PAPSS1, SLC35B2 and TPST2, as key molecules regulating sulfation of the major P-selectin glycoprotein ligand-1 in leukocytes. Approximately 80-90% of the sgRNA used in this study displayed high editing efficiency, and the CRISPR library picked up entire gene sets regulating specific biosynthetic pathways rather than only isolated genes. These data suggest that the glycoGene CRISPR library contains high-efficiency sgRNA. Further, this resource could be useful for the rapid screening of glycosylation-related genes and pathways that control lectin recognition in a variety of contexts.
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Affiliation(s)
- Yuqi Zhu
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Theodore Groth
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Anju Kelkar
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Yusen Zhou
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Sriram Neelamegham
- Chemical and Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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135
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Zecchin D, Moore C, Michailidis F, Horswell S, Rana S, Howell M, Downward J. Combined targeting of G protein-coupled receptor and EGF receptor signaling overcomes resistance to PI3K pathway inhibitors in PTEN-null triple negative breast cancer. EMBO Mol Med 2020; 12:e11987. [PMID: 32672423 PMCID: PMC7411640 DOI: 10.15252/emmm.202011987] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/09/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) has poorer prognosis compared to other types of breast cancers due to the lack of effective therapies and markers for patient stratification. Loss of PTEN tumor suppressor gene expression is a frequent event in TNBC, resulting in over-activation of the PI 3-kinase (PI3K) pathway and sensitivity to its inhibition. However, PI3K pathway inhibitors show limited efficacy as monotherapies on these tumors. We report a whole-genome screen to identify targets whose inhibition enhanced the effects of different PI3K pathway inhibitors on PTEN-null TNBC. This identified a signaling network that relies on both the G protein-coupled receptor for thrombin (PAR1/F2R) and downstream G protein βγ subunits and also epidermal growth factor receptor (EGFR) for the activation of the PI3K isoform p110β and AKT. Compensation mechanisms involving these two branches of the pathway could bypass PI3K blockade, but combination targeting of both EGFR and PI3Kβ suppressed ribosomal protein S6 phosphorylation and exerted anti-tumor activity both in vitro and in vivo, suggesting a new potential therapeutic strategy for PTEN-null TNBC.
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Affiliation(s)
| | | | | | | | - Sareena Rana
- Oncogene BiologyFrancis Crick InstituteLondonUK
- Lung Cancer GroupInstitute of Cancer ResearchLondonUK
| | - Michael Howell
- High Throughput Screening LaboratoriesFrancis Crick InstituteLondonUK
| | - Julian Downward
- Oncogene BiologyFrancis Crick InstituteLondonUK
- Lung Cancer GroupInstitute of Cancer ResearchLondonUK
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136
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Sun W, Wang H. Recent advances of genome editing and related technologies in China. Gene Ther 2020; 27:312-320. [DOI: 10.1038/s41434-020-0181-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/24/2020] [Accepted: 07/22/2020] [Indexed: 12/26/2022]
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137
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Zablocki-Thomas L, Menzies SA, Lehner PJ, Manel N, Benaroch P. A genome-wide CRISPR screen identifies regulation factors of the TLR3 signalling pathway. Innate Immun 2020; 26:459-472. [PMID: 32248720 PMCID: PMC7491238 DOI: 10.1177/1753425920915507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A subset of TLRs is specialised in the detection of incoming pathogens by sampling endosomes for nucleic acid contents. Among them, TLR3 senses the abnormal presence of double-stranded RNA in the endosomes and initiates a potent innate immune response via activation of NF-κB and IRF3. Nevertheless, mechanisms governing TLR3 regulation remain poorly defined. To identify new molecular players involved in the TLR3 pathway, we performed a genome-wide screen using CRISPR/Cas9 technology. We generated TLR3+ reporter cells carrying a NF-κB-responsive promoter that controls GFP expression. Cells were next transduced with a single-guide RNA (sgRNA) library, subjected to sequential rounds of stimulation with poly(I:C) and sorting of the GFP-negative cells. Enrichments in sgRNA estimated by deep sequencing identified genes required for TLR3-induced activation of NF-κB. Among the hits, five genes known to be critically involved in the TLR3 pathway, including TLR3 itself and the chaperone UNC93B1, were identified by the screen, thus validating our strategy. We further studied the top 40 hits and focused on the transcription factor aryl hydrocarbon receptor (AhR). Depletion of AhR had a dual effect on the TLR3 response, abrogating IL-8 production and enhancing IP-10 release. Moreover, in primary human macrophages exposed to poly(I:C), AhR activation enhanced IL-8 and diminished IP-10 release. Overall, these results reveal AhR plays a role in the TLR3 cellular innate immune response.
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Affiliation(s)
| | - Sam A Menzies
- Department of Medicine, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, UK
| | - Paul J Lehner
- Department of Medicine, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, UK
| | - Nicolas Manel
- Institut Curie, PSL Research University, INSERM U932, France
| | - Philippe Benaroch
- Institut Curie, PSL Research University, INSERM U932, France,Philippe Benaroch, Institut Curie, PSL Research University, INSERM U932, France. Nicolas Manel, Institut Curie, PSL Research University, INSERM U932, France.
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138
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Stein D, Thom V, Hubbuch J. High throughput screening setup of a scale-down device for membrane chromatography-aggregate removal of monoclonal antibodies. Biotechnol Prog 2020; 36:e3055. [PMID: 32710474 DOI: 10.1002/btpr.3055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/18/2020] [Accepted: 07/23/2020] [Indexed: 11/07/2022]
Abstract
In biopharmaceutical process development, resin-based high throughput screening (HTS) is well known for overcoming experimental limitations by permitting automated parallel processing at miniaturized scale, which results in fast data generation and reduced feed consumption. For membrane adsorber (MA), HTS solutions have so far only been available to a partial extent. Three case studies were performed with the aim of aligning HTS applications for MAs with those established for column chromatography: Process parameter range determination, mechanistic modeling (MM), and scalability. In order to exploit the MA typically features, such as high mass transfer and easy scalability, for scalable high throughput process development, a scale-down device (SDD) for MA was developed. Its applicability is confirmed for a monoclonal antibody aggregate removal step. The first case study explores the experimental application of the SDD developed. It uses bind and elute mode and variations of pH and salt concentration to obtain process operation windows for ion-exchange MAs Sartobind® S and Q. In the second case study, we successfully developed a mechanistic model based on parameters obtained from the SDD-HTS setup. The results proved to validate the use of the SDD developed for parameter estimation and thus model-based process development. The third case study shows the transferability and scalability of data from the SDD-HTS setup using both a direct scale factor and MM. Both approaches show good applicability with a deviation below 20% in the prediction of 10% dynamic breakthrough capacity and reliable scale-up from 0.42 to 800 ml.
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Affiliation(s)
- Dominik Stein
- Sartorius Stedim Biotech GmbH, Goettingen, Germany.,Department of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Volkmar Thom
- Sartorius Stedim Biotech GmbH, Goettingen, Germany
| | - Jürgen Hubbuch
- Department of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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139
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Liu X, Wei L, Dong Q, Liu L, Zhang MQ, Xie Z, Wang X. A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass. Aging (Albany NY) 2020; 11:4011-4031. [PMID: 31219803 PMCID: PMC6628988 DOI: 10.18632/aging.102034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/13/2019] [Indexed: 12/24/2022]
Abstract
Cellular senescence is an important mechanism of autonomous tumor suppression, while its consequence such as the senescence-associated secretory phenotype (SASP) may drive tumorigenesis and age-related diseases. Therefore, controlling the cell fate optimally when encountering senescence stress is helpful for anti-cancer or anti-aging treatments. To identify genes essential for senescence establishment or maintenance, we carried out a CRISPR-based screen with a deliberately designed single-guide RNA (sgRNA) library. The library comprised of about 12,000 kinds of sgRNAs targeting 1378 senescence-associated genes selected by integrating the information of literature mining, protein-protein interaction network, and differential gene expression. We successfully detected a dozen gene deficiencies potentially causing senescence bypass, and their phenotypes were further validated with a high true positive rate. RNA-seq analysis showed distinct transcriptome patterns of these bypass cells. Interestingly, in the bypass cells, the expression of SASP genes was maintained or elevated with CHEK2, HAS1, or MDK deficiency; but neutralized with MTOR, CRISPLD2, or MORF4L1 deficiency. Pathways of some age-related neurodegenerative disorders were also downregulated with MTOR, CRISPLD2, or MORF4L1 deficiency. The results demonstrated that disturbing these genes could lead to distinct cell fates as a consequence of senescence bypass, suggesting that they may play essential roles in cellular senescence.
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Affiliation(s)
- Xuehui Liu
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China.,Present address: State Key Laboratory of Medical Molecular Biology, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lei Wei
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Qiongye Dong
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China.,Present address: Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Liyang Liu
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China.,Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson, TX 75080, USA
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaowo Wang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic and Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
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140
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Lin X, Chemparathy A, La Russa M, Daley T, Qi LS. Computational Methods for Analysis of Large-Scale CRISPR Screens. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-020520-113523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Large-scale CRISPR-Cas pooled screens have shown great promise to investigate functional links between genotype and phenotype at the genome-wide scale. In addition to technological advancement, there is a need to develop computational methods to analyze the large datasets obtained from high-throughput CRISPR screens. Many computational methods have been developed to identify reliable gene hits from various screens. In this review, we provide an overview of the technology development of CRISPR screening platforms, with a focus on recent advances in computational methods to identify and model gene effects using CRISPR screen datasets. We also discuss existing challenges and opportunities for future computational methods development.
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Affiliation(s)
- Xueqiu Lin
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | | | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Timothy Daley
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
- Department of Statistics, Stanford University, Stanford, California 94305, USA
| | - Lei S. Qi
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
- Department of Chemical and Systems Biology and ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, California 94305, USA
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141
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Abstract
Neurodegenerative, neurodevelopmental and neuropsychiatric disorders are among the greatest public health challenges, as many lack disease-modifying treatments. A major reason for the absence of effective therapies is our limited understanding of the causative molecular and cellular mechanisms. Genome-wide association studies are providing a growing catalogue of disease-associated genetic variants, and the next challenge is to elucidate how these variants cause disease and to translate this understanding into therapies. This Review describes how new CRISPR-based functional genomics approaches can uncover disease mechanisms and therapeutic targets in neurological diseases. The bacterial CRISPR system can be used in experimental disease models to edit genomes and to control gene expression levels through CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa). These genetic perturbations can be implemented in massively parallel genetic screens to evaluate the functional consequences for human cells. CRISPR screens are particularly powerful in combination with induced pluripotent stem cell technology, which enables the derivation of differentiated cell types, such as neurons and glia, and brain organoids from cells obtained from patients. Modelling of disease-associated changes in gene expression via CRISPRi and CRISPRa can pinpoint causal changes. In addition, genetic modifier screens can be used to elucidate disease mechanisms and causal determinants of cell type-selective vulnerability and to identify therapeutic targets.
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142
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Arens R, Scheeren FA. Genetic Screening for Novel Regulators of Immune Checkpoint Molecules. Trends Immunol 2020; 41:692-705. [PMID: 32605801 DOI: 10.1016/j.it.2020.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/11/2020] [Accepted: 06/14/2020] [Indexed: 12/31/2022]
Abstract
Inhibitory and stimulatory immune checkpoint molecules play important roles in regulating immune responses. An increasing number of these immune regulators are currently being evaluated as targets in putative anti-cancer therapies. Recently, sophisticated genetic screens have been performed to increase our understanding of immune checkpoint pathways and their immunomodulatory regulators. Here, we summarize novel insights obtained by these screens and discuss new directions to advance possible strategies to treat malignancies.
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Affiliation(s)
- Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Ferenc A Scheeren
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, The Netherlands.
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143
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Clement K, Hsu JY, Canver MC, Joung JK, Pinello L. Technologies and Computational Analysis Strategies for CRISPR Applications. Mol Cell 2020; 79:11-29. [PMID: 32619467 PMCID: PMC7497852 DOI: 10.1016/j.molcel.2020.06.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 03/12/2020] [Accepted: 06/05/2020] [Indexed: 12/21/2022]
Abstract
The CRISPR-Cas system offers a programmable platform for eukaryotic genome and epigenome editing. The ability to perform targeted genetic and epigenetic perturbations enables researchers to perform a variety of tasks, ranging from investigating questions in basic biology to potentially developing novel therapeutics for the treatment of disease. While CRISPR systems have been engineered to target DNA and RNA with increased precision, efficiency, and flexibility, assays to identify off-target editing are becoming more comprehensive and sensitive. Furthermore, techniques to perform high-throughput genome and epigenome editing can be paired with a variety of readouts and are uncovering important cellular functions and mechanisms. These technological advances drive and are driven by accompanying computational approaches. Here, we briefly present available CRISPR technologies and review key computational advances and considerations for various CRISPR applications. In particular, we focus on the analysis of on- and off-target editing and CRISPR pooled screen data.
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Affiliation(s)
- Kendell Clement
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Y Hsu
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew C Canver
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Yu Y, Wu X, Guan N, Shao J, Li H, Chen Y, Ping Y, Li D, Ye H. Engineering a far-red light-activated split-Cas9 system for remote-controlled genome editing of internal organs and tumors. SCIENCE ADVANCES 2020; 6:eabb1777. [PMID: 32923591 PMCID: PMC7455487 DOI: 10.1126/sciadv.abb1777] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/14/2020] [Indexed: 05/22/2023]
Abstract
It is widely understood that CRISPR-Cas9 technology is revolutionary, with well-recognized issues including the potential for off-target edits and the attendant need for spatiotemporal control of editing. Here, we describe a far-red light (FRL)-activated split-Cas9 (FAST) system that can robustly induce gene editing in both mammalian cells and mice. Through light-emitting diode-based FRL illumination, the FAST system can efficiently edit genes, including nonhomologous end joining and homology-directed repair, for multiple loci in human cells. Further, we show that FAST readily achieves FRL-induced editing of internal organs in tdTomato reporter mice. Finally, FAST was demonstrated to achieve FRL-triggered editing of the PLK1 oncogene in a mouse xenograft tumor model. Beyond extending the spectrum of light energies in optogenetic toolbox for CRISPR-Cas9 technologies, this study demonstrates how FAST system can be deployed for programmable deep tissue gene editing in both biological and biomedical contexts toward high precision and spatial specificity.
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Affiliation(s)
- Yuanhuan Yu
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xin Wu
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Ningzi Guan
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jiawei Shao
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Huiying Li
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yuxuan Chen
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Dali Li
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
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145
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Wang S, Wei L, Wang JQ, Ji H, Xiong W, Liu J, Yin P, Tian T, Zhou X. Light-Driven Activation of RNA-Guided Nucleic Acid Cleavage. ACS Chem Biol 2020; 15:1455-1463. [PMID: 32378871 DOI: 10.1021/acschembio.0c00105] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As one of the most favorable stimuli, photoactivation provides an advantageous way to manipulate biological objects. In the current study, we have successfully demonstrated the use of light activation guide RNA (gRNA) strategy for controlling CRISPR systems. By conjugating photolabile protecting groups, the CRISPR functions became minimal, but exposure of acylated gRNAs to 365 nm light triggers the removal of masking groups, leading to the rescue of CRISPR functions. Furthermore, our strategy has been successfully used to control gene editing in human cells. This proof-of-concept study therefore demonstrates the promising potential of our strategy to versatile applications in chemical biology.
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Affiliation(s)
- Shaoru Wang
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Lai Wei
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Jia-Qi Wang
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Huimin Ji
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Wei Xiong
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Jian Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Tian Tian
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
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146
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Liu D, Ndongwe TP, Puray-Chavez M, Casey MC, Izumi T, Pathak VK, Tedbury PR, Sarafianos SG. Effect of P-body component Mov10 on HCV virus production and infectivity. FASEB J 2020; 34:9433-9449. [PMID: 32496609 DOI: 10.1096/fj.201800641r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 03/28/2020] [Accepted: 05/04/2020] [Indexed: 12/11/2022]
Abstract
Mov10 is a processing body (P-body) protein and an interferon-stimulated gene that can affect replication of retroviruses, hepatitis B virus, and hepatitis C virus (HCV). The mechanism of HCV inhibition by Mov10 is unknown. Here, we investigate the effect of Mov10 on HCV infection and determine the virus life cycle steps affected by changes in Mov10 overexpression. Mov10 overexpression suppresses HCV RNA in both infectious virus and subgenomic replicon systems. Additionally, Mov10 overexpression decreases the infectivity of released virus, unlike control P-body protein DCP1a that has no effect on HCV RNA production or infectivity of progeny virus. Confocal imaging of uninfected cells shows endogenous Mov10 localized at P-bodies. However, in HCV-infected cells, Mov10 localizes in circular structures surrounding cytoplasmic lipid droplets with NS5A and core protein. Mutagenesis experiments show that the RNA binding activity of Mov10 is required for HCV inhibition, while its P-body localization, helicase, and ATP-binding functions are not required. Unexpectedly, endogenous Mov10 promotes HCV replication, as CRISPR-Cas9-based Mov10 depletion decreases HCV replication and infection levels. Our data reveal an important and complex role for Mov10 in HCV replication, which can be perturbed by excess or insufficient Mov10.
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Affiliation(s)
- Dandan Liu
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Tanyaradzwa P Ndongwe
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Maritza Puray-Chavez
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Mary C Casey
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Taisuke Izumi
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
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147
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Wu X, Ma W, Mei C, Chen X, Yao Y, Liu Y, Qin X, Yuan Y. Description of CRISPR/Cas9 development and its prospect in hepatocellular carcinoma treatment. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:97. [PMID: 32487115 PMCID: PMC7268395 DOI: 10.1186/s13046-020-01603-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/25/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies today. Patients suffer from HCC since its high malignancy and limited treatment means. With the development of genetic research, new therapeutic strategy comes up in the way of gene editing. Clustered regularly interspaced short palindromic repeat/CRISPR-associated nuclease 9 (CRISPR/Cas9) was discovered as an immune sequence in bacteria and archaea. After artificial transformation and follow-up research, it is widely used as a gene editing tool. In this review, the development of CRISPR/Cas9 is summarized in retrospect. Through the evaluation of novel research in HCC, it is concluded that CRISPR/Cas9 would promote cancer research and provide a new tool for genetic treatment in prospect.
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Affiliation(s)
- Xiaoling Wu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Weijie Ma
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Chengjie Mei
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Xi Chen
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Ye Yao
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Yingyi Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Xian Qin
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Yufeng Yuan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, China.
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148
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Blanck M, Budnik-Zawilska MB, Lenger SR, McGonigle JE, Martin GR, le Sage C, Lawo S, Pemberton HN, Tiwana GS, Sorrell DA, Cross BC. A Flexible, Pooled CRISPR Library for Drug Development Screens. CRISPR J 2020; 3:211-222. [PMID: 33054419 PMCID: PMC7567641 DOI: 10.1089/crispr.2019.0066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Functional genomic screening with CRISPR has provided a powerful and precise new way to interrogate the phenotypic consequences of gene manipulation in high-throughput, unbiased analyses. However, some experimental paradigms prove especially challenging and require carefully and appropriately adapted screening approaches. In particular, negative selection (or sensitivity) screening, often the most experimentally desirable modality of screening, has remained a challenge in drug discovery. Here we assess whether our new, modular genome-wide pooled CRISPR library can improve negative selection CRISPR screening and add utility throughout the drug development pipeline. Our pooled library is split into three parts, allowing it to be scaled to accommodate the experimental challenges encountered during drug development, such as target identification using unlimited cell numbers compared with target identification studies for cell populations where cell numbers are limiting. To test our new library, we chose to look for drug-gene interactions using a well-described small molecule inhibitor targeting poly(ADP-ribose) polymerase 1 (PARP1), and in particular to identify genes which sensitise cells to this drug. We simulate hit identification and performance using each library partition and support these findings through orthogonal drug combination cell panel screening. We also compare our data with a recently published CRISPR sensitivity dataset obtained using the same PARP1 inhibitor. Overall, our data indicate that generating a comprehensive CRISPR knockout screening library where the number of guides can be scaled to suit the biological question being addressed allows a library to have multiple uses throughout the drug development pipeline, and that initial validation of hits can be achieved through high-throughput cell panels screens where clinical grade chemical or biological matter exist.
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Affiliation(s)
| | | | | | | | | | | | - Steffen Lawo
- Max Planck Institute for Biology of Ageing, Cologne, Germany
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149
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Rehman T, Thornell IM, Pezzulo AA, Thurman AL, Romano Ibarra GS, Karp PH, Tan P, Duffey ME, Welsh MJ. TNFα and IL-17 alkalinize airway surface liquid through CFTR and pendrin. Am J Physiol Cell Physiol 2020; 319:C331-C344. [PMID: 32432926 PMCID: PMC7500220 DOI: 10.1152/ajpcell.00112.2020] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The pH of airway surface liquid (ASL) is a key factor that determines respiratory host defense; ASL acidification impairs and alkalinization enhances key defense mechanisms. Under healthy conditions, airway epithelia secrete base ([Formula: see text]) and acid (H+) to control ASL pH (pHASL). Neutrophil-predominant inflammation is a hallmark of several airway diseases, and TNFα and IL-17 are key drivers. However, how these cytokines perturb pHASL regulation is uncertain. In primary cultures of differentiated human airway epithelia, TNFα decreased and IL-17 did not change pHASL. However, the combination (TNFα+IL-17) markedly increased pHASL by increasing [Formula: see text] secretion. TNFα+IL-17 increased expression and function of two apical [Formula: see text] transporters, CFTR anion channels and pendrin Cl-/[Formula: see text] exchangers. Both were required for maximal alkalinization. TNFα+IL-17 induced pendrin expression primarily in secretory cells where it was coexpressed with CFTR. Interestingly, significant pendrin expression was not detected in CFTR-rich ionocytes. These results indicate that TNFα+IL-17 stimulate [Formula: see text] secretion via CFTR and pendrin to alkalinize ASL, which may represent an important defense mechanism in inflamed airways.
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Affiliation(s)
- Tayyab Rehman
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Ian M Thornell
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Alejandro A Pezzulo
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Andrew L Thurman
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Guillermo S Romano Ibarra
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Philip H Karp
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa.,Howard Hughes Medical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Ping Tan
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Michael E Duffey
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Michael J Welsh
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa.,Howard Hughes Medical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa.,Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
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150
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Liu D, Zhao X, Tang A, Xu X, Liu S, Zha L, Ma W, Zheng J, Shi M. CRISPR screen in mechanism and target discovery for cancer immunotherapy. Biochim Biophys Acta Rev Cancer 2020; 1874:188378. [PMID: 32413572 DOI: 10.1016/j.bbcan.2020.188378] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
Abstract
CRISPR/Cas-based genetic perturbation screens have emerged as powerful tools for large-scale identification of new targets for cancer immunotherapy. Various strategies of CRISPR screen have been used for immune-oncology (IO) target discovery. The genomic sequences targeted by CRISPR/Cas system range from coding sequences to non-coding RNA/DNA, including miRNAs, LncRNAs, circRNAs, promoters, and enhancers, which may be potential targets for future pharmacological and therapeutic interventions. Rapid progresses have been witnessed in finding novel targets for enhancing tumor antigen presentation, sensitizing of tumor cells to immune-mediated cytotoxicity, and reinvigorating tumor-specific T cells by using CRISPR technologies. In combination with other strategies, the detailed characteristics of the targets for immunotherapy have been obtained by CRISPR screen. In this review, we present an overview of recent progresses in the development of CRISPR-based screens for IO target identification and discuss the challenges and possible solutions in this rapidly growing field.
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Affiliation(s)
- Dan Liu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Xuan Zhao
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Anqun Tang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Xiyue Xu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Shuci Liu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Li Zha
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Wen Ma
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China
| | - Junnian Zheng
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China.
| | - Ming Shi
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221000, Jiangsu, China.
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