1
|
Wang Y, Ding G, Chu C, Cheng XD, Qin JJ. Genomic biology and therapeutic strategies of liver metastasis from gastric cancer. Crit Rev Oncol Hematol 2024; 202:104470. [PMID: 39111457 DOI: 10.1016/j.critrevonc.2024.104470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
The liver is a frequent site of metastasis in advanced gastric cancer (GC). Despite significant advancements in diagnostic and therapeutic techniques, the overall survival rate for patients afflicted with gastric cancer liver metastasis (GCLM) remains dismally low. Precision oncology has made significant progress in identifying therapeutic targets and enhancing our understanding of metastasis mechanisms through genome sequencing and molecular characterization. Therefore, it is crucial to have a comprehensive understanding of the various molecular processes involved in GCLM and the fundamental principles of systemic therapy to develop new treatment approaches. This paper aims to review recent findings on the diagnosis, potential biomarkers, and therapies targeting the multiple molecular processes of GCLM, with the goal of improving treatment strategies for patients with GCLM.
Collapse
Affiliation(s)
- Yichao Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 313200, China; Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Guangyu Ding
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Chu Chu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 313200, China
| | - Xiang-Dong Cheng
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China; Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou 310022, China.
| | - Jiang-Jiang Qin
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China; Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou 310022, China; Key Laboratory for Molecular Medicine and Chinese Medicine Preparations, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China.
| |
Collapse
|
2
|
Zhao M, Shuai W, Su Z, Xu P, Wang A, Sun Q, Wang G. Protein tyrosine phosphatases: emerging role in cancer therapy resistance. Cancer Commun (Lond) 2024; 44:637-653. [PMID: 38741380 PMCID: PMC11194456 DOI: 10.1002/cac2.12548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Tyrosine phosphorylation of intracellular proteins is a post-translational modification that plays a regulatory role in signal transduction during cellular events. Dephosphorylation of signal transduction proteins caused by protein tyrosine phosphatases (PTPs) contributed their role as a convergent node to mediate cross-talk between signaling pathways. In the context of cancer, PTP-mediated pathways have been identified as signaling hubs that enabled cancer cells to mitigate stress induced by clinical therapy. This is achieved by the promotion of constitutive activation of growth-stimulatory signaling pathways or modulation of the immune-suppressive tumor microenvironment. Preclinical evidences suggested that anticancer drugs will release their greatest therapeutic potency when combined with PTP inhibitors, reversing drug resistance that was responsible for clinical failures during cancer therapy. AREAS COVERED This review aimed to elaborate recent insights that supported the involvement of PTP-mediated pathways in the development of resistance to targeted therapy and immune-checkpoint therapy. EXPERT OPINION This review proposed the notion of PTP inhibition in anticancer combination therapy as a potential strategy in clinic to achieve long-term tumor regression. Ongoing clinical trials are currently underway to assess the safety and efficacy of combination therapy in advanced-stage tumors.
Collapse
Affiliation(s)
- Min Zhao
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Wen Shuai
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Zehao Su
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
- West China Biomedical Big Data CenterMed‐X Center for InformaticsSichuan UniversityChengduSichuanP. R. China
| | - Ping Xu
- Emergency DepartmentZigong Fourth People's HospitalChengduSichuanP. R. China
| | - Aoxue Wang
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Qiu Sun
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| | - Guan Wang
- Innovation Center of Nursing ResearchNursing Key Laboratory of Sichuan ProvinceDepartment of BiotherapyCancer Center and State Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China Hospital, West China School of Nursing, Sichuan UniversityChengduSichuanP. R. China
| |
Collapse
|
3
|
Francis JC, Capper A, Rust AG, Ferro K, Ning J, Yuan W, de Bono J, Pettitt SJ, Swain A. Identification of genes that promote PI3K pathway activation and prostate tumour formation. Oncogene 2024; 43:1824-1835. [PMID: 38654106 PMCID: PMC11164682 DOI: 10.1038/s41388-024-03028-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
We have performed a functional in vivo mutagenesis screen to identify genes that, when altered, cooperate with a heterozygous Pten mutation to promote prostate tumour formation. Two genes, Bzw2 and Eif5a2, which have been implicated in the process of protein translation, were selected for further validation. Using prostate organoid models, we show that either Bzw2 downregulation or EIF5A2 overexpression leads to increased organoid size and in vivo prostate growth. We show that both genes impact the PI3K pathway and drive a sustained increase in phospho-AKT expression, with PTEN protein levels reduced in both models. Mechanistic studies reveal that EIF5A2 is directly implicated in PTEN protein translation. Analysis of patient datasets identified EIF5A2 amplifications in many types of human cancer, including the prostate. Human prostate cancer samples in two independent cohorts showed a correlation between increased levels of EIF5A2 and upregulation of a PI3K pathway gene signature. Consistent with this, organoids with high levels of EIF5A2 were sensitive to AKT inhibitors. Our study identified novel genes that promote prostate cancer formation through upregulation of the PI3K pathway, predicting a strategy to treat patients with genetic aberrations in these genes particularly relevant for EIF5A2 amplified tumours.
Collapse
Affiliation(s)
- Jeffrey C Francis
- Division of Cancer Biology, Institute of Cancer Research, London, SW3 6JB, UK
| | - Amy Capper
- Division of Cancer Biology, Institute of Cancer Research, London, SW3 6JB, UK
| | - Alistair G Rust
- Genomics Facility, Institute of Cancer Research, London, UK
- Genomic Data Sciences, GlaxoSmithKline, Stevenage, UK
| | - Klea Ferro
- Division of Cancer Biology, Institute of Cancer Research, London, SW3 6JB, UK
| | - Jian Ning
- Tumour Modelling Facility, Institute of Cancer Research, London, SW3 6JB, UK
| | - Wei Yuan
- Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Johann de Bono
- Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory, Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, SW3 6JB, UK
| | - Amanda Swain
- Division of Cancer Biology, Institute of Cancer Research, London, SW3 6JB, UK.
| |
Collapse
|
4
|
Fang Y, Li X, Tian R. Unlocking Glioblastoma Vulnerabilities with CRISPR-Based Genetic Screening. Int J Mol Sci 2024; 25:5702. [PMID: 38891890 PMCID: PMC11171782 DOI: 10.3390/ijms25115702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Glioblastoma (GBM) is the most common malignant brain tumor in adults. Despite advancements in treatment, the prognosis for patients with GBM remains poor due to its aggressive nature and resistance to therapy. CRISPR-based genetic screening has emerged as a powerful tool for identifying genes crucial for tumor progression and treatment resistance, offering promising targets for tumor therapy. In this review, we provide an overview of the recent advancements in CRISPR-based genetic screening approaches and their applications in GBM. We highlight how these approaches have been used to uncover the genetic determinants of GBM progression and responsiveness to various therapies. Furthermore, we discuss the ongoing challenges and future directions of CRISPR-based screening methods in advancing GBM research.
Collapse
Affiliation(s)
- Yitong Fang
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.F.); (X.L.)
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xing Li
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.F.); (X.L.)
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruilin Tian
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.F.); (X.L.)
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
5
|
Iida N, Muranaka Y, Park JW, Sekine S, Copeland NG, Jenkins NA, Shiraishi Y, Oshima M, Takeda H. Sleeping Beauty transposon mutagenesis in mouse intestinal organoids identifies genes involved in tumor progression and metastasis. Cancer Gene Ther 2024; 31:527-536. [PMID: 38177308 DOI: 10.1038/s41417-023-00723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
To identify genes important for colorectal cancer (CRC) development and metastasis, we established a new metastatic mouse organoid model using Sleeping Beauty (SB) transposon mutagenesis. Intestinal organoids derived from mice carrying actively mobilizing SB transposons, an activating KrasG12D, and an inactivating ApcΔ716 allele, were transplanted to immunodeficient mice. While 66.7% of mice developed primary tumors, 7.6% also developed metastatic tumors. Analysis of SB insertion sites in tumors identified numerous candidate cancer genes (CCGs) identified previously in intestinal SB screens performed in vivo, in addition to new CCGs, such as Slit2 and Atxn1. Metastatic tumors from the same mouse were clonally related to each other and to primary tumors, as evidenced by the transposon insertion site. To provide functional validation, we knocked out Slit2, Atxn1, and Cdkn2a in mouse tumor organoids and transplanted to mice. Tumor development was promoted when these gene were knocked out, demonstrating that these are potent tumor suppressors. Cdkn2a knockout cells also metastasized to the liver in 100% of the mice, demonstrating that Cdkn2a loss confers metastatic ability. Our organoid model thus provides a new approach that can be used to understand the evolutionary forces driving CRC metastasis and a rich resource to uncover CCGs promoting CRC.
Collapse
Affiliation(s)
- Naoko Iida
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Yukari Muranaka
- Laboratory of Molecular Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Jun Won Park
- Division of Biomedical Convergence, College of Biomedical Science, Kang-won National University, Chuncheon-si, Republic of Korea
| | - Shigeki Sekine
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Neal G Copeland
- Genetics Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nancy A Jenkins
- Genetics Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Ishikawa, Japan
- Nano-Life Science Institute, Kanazawa University, Ishikawa, Japan
| | - Haruna Takeda
- Laboratory of Molecular Genetics, National Cancer Center Research Institute, Tokyo, Japan.
- Cancer genes and genomes unit, Cancer Research Institute, Kanazawa University, Ishikawa, Japan.
| |
Collapse
|
6
|
Montero JJ, Trozzo R, Sugden M, Öllinger R, Belka A, Zhigalova E, Waetzig P, Engleitner T, Schmidt-Supprian M, Saur D, Rad R. Genome-scale pan-cancer interrogation of lncRNA dependencies using CasRx. Nat Methods 2024; 21:584-596. [PMID: 38409225 PMCID: PMC11009108 DOI: 10.1038/s41592-024-02190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024]
Abstract
Although long noncoding RNAs (lncRNAs) dominate the transcriptome, their functions are largely unexplored. The extensive overlap of lncRNAs with coding and regulatory sequences restricts their systematic interrogation by DNA-directed perturbation. Here we developed genome-scale lncRNA transcriptome screening using Cas13d/CasRx. We show that RNA targeting overcomes limitations inherent to other screening methods, thereby considerably expanding the explorable space of the lncRNAome. By evolving the screening system toward pan-cancer applicability, it supports molecular and phenotypic data integration to contextualize screening hits or infer lncRNA function. We thereby addressed challenges posed by the enormous transcriptome size and tissue specificity through a size-reduced multiplexed gRNA library termed Albarossa, targeting 24,171 lncRNA genes. Its rational design incorporates target prioritization based on expression, evolutionary conservation and tissue specificity, thereby reconciling high discovery power and pan-cancer representation with scalable experimental throughput. Applied across entities, the screening platform identified numerous context-specific and common essential lncRNAs. Our work sets the stage for systematic exploration of lncRNA biology in health and disease.
Collapse
Affiliation(s)
- Juan J Montero
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
| | - Riccardo Trozzo
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Maya Sugden
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Alexander Belka
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Ekaterina Zhigalova
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Paul Waetzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
7
|
Zhang J, Zhou Y, Lei J, Liu X, Zhang N, Wu L, Li Y. Retention time prediction and MRM validation reinforce the biomarker identification of LC-MS based phospholipidomics. Analyst 2024; 149:515-527. [PMID: 38078496 DOI: 10.1039/d3an01735d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Dysfunctional lipid metabolism plays a crucial role in the development and progression of various diseases. Accurate measurement of lipidomes can help uncover the complex interactions between genes, proteins, and lipids in health and diseases. The prediction of retention time (RT) has become increasingly important in both targeted and untargeted metabolomics. However, the potential impact of RT prediction on targeted LC-MS based lipidomics is still not fully understood. Herein, we propose a simplified workflow for predicting RT in phospholipidomics. Our approach involves utilizing the fatty acyl chain length or carbon-carbon double bond (DB) number in combination with multiple reaction monitoring (MRM) validation. We found that our model's predictive capacity for RT was comparable to that of a publicly accessible program (QSRR Automator). Additionally, MRM validation helped in further mitigating the interference in signal recognition. Using this developed workflow, we conducted phospholipidomics of sorafenib resistant hepatocellular carcinoma (HCC) cell lines, namely MHCC97H and Hep3B. Our findings revealed an abundance of monounsaturated fatty acyl (MUFA) or polyunsaturated fatty acyl (PUFA) phospholipids in these cell lines after developing drug resistance. In both cell lines, a total of 29 lipids were found to be co-upregulated and 5 lipids were co-downregulated. Further validation was conducted on seven of the upregulated lipids using an independent dataset, which demonstrates the potential for translation of the established workflow or the lipid biomarkers.
Collapse
Affiliation(s)
- Jiangang Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Yu Zhou
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Juan Lei
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Xudong Liu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Nan Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| |
Collapse
|
8
|
Dziubańska-Kusibab PJ, Nevedomskaya E, Haendler B. Preclinical Anticipation of On- and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review. Int J Mol Sci 2024; 25:705. [PMID: 38255778 PMCID: PMC10815614 DOI: 10.3390/ijms25020705] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The advent of targeted therapies has led to tremendous improvements in treatment options and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by developing on-target or off-target resistance mechanisms. Gaining the ability to resist treatment is the rule rather than the exception in tumors, and it remains a major healthcare challenge to achieve long-lasting remission in most cancer patients. Here, we discuss emerging strategies that take advantage of innovative high-throughput screening technologies to anticipate on- and off-target resistance mechanisms before they occur in treated cancer patients. We divide the methods into non-systematic approaches, such as random mutagenesis or long-term drug treatment, and systematic approaches, relying on the clustered regularly interspaced short palindromic repeats (CRISPR) system, saturated mutagenesis, or computational methods. All these new developments, especially genome-wide CRISPR-based screening platforms, have significantly accelerated the processes for identification of the mechanisms responsible for cancer drug resistance and opened up new avenues for future treatments.
Collapse
Affiliation(s)
| | | | - Bernard Haendler
- Research and Early Development Oncology, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (P.J.D.-K.); (E.N.)
| |
Collapse
|
9
|
Li X, Chen Z, Ye W, Yu J, Zhang X, Li Y, Niu Y, Ran S, Wang S, Luo Z, Zhao J, Hao Y, Zong J, Xia C, Xia J, Wu J. High-throughput CRISPR technology: a novel horizon for solid organ transplantation. Front Immunol 2024; 14:1295523. [PMID: 38239344 PMCID: PMC10794540 DOI: 10.3389/fimmu.2023.1295523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024] Open
Abstract
Organ transplantation is the gold standard therapy for end-stage organ failure. However, the shortage of available grafts and long-term graft dysfunction remain the primary barriers to organ transplantation. Exploring approaches to solve these issues is urgent, and CRISPR/Cas9-based transcriptome editing provides one potential solution. Furthermore, combining CRISPR/Cas9-based gene editing with an ex vivo organ perfusion system would enable pre-implantation transcriptome editing of grafts. How to determine effective intervention targets becomes a new problem. Fortunately, the advent of high-throughput CRISPR screening has dramatically accelerated the effective targets. This review summarizes the current advancements, utilization, and workflow of CRISPR screening in various immune and non-immune cells. It also discusses the ongoing applications of CRISPR/Cas-based gene editing in transplantation and the prospective applications of CRISPR screening in solid organ transplantation.
Collapse
Affiliation(s)
- Xiaohan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhang Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weicong Ye
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizhang Yu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Zhang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqing Niu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuan Ran
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Song Wang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zilong Luo
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiulu Zhao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanglin Hao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junjie Zong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengkun Xia
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Xia
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Jie Wu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| |
Collapse
|
10
|
Wang X, Istvanffy R, Ye L, Teller S, Laschinger M, Diakopoulos KN, Görgülü K, Li Q, Ren L, Jäger C, Steiger K, Muckenhuber A, Vilne B, Çifcibaşı K, Reyes CM, Yurteri Ü, Kießler M, Gürçınar IH, Sugden M, Yıldızhan SE, Sezerman OU, Çilingir S, Süyen G, Reichert M, Schmid RM, Bärthel S, Oellinger R, Krüger A, Rad R, Saur D, Algül H, Friess H, Lesina M, Ceyhan GO, Demir IE. Phenotype screens of murine pancreatic cancer identify a Tgf-α-Ccl2-paxillin axis driving human-like neural invasion. J Clin Invest 2023; 133:e166333. [PMID: 37607005 PMCID: PMC10617783 DOI: 10.1172/jci166333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
Solid cancers like pancreatic ductal adenocarcinoma (PDAC), a type of pancreatic cancer, frequently exploit nerves for rapid dissemination. This neural invasion (NI) is an independent prognostic factor in PDAC, but insufficiently modeled in genetically engineered mouse models (GEMM) of PDAC. Here, we systematically screened for human-like NI in Europe's largest repository of GEMM of PDAC, comprising 295 different genotypes. This phenotype screen uncovered 2 GEMMs of PDAC with human-like NI, which are both characterized by pancreas-specific overexpression of transforming growth factor α (TGF-α) and conditional depletion of p53. Mechanistically, cancer-cell-derived TGF-α upregulated CCL2 secretion from sensory neurons, which induced hyperphosphorylation of the cytoskeletal protein paxillin via CCR4 on cancer cells. This activated the cancer migration machinery and filopodia formation toward neurons. Disrupting CCR4 or paxillin activity limited NI and dampened tumor size and tumor innervation. In human PDAC, phospho-paxillin and TGF-α-expression constituted strong prognostic factors. Therefore, we believe that the TGF-α-CCL2-CCR4-p-paxillin axis is a clinically actionable target for constraining NI and tumor progression in PDAC.
Collapse
Affiliation(s)
- Xiaobo Wang
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Rouzanna Istvanffy
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Neural Influences in Cancer (NIC) International Research Consortium
| | - Linhan Ye
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Pain Clinic, Department of Anesthesiology, First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Steffen Teller
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Melanie Laschinger
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Kalliope N. Diakopoulos
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Department of Internal Medicine II & Comprehensive Cancer Center Munich, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Kıvanç Görgülü
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Department of Internal Medicine II & Comprehensive Cancer Center Munich, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Qiaolin Li
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lei Ren
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Carsten Jäger
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Katja Steiger
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Comparative Experimental Pathology and Institute of Pathology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Alexander Muckenhuber
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Comparative Experimental Pathology and Institute of Pathology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Baiba Vilne
- Bioinformatics laboratory, Riga Stradins University, Riga, Latvia
| | - Kaan Çifcibaşı
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Carmen Mota Reyes
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Neural Influences in Cancer (NIC) International Research Consortium
| | - Ümmügülsüm Yurteri
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Maximilian Kießler
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Ibrahim Halil Gürçınar
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Maya Sugden
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | | | - Sümeyye Çilingir
- Department of Physiology, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Güldal Süyen
- Department of Physiology, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Maximilian Reichert
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Roland M. Schmid
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Stefanie Bärthel
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Translational Cancer Research (TranslaTUM) and Experimental Cancer Therapy
| | - Rupert Oellinger
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics
| | - Achim Krüger
- Institute of Experimental Oncology and Therapy Research, School of Medicine, Technical University Munich, Munich, Germany
| | - Roland Rad
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics
| | - Dieter Saur
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Institute of Translational Cancer Research (TranslaTUM) and Experimental Cancer Therapy
| | - Hana Algül
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Department of Internal Medicine II & Comprehensive Cancer Center Munich, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Helmut Friess
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Neural Influences in Cancer (NIC) International Research Consortium
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Marina Lesina
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Department of Internal Medicine II & Comprehensive Cancer Center Munich, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Güralp Onur Ceyhan
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Neural Influences in Cancer (NIC) International Research Consortium
- Department of General Surgery, HPB-Unit, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ihsan Ekin Demir
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CRC 1321 Modelling and Targeting Pancreatic Cancer, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Neural Influences in Cancer (NIC) International Research Consortium
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Department of General Surgery, HPB-Unit, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Else Kröner Clinician Scientist Professor for Translational Pancreatic Surgery, Technical University of Munich, Munich, Germany
| |
Collapse
|
11
|
Zhou H, Hao X, Zhang P, He S. Noncoding RNA mutations in cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1812. [PMID: 37544928 DOI: 10.1002/wrna.1812] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Cancer is driven by both germline and somatic genetic changes. Efforts have been devoted to characterizing essential genetic variations in cancer initiation and development. Most attention has been given to mutations in protein-coding genes and associated regulatory elements such as promoters and enhancers. The development of sequencing technologies and in silico and experimental methods has allowed further exploration of cancer predisposition variants and important somatic mutations in noncoding RNAs, mainly for long noncoding RNAs and microRNAs. Association studies including GWAS have revealed hereditary variations including SNPs and indels in lncRNA or miRNA genes and regulatory regions. These mutations altered RNA secondary structures, expression levels, and target recognition and then conferred cancer predisposition to carriers. Whole-exome/genome sequencing comparing cancer and normal tissues has revealed important somatic mutations in noncoding RNA genes. Mutation hotspots and somatic copy number alterations have been identified in various tumor-associated noncoding RNAs. Increasing focus and effort have been devoted to studying the noncoding region of the genome. The complex genetic network of cancer initiation is being unveiled. This article is categorized under: RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Honghong Zhou
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xinpei Hao
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
12
|
Zhou Y, Luo K, Liang L, Chen M, He X. A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening. Nat Methods 2023; 20:1693-1703. [PMID: 37770710 PMCID: PMC10630124 DOI: 10.1038/s41592-023-02017-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/18/2023] [Indexed: 09/30/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) screening coupled with single-cell RNA sequencing has emerged as a powerful tool to characterize the effects of genetic perturbations on the whole transcriptome at a single-cell level. However, due to its sparsity and complex structure, analysis of single-cell CRISPR screening data is challenging. In particular, standard differential expression analysis methods are often underpowered to detect genes affected by CRISPR perturbations. We developed a statistical method for such data, called guided sparse factor analysis (GSFA). GSFA infers latent factors that represent coregulated genes or gene modules; by borrowing information from these factors, it infers the effects of genetic perturbations on individual genes. We demonstrated through extensive simulation studies that GSFA detects perturbation effects with much higher power than state-of-the-art methods. Using single-cell CRISPR data from human CD8+ T cells and neural progenitor cells, we showed that GSFA identified biologically relevant gene modules and specific genes affected by CRISPR perturbations, many of which were missed by existing methods, providing new insights into the functions of genes involved in T cell activation and neurodevelopment.
Collapse
Affiliation(s)
- Yifan Zhou
- Graduate Program of Biophysical Sciences, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Lifan Liang
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Mengjie Chen
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
13
|
Blair LM, Juan JM, Sebastian L, Tran VB, Nie W, Wall GD, Gerceker M, Lai IK, Apilado EA, Grenot G, Amar D, Foggetti G, Do Carmo M, Ugur Z, Deng D, Chenchik A, Paz Zafra M, Dow LE, Politi K, MacQuitty JJ, Petrov DA, Winslow MM, Rosen MJ, Winters IP. Oncogenic context shapes the fitness landscape of tumor suppression. Nat Commun 2023; 14:6422. [PMID: 37828026 PMCID: PMC10570323 DOI: 10.1038/s41467-023-42156-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Tumors acquire alterations in oncogenes and tumor suppressor genes in an adaptive walk through the fitness landscape of tumorigenesis. However, the interactions between oncogenes and tumor suppressor genes that shape this landscape remain poorly resolved and cannot be revealed by human cancer genomics alone. Here, we use a multiplexed, autochthonous mouse platform to model and quantify the initiation and growth of more than one hundred genotypes of lung tumors across four oncogenic contexts: KRAS G12D, KRAS G12C, BRAF V600E, and EGFR L858R. We show that the fitness landscape is rugged-the effect of tumor suppressor inactivation often switches between beneficial and deleterious depending on the oncogenic context-and shows no evidence of diminishing-returns epistasis within variants of the same oncogene. These findings argue against a simple linear signaling relationship amongst these three oncogenes and imply a critical role for off-axis signaling in determining the fitness effects of inactivating tumor suppressors.
Collapse
Affiliation(s)
| | | | | | - Vy B Tran
- D2G Oncology, Mountain View, CA, USA
| | | | | | | | - Ian K Lai
- D2G Oncology, Mountain View, CA, USA
| | | | | | - David Amar
- D2G Oncology, Mountain View, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Cardiovascular Medicine and the Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Mariana Do Carmo
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Zeynep Ugur
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Maria Paz Zafra
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Excellence Research Unit "Modeling Nature" (MNat), University of Granada, E-18016, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18071, Granada, Spain
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Katerina Politi
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg BioHub, San Francisco, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | |
Collapse
|
14
|
Kendirli A, de la Rosa C, Lämmle KF, Eglseer K, Bauer IJ, Kavaka V, Winklmeier S, Zhuo L, Wichmann C, Gerdes LA, Kümpfel T, Dornmair K, Beltrán E, Kerschensteiner M, Kawakami N. A genome-wide in vivo CRISPR screen identifies essential regulators of T cell migration to the CNS in a multiple sclerosis model. Nat Neurosci 2023; 26:1713-1725. [PMID: 37709997 PMCID: PMC10545543 DOI: 10.1038/s41593-023-01432-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Multiple sclerosis (MS) involves the infiltration of autoreactive T cells into the CNS, yet we lack a comprehensive understanding of the signaling pathways that regulate this process. Here, we conducted a genome-wide in vivo CRISPR screen in a rat MS model and identified 5 essential brakes and 18 essential facilitators of T cell migration to the CNS. While the transcription factor ETS1 limits entry to the CNS by controlling T cell responsiveness, three functional modules, centered around the adhesion molecule α4-integrin, the chemokine receptor CXCR3 and the GRK2 kinase, are required for CNS migration of autoreactive CD4+ T cells. Single-cell analysis of T cells from individuals with MS confirmed that the expression of these essential regulators correlates with the propensity of CD4+ T cells to reach the CNS. Our data thus reveal key regulators of the fundamental step in the induction of MS lesions.
Collapse
Affiliation(s)
- Arek Kendirli
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Clara de la Rosa
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Katrin F Lämmle
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Klara Eglseer
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Isabel J Bauer
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Vladyslav Kavaka
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Stephan Winklmeier
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - La Zhuo
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Christian Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lisa Ann Gerdes
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Eduardo Beltrán
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Martin Kerschensteiner
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Naoto Kawakami
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany.
| |
Collapse
|
15
|
Bresci A, Kim JH, Ghislanzoni S, Manetti F, Wu L, Vernuccio F, Ceconello C, Sorrentino S, Barman I, Bongarzone I, Cerullo G, Vanna R, Polli D. Noninvasive morpho-molecular imaging reveals early therapy-induced senescence in human cancer cells. SCIENCE ADVANCES 2023; 9:eadg6231. [PMID: 37703362 PMCID: PMC10881071 DOI: 10.1126/sciadv.adg6231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 08/11/2023] [Indexed: 09/15/2023]
Abstract
Anticancer therapy screening in vitro identifies additional treatments and improves clinical outcomes. Systematically, although most tested cells respond to cues with apoptosis, an appreciable portion enters a senescent state, a critical condition potentially driving tumor resistance and relapse. Conventional screening protocols would strongly benefit from prompt identification and monitoring of therapy-induced senescent (TIS) cells in their native form. We combined complementary all-optical, label-free, and quantitative microscopy techniques, based on coherent Raman scattering, multiphoton absorption, and interferometry, to explore the early onset and progression of this phenotype, which has been understudied in unperturbed conditions. We identified TIS manifestations as early as 24 hours following treatment, consisting of substantial mitochondrial rearrangement and increase of volume and dry mass, followed by accumulation of lipid vesicles starting at 72 hours. This work holds the potential to affect anticancer treatment research, by offering a label-free, rapid, and accurate method to identify initial TIS in tumor cells.
Collapse
Affiliation(s)
- Arianna Bresci
- Department of Physics, Politecnico di Milano, Milan, Italy
| | - Jeong Hee Kim
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Silvia Ghislanzoni
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | - Lintong Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Italia Bongarzone
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Giulio Cerullo
- Department of Physics, Politecnico di Milano, Milan, Italy
- CNR-Institute for Photonics and Nanotechnologies (CNR-IFN), Milan, Italy
| | - Renzo Vanna
- CNR-Institute for Photonics and Nanotechnologies (CNR-IFN), Milan, Italy
| | - Dario Polli
- Department of Physics, Politecnico di Milano, Milan, Italy
- CNR-Institute for Photonics and Nanotechnologies (CNR-IFN), Milan, Italy
| |
Collapse
|
16
|
Zhang L, Wirth M, Patra U, Stroh J, Isaakidis K, Rieger L, Kossatz S, Milanovic M, Zang C, Demel U, Keiten‐Schmitz J, Wagner K, Steiger K, Rad R, Bassermann F, Müller S, Keller U, Schick M. Actionable loss of SLF2 drives B-cell lymphomagenesis and impairs the DNA damage response. EMBO Mol Med 2023; 15:e16431. [PMID: 37485814 PMCID: PMC10493575 DOI: 10.15252/emmm.202216431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
The DNA damage response (DDR) acts as a barrier to malignant transformation and is often impaired during tumorigenesis. Exploiting the impaired DDR can be a promising therapeutic strategy; however, the mechanisms of inactivation and corresponding biomarkers are incompletely understood. Starting from an unbiased screening approach, we identified the SMC5-SMC6 Complex Localization Factor 2 (SLF2) as a regulator of the DDR and biomarker for a B-cell lymphoma (BCL) patient subgroup with an adverse prognosis. SLF2-deficiency leads to loss of DDR factors including Claspin (CLSPN) and consequently impairs CHK1 activation. In line with this mechanism, genetic deletion of Slf2 drives lymphomagenesis in vivo. Tumor cells lacking SLF2 are characterized by a high level of DNA damage, which leads to alterations of the post-translational SUMOylation pathway as a safeguard. The resulting co-dependency confers synthetic lethality to a clinically applicable SUMOylation inhibitor (SUMOi), and inhibitors of the DDR pathway act highly synergistic with SUMOi. Together, our results identify SLF2 as a DDR regulator and reveal co-targeting of the DDR and SUMOylation as a promising strategy for treating aggressive lymphoma.
Collapse
Affiliation(s)
- Le Zhang
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Upayan Patra
- Institute of Biochemistry IIGoethe University Frankfurt, Medical SchoolFrankfurtGermany
| | - Jacob Stroh
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of Medicine III, Klinikum rechts der IsarTechnical University of MunichMunichGermany
| | - Konstandina Isaakidis
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Leonie Rieger
- Department of Medicine III, Klinikum rechts der IsarTechnical University of MunichMunichGermany
- Center for Translational Cancer Research (TranslaTUM)Technische Universität MünchenMunichGermany
| | - Susanne Kossatz
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Center for Translational Cancer Research (TranslaTUM)Technische Universität MünchenMunichGermany
- Nuclear Medicine, Klinikum rechts der IsarTechnical University of MunichMunichGermany
| | - Maja Milanovic
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Chuanbing Zang
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Uta Demel
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
- Clinician Scientist ProgramBerlin Institute of Health (BIH)BerlinGermany
| | - Jan Keiten‐Schmitz
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Institute of Biochemistry IIGoethe University Frankfurt, Medical SchoolFrankfurtGermany
| | - Kristina Wagner
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Institute of Biochemistry IIGoethe University Frankfurt, Medical SchoolFrankfurtGermany
| | - Katja Steiger
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Comparative Experimental Pathology, Institute of PathologyTechnical University of MunichMunichGermany
| | - Roland Rad
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Center for Translational Cancer Research (TranslaTUM)Technische Universität MünchenMunichGermany
- Institute of Molecular Oncology and Functional Genomics, TUM School of MedicineTechnische Universität MünchenMunichGermany
| | - Florian Bassermann
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of Medicine III, Klinikum rechts der IsarTechnical University of MunichMunichGermany
- Center for Translational Cancer Research (TranslaTUM)Technische Universität MünchenMunichGermany
| | - Stefan Müller
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Institute of Biochemistry IIGoethe University Frankfurt, Medical SchoolFrankfurtGermany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Markus Schick
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| |
Collapse
|
17
|
Weiner L, Brissette JL. Finding meaning in chaos: a selection signature for functional interactions and its use in molecular biology. FEBS J 2023; 290:3914-3927. [PMID: 35653424 DOI: 10.1111/febs.16542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/18/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022]
Abstract
A primary goal of biomedical research is to elucidate molecular mechanisms, particularly those responsible for human traits, either normal or pathological. Yet achieving this goal is difficult if not impossible when the traits of interest lack tractable models and so cannot be dissected through time-honoured approaches like forward genetics or reconstitution. Arguably, no biological problem has hindered scientific progress more than this: the inability to dissect a trait's mechanism without a tractable likeness of the trait. At root, forward genetics and reconstitution are powerful approaches because they assay for specific molecular functions. Here, we discuss an alternative way to uncover important mechanistic interactions, namely, to assay for positive natural selection. If an interaction has been selected for, then it must perform an important function, a function that significantly promotes reproductive success. Accordingly, selection is a consequence and indicator of function, and uncovering multimolecular selection will reveal important functional interactions. We propose a selection signature for interactions and review recent selection-based approaches through which to dissect traits that are not inherently tractable. The review includes proof-of-principle studies in which important interactions were uncovered by screening for selection. In sum, screens for selection appear feasible when screens for specific functions are not. Selection screens thus constitute a novel tool through which to reveal the mechanisms that shape the fates of organisms.
Collapse
Affiliation(s)
- Lorin Weiner
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Janice L Brissette
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| |
Collapse
|
18
|
Cao F, Jiang Y, Chang L, Du H, Chang D, Pan C, Huang X, Yu D, Zhang M, Fan Y, Bian X, Li K. High-throughput functional screen identifies YWHAZ as a key regulator of pancreatic cancer metastasis. Cell Death Dis 2023; 14:431. [PMID: 37452033 PMCID: PMC10349114 DOI: 10.1038/s41419-023-05951-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Pancreatic cancer is a leading cause of cancer death due to its early metastasis and limited response to the current therapies. Metastasis is a complicated multistep process, which is determined by complex genetic alterations. Despite the identification of many metastasis-related genes, distinguishing the drivers from numerous passengers and establishing the causality in cancer pathophysiology remains challenging. Here, we established a high-throughput and piggyBac transposon-based genetic screening platform, which enables either reduced or increased expression of chromosomal genes near the incorporation site of the gene search vector cassette that contains a doxycycline-regulated promoter. Using this strategy, we identified YWHAZ as a key regulator of pancreatic cancer metastasis. We demonstrated that functional activation of Ywhaz by the gene search vector led to enhanced metastatic capability in mouse pancreatic cancer cells. The metastasis-promoting role of YWHAZ was further validated in human pancreatic cancer cells. Overexpression of YWHAZ resulted in more aggressive metastatic phenotypes in vitro and a shorter survival rate in vivo by modulating epithelial-to-mesenchymal transition. Hence, our study established a high-throughput screening method to investigate the functional relevance of novel genes and validated YWHAZ as a key regulator of pancreatic cancer metastasis.
Collapse
Affiliation(s)
- Fang Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yunpeng Jiang
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lin Chang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Endoscopy Center, Peking University Cancer Hospital & Institute, Beijing, China
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Hongzhen Du
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - De Chang
- Department of Pulmonary and Critical Care Medicine, 7th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chunxiao Pan
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Xiaozheng Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Donglin Yu
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Mi Zhang
- Department of Pulmonary and Critical Care Medicine, 7th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yongna Fan
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China
| | - Xiaocui Bian
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing, China.
| | - Kailong Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
| |
Collapse
|
19
|
Tang YJ, Shuldiner EG, Karmakar S, Winslow MM. High-Throughput Identification, Modeling, and Analysis of Cancer Driver Genes In Vivo. Cold Spring Harb Perspect Med 2023; 13:a041382. [PMID: 37277208 PMCID: PMC10317066 DOI: 10.1101/cshperspect.a041382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The vast number of genomic and molecular alterations in cancer pose a substantial challenge to uncovering the mechanisms of tumorigenesis and identifying therapeutic targets. High-throughput functional genomic methods in genetically engineered mouse models allow for rapid and systematic investigation of cancer driver genes. In this review, we discuss the basic concepts and tools for multiplexed investigation of functionally important cancer genes in vivo using autochthonous cancer models. Furthermore, we highlight emerging technical advances in the field, potential opportunities for future investigation, and outline a vision for integrating multiplexed genetic perturbations with detailed molecular analyses to advance our understanding of the genetic and molecular basis of cancer.
Collapse
Affiliation(s)
- Yuning J Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Emily G Shuldiner
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Saswati Karmakar
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
20
|
Datta I, Vassel T, Linkous B, Odum T, Drew C, Taylor A, Bangi E. A targeted genetic modifier screen in Drosophila uncovers vulnerabilities in a genetically complex model of colon cancer. G3 (BETHESDA, MD.) 2023; 13:jkad053. [PMID: 36880303 PMCID: PMC10151408 DOI: 10.1093/g3journal/jkad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 01/16/2023] [Accepted: 02/21/2023] [Indexed: 03/08/2023]
Abstract
Received on 16 January 2023; accepted on 21 February 2023Kinases are key regulators of cellular signal transduction pathways. Many diseases, including cancer, are associated with global alterations in protein phosphorylation networks. As a result, kinases are frequent targets of drug discovery efforts. However, target identification and assessment, a critical step in targeted drug discovery that involves identifying essential genetic mediators of disease phenotypes, can be challenging in complex, heterogeneous diseases like cancer, where multiple concurrent genomic alterations are common. Drosophila is a particularly useful genetic model system to identify novel regulators of biological processes through unbiased genetic screens. Here, we report 2 classic genetic modifier screens focusing on the Drosophila kinome to identify kinase regulators in 2 different backgrounds: KRAS TP53 PTEN APC, a multigenic cancer model that targets 4 genes recurrently mutated in human colon tumors and KRAS alone, a simpler model that targets one of the most frequently altered pathways in cancer. These screens identified hits unique to each model and one shared by both, emphasizing the importance of capturing the genetic complexity of human tumor genome landscapes in experimental models. Our follow-up analysis of 2 hits from the KRAS-only screen suggests that classical genetic modifier screens in heterozygous mutant backgrounds that result in a modest, nonlethal reduction in candidate gene activity in the context of a whole animal-a key goal of systemic drug treatment-may be a particularly useful approach to identify the most rate-limiting genetic vulnerabilities in disease models as ideal candidate drug targets.
Collapse
Affiliation(s)
- Ishwaree Datta
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Tajah Vassel
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Benjamin Linkous
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Tyler Odum
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Christian Drew
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Andrew Taylor
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Erdem Bangi
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| |
Collapse
|
21
|
Fischer A, Lersch R, de Andrade Krätzig N, Strong A, Friedrich MJ, Weber J, Engleitner T, Öllinger R, Yen HY, Kohlhofer U, Gonzalez-Menendez I, Sailer D, Kogan L, Lahnalampi M, Laukkanen S, Kaltenbacher T, Klement C, Rezaei M, Ammon T, Montero JJ, Schneider G, Mayerle J, Heikenwälder M, Schmidt-Supprian M, Quintanilla-Martinez L, Steiger K, Liu P, Cadiñanos J, Vassiliou GS, Saur D, Lohi O, Heinäniemi M, Conte N, Bradley A, Rad L, Rad R. In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution. CELL GENOMICS 2023; 3:100276. [PMID: 36950387 PMCID: PMC10025556 DOI: 10.1016/j.xgen.2023.100276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/05/2022] [Accepted: 02/08/2023] [Indexed: 03/10/2023]
Abstract
In contrast to mono- or biallelic loss of tumor-suppressor function, effects of discrete gene dysregulations, as caused by non-coding (epi)genome alterations, are poorly understood. Here, by perturbing the regulatory genome in mice, we uncover pervasive roles of subtle gene expression variation in cancer evolution. Genome-wide screens characterizing 1,450 tumors revealed that such quasi-insufficiency is extensive across entities and displays diverse context dependencies, such as distinct cell-of-origin associations in T-ALL subtypes. We compile catalogs of non-coding regions linked to quasi-insufficiency, show their enrichment with human cancer risk variants, and provide functional insights by engineering regulatory alterations in mice. As such, kilo-/megabase deletions in a Bcl11b-linked non-coding region triggered aggressive malignancies, with allele-specific tumor spectra reflecting gradual gene dysregulations through modular and cell-type-specific enhancer activities. Our study constitutes a first survey toward a systems-level understanding of quasi-insufficiency in cancer and gives multifaceted insights into tumor evolution and the tissue-specific effects of non-coding mutations.
Collapse
Affiliation(s)
- Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Robert Lersch
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Mathias J. Friedrich
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Hsi-Yu Yen
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Ursula Kohlhofer
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Irene Gonzalez-Menendez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - David Sailer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Liz Kogan
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Mari Lahnalampi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Saara Laukkanen
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Thorsten Kaltenbacher
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Christine Klement
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Majdaddin Rezaei
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Tim Ammon
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Juan J. Montero
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Julia Mayerle
- Medical Department II, University Hospital, LMU Munich, Munich, Germany
| | - Mathias Heikenwälder
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Li Ka Shing Faculty of Medicine, Stem Cell and Regenerative Medicine Consortium, School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), 33193 Oviedo, Spain
| | - George S. Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0PT, UK
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Olli Lohi
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Nathalie Conte
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
| |
Collapse
|
22
|
Zhang N, Huang D, Ruan X, Ng ATL, Tsu JHL, Jiang G, Huang J, Zhan Y, Na R. CRISPR screening reveals gleason score and castration resistance related oncodriver ring finger protein 19 A (RNF19A) in prostate cancer. Drug Resist Updat 2023; 67:100912. [PMID: 36623445 DOI: 10.1016/j.drup.2022.100912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/11/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023]
Abstract
Prostate cancer (PCa) is one of the most lethal causes of cancer-related death in male. It is characterized by chromosomal instability and disturbed signaling transduction. E3 ubiquitin ligases are well-recognized as mediators leading to genomic alterations and malignant phenotypes. There is a lack of systematic study on novel oncodrivers with genomic and clinical significance in PCa. In this study we used clustered regularly interspaced short palindromic repeats (CRISPR) system to screen 656 E3 ubiquitin ligases as oncodrivers or tumor repressors in PCa cells. We identified 51 significantly changed genes, and conducted genomic and clinical analysis on these genes. It was found that the Ring Finger Protein 19 A (RNF19A) was a novel oncodriver in PCa. RNF19A was frequently amplified and highly expressed in PCa and other cancer types. Clinically, higher RNF19A expression correlated with advanced Gleason Score and predicted castration resistance. Mechanistically, transcriptomics, quantitative and ubiquitination proteomic analysis showed that RNF19A ubiquitylated Thyroid Hormone Receptor Interactor 13 (TRIP13) and was transcriptionally activated by androgen receptor (AR) and Hypoxia Inducible Factor 1 Subunit Alpha (HIF1A). This study uncovers the genomic and clinical significance of a oncodriver RNF19A in PCa. The results of this study indicate that targeting AR/HIF1A-RNF19A-TRIP13 signaling axis could be an alternative option for PCa diagnosis and therapy.
Collapse
Affiliation(s)
- Ning Zhang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Da Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohao Ruan
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ada Tsui-Lin Ng
- Division of Urology, Department of Surgery, Queen Mary Hospital, Hong Kong, China; Division of Urology, Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - James Hok-Leung Tsu
- Division of Urology, Department of Surgery, Queen Mary Hospital, Hong Kong, China; Division of Urology, Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Guangliang Jiang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingyi Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongle Zhan
- Division of Urology, Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Rong Na
- Division of Urology, Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
23
|
Bredthauer C, Fischer A, Ahari AJ, Cao X, Weber J, Rad L, Rad R, Wachutka L, Gagneur J. Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens. Nucleic Acids Res 2023; 51:e21. [PMID: 36617985 PMCID: PMC9976929 DOI: 10.1093/nar/gkac1215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/06/2022] [Accepted: 12/17/2022] [Indexed: 01/10/2023] Open
Abstract
Transposon screens are powerful in vivo assays used to identify loci driving carcinogenesis. These loci are identified as Common Insertion Sites (CISs), i.e. regions with more transposon insertions than expected by chance. However, the identification of CISs is affected by biases in the insertion behaviour of transposon systems. Here, we introduce Transmicron, a novel method that differs from previous methods by (i) modelling neutral insertion rates based on chromatin accessibility, transcriptional activity and sequence context and (ii) estimating oncogenic selection for each genomic region using Poisson regression to model insertion counts while controlling for neutral insertion rates. To assess the benefits of our approach, we generated a dataset applying two different transposon systems under comparable conditions. Benchmarking for enrichment of known cancer genes showed improved performance of Transmicron against state-of-the-art methods. Modelling neutral insertion rates allowed for better control of false positives and stronger agreement of the results between transposon systems. Moreover, using Poisson regression to consider intra-sample and inter-sample information proved beneficial in small and moderately-sized datasets. Transmicron is open-source and freely available. Overall, this study contributes to the understanding of transposon biology and introduces a novel approach to use this knowledge for discovering cancer driver genes.
Collapse
Affiliation(s)
- Carl Bredthauer
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ata Jadid Ahari
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Xueqi Cao
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Institute for Experimental Cancer Therapy, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Medicine II, Klinikum rechts der Isar, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leonhard Wachutka
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Julien Gagneur
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany.,Institute of Human Genetics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| |
Collapse
|
24
|
Vaishnavi A, Juan J, Jacob M, Stehn C, Gardner EE, Scherzer MT, Schuman S, Van Veen JE, Murphy B, Hackett CS, Dupuy AJ, Chmura SA, van der Weyden L, Newberg JY, Liu A, Mann K, Rust AG, Weiss WA, Kinsey CG, Adams DJ, Grossmann A, Mann MB, McMahon M. Transposon Mutagenesis Reveals RBMS3 Silencing as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis. Cancer Res 2022; 82:4261-4273. [PMID: 36112789 PMCID: PMC9664136 DOI: 10.1158/0008-5472.can-21-3214] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 06/29/2022] [Accepted: 09/13/2022] [Indexed: 01/09/2023]
Abstract
Mutationally activated BRAF is detected in approximately 7% of human lung adenocarcinomas, with BRAFT1799A serving as a predictive biomarker for treatment of patients with FDA-approved inhibitors of BRAFV600E oncoprotein signaling. In genetically engineered mouse (GEM) models, expression of BRAFV600E in the lung epithelium initiates growth of benign lung tumors that, without additional genetic alterations, rarely progress to malignant lung adenocarcinoma. To identify genes that cooperate with BRAFV600E for malignant progression, we used Sleeping Beauty-mediated transposon mutagenesis, which dramatically accelerated the emergence of lethal lung cancers. Among the genes identified was Rbms3, which encodes an RNA-binding protein previously implicated as a putative tumor suppressor. Silencing of RBMS3 via CRISPR/Cas9 gene editing promoted growth of BRAFV600E lung organoids and promoted development of malignant lung cancers with a distinct micropapillary architecture in BRAFV600E and EGFRL858R GEM models. BRAFV600E/RBMS3Null lung tumors displayed elevated expression of Ctnnb1, Ccnd1, Axin2, Lgr5, and c-Myc mRNAs, suggesting that RBMS3 silencing elevates signaling through the WNT/β-catenin signaling axis. Although RBMS3 silencing rendered BRAFV600E-driven lung tumors resistant to the effects of dabrafenib plus trametinib, the tumors were sensitive to inhibition of porcupine, an acyltransferase of WNT ligands necessary for their secretion. Analysis of The Cancer Genome Atlas patient samples revealed that chromosome 3p24, which encompasses RBMS3, is frequently lost in non-small cell lung cancer and correlates with poor prognosis. Collectively, these data reveal the role of RBMS3 as a lung cancer suppressor and suggest that RBMS3 silencing may contribute to malignant NSCLC progression. SIGNIFICANCE Loss of RBMS3 cooperates with BRAFV600E to induce lung tumorigenesis, providing a deeper understanding of the molecular mechanisms underlying mutant BRAF-driven lung cancer and potential strategies to more effectively target this disease.
Collapse
Affiliation(s)
- Aria Vaishnavi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Joseph Juan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Maebh Jacob
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | - Eric E. Gardner
- Meyer Cancer Center, Weill Cornell Medicine, New York City, New York
- Palo Alto Wellness, Menlo Park, California
| | - Michael T. Scherzer
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - Sophia Schuman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - J. Edward Van Veen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Brandon Murphy
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Christopher S. Hackett
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
| | - Steven A. Chmura
- Meyer Cancer Center, Weill Cornell Medicine, New York City, New York
- Palo Alto Wellness, Menlo Park, California
| | - Louise van der Weyden
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Justin Y. Newberg
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Annie Liu
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Karen Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Alistair G. Rust
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - William A. Weiss
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Conan G. Kinsey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - David J. Adams
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
| | - Allie Grossmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Michael B. Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Martin McMahon
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
| |
Collapse
|
25
|
Braun CJ, Adames AC, Saur D, Rad R. Tutorial: design and execution of CRISPR in vivo screens. Nat Protoc 2022; 17:1903-1925. [PMID: 35840661 DOI: 10.1038/s41596-022-00700-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022]
Abstract
Here we provide a detailed tutorial on CRISPR in vivo screening. Using the mouse as the model organism, we introduce a range of CRISPR tools and applications, delineate general considerations for 'transplantation-based' or 'direct in vivo' screening design, and provide details on technical execution, sequencing readouts, computational analyses and data interpretation. In vivo screens face unique pitfalls and limitations, such as delivery issues or library bottlenecking, which must be counteracted to avoid screening failure or flawed conclusions. A broad variety of in vivo phenotypes can be interrogated such as organ development, hematopoietic lineage decision and evolutionary licensing in oncogenesis. We describe experimental strategies to address various biological questions and provide an outlook on emerging CRISPR applications, such as genetic interaction screening. These technological advances create potent new opportunities to dissect the molecular underpinnings of complex organismal phenotypes.
Collapse
Affiliation(s)
- Christian J Braun
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany. .,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Andrés Carbonell Adames
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Dieter Saur
- Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany. .,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
26
|
Ji P, Gong Y, Jin ML, Wu HL, Guo LW, Pei YC, Chai WJ, Jiang YZ, Liu Y, Ma XY, Di GH, Hu X, Shao ZM. In vivo multidimensional CRISPR screens identify Lgals2 as an immunotherapy target in triple-negative breast cancer. SCIENCE ADVANCES 2022; 8:eabl8247. [PMID: 35767614 PMCID: PMC9242595 DOI: 10.1126/sciadv.abl8247] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Immune checkpoint inhibitors exhibit limited response rates in patients with triple-negative breast cancer (TNBC), suggesting that additional immune escape mechanisms may exist. Here, we performed two-step customized in vivo CRISPR screens targeting disease-related immune genes using different mouse models with multidimensional immune-deficiency characteristics. In vivo screens characterized gene functions in the different tumor microenvironments and recovered canonical immunotherapy targets such as Ido1. In addition, functional screening and transcriptomic analysis identified Lgals2 as a candidate regulator in TNBC involving immune escape. Mechanistic studies demonstrated that tumor cell-intrinsic Lgals2 induced the increased number of tumor-associated macrophages, as well as the M2-like polarization and proliferation of macrophages through the CSF1/CSF1R axis, which resulted in the immunosuppressive nature of the TNBC microenvironment. Blockade of LGALS2 using an inhibitory antibody successfully arrested tumor growth and reversed the immune suppression. Collectively, our results provide a theoretical basis for LGALS2 as a potential immunotherapy target in TNBC.
Collapse
Affiliation(s)
- Peng Ji
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yue Gong
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Ming-liang Jin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huai-liang Wu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lin-Wei Guo
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yu-Chen Pei
- Precision Cancer Medical Center, Fudan University Shanghai Cancer Center, Shanghai 201315, China
| | - Wen-Jun Chai
- Laboratory Animal Center, Fudan University Shanghai Cancer Center, Shanghai 201315, China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yin Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Xiao-Yan Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Precision Cancer Medical Center, Fudan University Shanghai Cancer Center, Shanghai 201315, China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Precision Cancer Medical Center, Fudan University Shanghai Cancer Center, Shanghai 201315, China
| |
Collapse
|
27
|
Inflammatory burden as a prognostic biomarker for cancer. Clin Nutr 2022; 41:1236-1243. [PMID: 35504166 DOI: 10.1016/j.clnu.2022.04.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND AIMS Systemic inflammation is the most representative host-tumor interaction in cancer. This study aimed to develop a novel inflammatory burden index (IBI) to assess the inflammatory burden of different cancers and predict the prognosis of patients with cancer. METHODS A total of 6359 cancer patients admitted to multiple centers from 2012 through 2019 were included in this study. The IBI was formulated as C-reaction protein × neutrophil/lymphocyte. Survival differences between the groups were compared using the Kaplan-Meier method. Cox proportional hazard regression analysis was used to estimate the hazard ratio (HR) and 95% confidence interval (CI). Logistic regression analysis was used to assess the association between the inflammatory burden index and outcomes. RESULTS Cancers assessed by the IBI could be classified as high, moderate, or low inflammatory burden and had different prognostic stratification effects (46.5% vs 61.0% vs 83.0%; P < .001). Compared with other systemic inflammation biomarkers, the IBI had the highest accuracy in predicting survival. Patients with a high IBI had significantly lower survival rates than those with a low IBI (45.7% vs 69.1%; P < .001). For every standard deviation increase in the IBI, the risk of poor prognosis for patients with cancer increased by 10.3% (HR, 1.103; 95% CI, 1.072-1.136; P < .001). The IBI could be used as a useful prognostic supplement in the pathological stage. A high IBI was an independent high-risk factor that affected patient's physical condition, malnutrition, cachexia, and short-term outcomes and an independent risk factor for patients with cancer in both validation cohorts a (hazard ratio, 1.114; 95% confidence interval, 1.072-1.157; P < .001) and b (hazard ratio, 1.125; 95% confidence interval, 1.060-1.193; P < .001). CONCLUSIONS The IBI, as a novel indicator of systemic inflammation, is a feasible and promising predictive biomarker in patients with cancer and can be used to assess the inflammatory burden of different cancers.
Collapse
|
28
|
Farooqi AA, Zahid R, Naureen H, Attar R, Gazouli M, Berardi R, Szelachowska J, Matkowski R, Pawlak E. Regulation of ROCK1/2 by long non-coding RNAs and circular RNAs in different cancer types. Oncol Lett 2022; 23:159. [PMID: 35399329 PMCID: PMC8987920 DOI: 10.3892/ol.2022.13279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 05/19/2021] [Indexed: 11/30/2022] Open
Abstract
Recent breakthroughs in high-throughput technologies have enabled the development of a better understanding of the functionalities of rho-associated protein kinases (ROCKs) under various physiological and pathological conditions. Since their discovery in the late 1990s, ROCKs have attracted the attention of interdisciplinary researchers due to their ability to pleiotropically modulate a myriad of cellular mechanisms. A rapidly growing number of published studies have started to shed light on the mechanisms underlying the regulation of ROCK1 and ROCK2 via long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in different types of cancer. Detailed analyses have suggested that lncRNAs may be characteristically divided into oncogenic and tumor suppressor lncRNAs. Several exciting recent discoveries have also indicated how different lncRNAs and circRNAs modulate ROCK1/2 and mediate multistep cancer onset and progression. The present review chronicles the major advances that have been made in our understanding of the regulatory role of ROCK1/2 in different types of cancer, and how wide-ranging lncRNAs and circRNAs potentiate ROCK-driven signaling by blocking the targeting activities of tumor suppressor microRNAs.
Collapse
Affiliation(s)
- Ammad Ahmad Farooqi
- Department of Molecular Oncology, Institute of Biomedical and Genetic Engineering, Islamabad 54000, Pakistan
| | - Rabbia Zahid
- Institute of Chemistry, University of Punjab, Lahore 43000, Pakistan
| | - Humaira Naureen
- Faculty of Pharmaceutical Sciences, Riphah International University, Islamabad 54000, Pakistan
| | - Rukset Attar
- Department of Obstetrics and Gynecology, Yeditepe University 34280, Turkey
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens 54634, Greece
| | - Rossana Berardi
- Oncology Clinic-Marche Polytechnic University, Azienda Ospedaliero-Universitaria Ospedali Riuniti Umberto I-GM Lancisi-G Salesi di Ancona, I-60126 Ancona, Italy
| | - Jolanta Szelachowska
- Department of Oncology, Wroclaw Medical University, 53-413 Wroclaw, Poland
- Wroclaw Comprehensive Cancer Centre, 53-413 Wroclaw, Poland
| | - Rafał Matkowski
- Department of Oncology, Wroclaw Medical University, 53-413 Wroclaw, Poland
- Wroclaw Comprehensive Cancer Centre, 53-413 Wroclaw, Poland
| | - Edyta Pawlak
- Department of Experimental Therapy, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 50-013 Wroclaw, Poland
| |
Collapse
|
29
|
Genome-wide CRISPR screen identified Rad18 as a determinant of doxorubicin sensitivity in osteosarcoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:154. [PMID: 35459258 PMCID: PMC9034549 DOI: 10.1186/s13046-022-02344-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/25/2022] [Indexed: 12/14/2022]
Abstract
Background Osteosarcoma (OS) is a malignant bone tumor mostly occurring in children and adolescents, while chemotherapy resistance often develops and the mechanisms involved remain challenging to be fully investigated. Methods Genome-wide CRISPR screening combined with transcriptomic sequencing were used to identify the critical genes of doxorubicin resistance. Analysis of clinical samples and datasets, and in vitro and in vivo experiments (including CCK-8, apoptosis, western blot, qRT-PCR and mouse models) were applied to confirm the function of these genes. The bioinformatics and IP-MS assays were utilized to further verify the downstream pathway. RGD peptide-directed and exosome-delivered siRNA were developed for the novel therapy strategy. Results We identified that E3 ubiquitin-protein ligase Rad18 (Rad18) contributed to doxorubicin-resistance in OS. Further exploration revealed that Rad18 interact with meiotic recombination 11 (MRE11) to promote the formation of the MRE11-RAD50-NBS1 (MRN) complex, facilitating the activation of the homologous recombination (HR) pathway, which ultimately mediated DNA damage tolerance and leaded to a poor prognosis and chemotherapy response in patients with OS. Rad18-knockout effectively restored the chemotherapy response in vitro and in vivo. Also, RGD-exosome loading chemically modified siRad18 combined with doxorubicin, where exosome and chemical modification guaranteed the stability of siRad18 and the RGD peptide provided prominent targetability, had significantly improved antitumor activity of doxorubicin. Conclusions Collectively, our study identifies Rad18 as a driver of OS doxorubicin resistance that promotes the HR pathway and indicates that targeting Rad18 is an effective approach to overcome chemotherapy resistance in OS. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02344-y.
Collapse
|
30
|
Exploring liver cancer biology through functional genetic screens. Nat Rev Gastroenterol Hepatol 2021; 18:690-704. [PMID: 34163045 DOI: 10.1038/s41575-021-00465-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
As the fourth leading cause of cancer-related death in the world, liver cancer poses a major threat to human health. Although a growing number of therapies have been approved for the treatment of hepatocellular carcinoma in the past few years, most of them only provide a limited survival benefit. Therefore, an urgent need exists to identify novel targetable vulnerabilities and powerful drug combinations for the treatment of liver cancer. The advent of functional genetic screening has contributed to the advancement of liver cancer biology, uncovering many novel genes involved in tumorigenesis and cancer progression in a high-throughput manner. In addition, this unbiased screening platform also provides an efficient tool for the exploration of the mechanisms involved in therapy resistance as well as identifying potential targets for therapy. In this Review, we describe how functional screens can help to deepen our understanding of liver cancer and guide the development of new therapeutic strategies.
Collapse
|
31
|
Abstract
The past 25 years of genomics research first revealed which genes are encoded by the human genome and then a detailed catalogue of human genome variation associated with many diseases. Despite this, the function of many genes and gene regulatory elements remains poorly characterized, which limits our ability to apply these insights to human disease. The advent of new CRISPR functional genomics tools allows for scalable and multiplexable characterization of genes and gene regulatory elements encoded by the human genome. These approaches promise to reveal mechanisms of gene function and regulation, and to enable exploration of how genes work together to modulate complex phenotypes.
Collapse
|
32
|
Dawes JC, Uren AG. Forward and Reverse Genetics of B Cell Malignancies: From Insertional Mutagenesis to CRISPR-Cas. Front Immunol 2021; 12:670280. [PMID: 34484175 PMCID: PMC8414522 DOI: 10.3389/fimmu.2021.670280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022] Open
Abstract
Cancer genome sequencing has identified dozens of mutations with a putative role in lymphomagenesis and leukemogenesis. Validation of driver mutations responsible for B cell neoplasms is complicated by the volume of mutations worthy of investigation and by the complex ways that multiple mutations arising from different stages of B cell development can cooperate. Forward and reverse genetic strategies in mice can provide complementary validation of human driver genes and in some cases comparative genomics of these models with human tumors has directed the identification of new drivers in human malignancies. We review a collection of forward genetic screens performed using insertional mutagenesis, chemical mutagenesis and exome sequencing and discuss how the high coverage of subclonal mutations in insertional mutagenesis screens can identify cooperating mutations at rates not possible using human tumor genomes. We also compare a set of independently conducted screens from Pax5 mutant mice that converge upon a common set of mutations observed in human acute lymphoblastic leukemia (ALL). We also discuss reverse genetic models and screens that use CRISPR-Cas, ORFs and shRNAs to provide high throughput in vivo proof of oncogenic function, with an emphasis on models using adoptive transfer of ex vivo cultured cells. Finally, we summarize mouse models that offer temporal regulation of candidate genes in an in vivo setting to demonstrate the potential of their encoded proteins as therapeutic targets.
Collapse
Affiliation(s)
- Joanna C Dawes
- Medical Research Council, London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Anthony G Uren
- Medical Research Council, London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
33
|
Cervera ST, Rodríguez-Martín C, Fernández-Tabanera E, Melero-Fernández de Mera RM, Morin M, Fernández-Peñalver S, Iranzo-Martínez M, Amhih-Cardenas J, García-García L, González-González L, Moreno-Pelayo MA, Alonso J. Therapeutic Potential of EWSR1-FLI1 Inactivation by CRISPR/Cas9 in Ewing Sarcoma. Cancers (Basel) 2021; 13:cancers13153783. [PMID: 34359682 PMCID: PMC8345183 DOI: 10.3390/cancers13153783] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 01/14/2023] Open
Abstract
Simple Summary Ewing sarcoma is an aggressive tumor with still unacceptable survival rates, particularly in patients with metastatic disease and for which it is necessary to develop new and innovative therapies. These tumors are characterized by the presence of chromosomal translocations that give rise to chimeric transcription factors (i.e., EWSR1–FLI1) that govern the oncogenic process. In this article, we describe an efficient strategy to permanently inactivate the EWSR1–FLI1 oncogene characteristic of Ewing sarcoma using CRISPR/Cas9 gene editing technology. Although the application of gene therapy in cancer still has many limitations, for example, the strategy for delivery, studies like ours show that gene therapy can be a promising alternative, particularly for those tumors that are highly dependent on a particular oncogene as is the case in Ewing sarcoma. Abstract Ewing sarcoma is an aggressive bone cancer affecting children and young adults. The main molecular hallmark of Ewing sarcoma are chromosomal translocations that produce chimeric oncogenic transcription factors, the most frequent of which is the aberrant transcription factor EWSR1–FLI1. Because this is the principal oncogenic driver of Ewing sarcoma, its inactivation should be the best therapeutic strategy to block tumor growth. In this study, we genetically inactivated EWSR1–FLI1 using CRISPR-Cas9 technology in order to cause permanent gene inactivation. We found that gene editing at the exon 9 of FLI1 was able to block cell proliferation drastically and induce senescence massively in the well-studied Ewing sarcoma cell line A673. In comparison with an extensively used cellular model of EWSR1–FLI1 knockdown (A673/TR/shEF), genetic inactivation was more effective, particularly in its capability to block cell proliferation. In summary, genetic inactivation of EWSR1–FLI1 in A673 Ewing sarcoma cells blocks cell proliferation and induces a senescence phenotype that could be exploited therapeutically. Although efficient and specific in vivo CRISPR-Cas9 editing still presents many challenges today, our data suggest that complete inactivation of EWSR1–FLI1 at the cell level should be considered a therapeutic approach to develop in the future.
Collapse
Affiliation(s)
- Saint T. Cervera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Carlos Rodríguez-Martín
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Enrique Fernández-Tabanera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Raquel M. Melero-Fernández de Mera
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Matias Morin
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.M.); (S.F.-P.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/0048; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Sergio Fernández-Peñalver
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.M.); (S.F.-P.); (M.A.M.-P.)
| | - Maria Iranzo-Martínez
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
| | - Jorge Amhih-Cardenas
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
| | - Laura García-García
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
| | - Laura González-González
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
| | - Miguel Angel Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.M.); (S.F.-P.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/0048; CIBERER-ISCIII), 28029 Madrid, Spain
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain; (S.T.C.); (C.R.-M.); (E.F.-T.); (R.M.M.-F.d.M.); (M.I.-M.); (J.A.-C.); (L.G.-G.); (L.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III (CB06/07/1009; CIBERER-ISCIII), 28029 Madrid, Spain
- Correspondence:
| |
Collapse
|
34
|
Cai H, Chew SK, Li C, Tsai MK, Andrejka L, Murray CW, Hughes NW, Shuldiner EG, Ashkin EL, Tang R, Hung KL, Chen LC, Lee SYC, Yousefi M, Lin WY, Kunder CA, Cong L, McFarland CD, Petrov DA, Swanton C, Winslow MM. A Functional Taxonomy of Tumor Suppression in Oncogenic KRAS-Driven Lung Cancer. Cancer Discov 2021; 11:1754-1773. [PMID: 33608386 PMCID: PMC8292166 DOI: 10.1158/2159-8290.cd-20-1325] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/25/2020] [Accepted: 02/12/2021] [Indexed: 12/13/2022]
Abstract
Cancer genotyping has identified a large number of putative tumor suppressor genes. Carcinogenesis is a multistep process, but the importance and specific roles of many of these genes during tumor initiation, growth, and progression remain unknown. Here we use a multiplexed mouse model of oncogenic KRAS-driven lung cancer to quantify the impact of 48 known and putative tumor suppressor genes on diverse aspects of carcinogenesis at an unprecedented scale and resolution. We uncover many previously understudied functional tumor suppressors that constrain cancer in vivo. Inactivation of some genes substantially increased growth, whereas the inactivation of others increases tumor initiation and/or the emergence of exceptionally large tumors. These functional in vivo analyses revealed an unexpectedly complex landscape of tumor suppression that has implications for understanding cancer evolution, interpreting clinical cancer genome sequencing data, and directing approaches to limit tumor initiation and progression. SIGNIFICANCE: Our high-throughput and high-resolution analysis of tumor suppression uncovered novel genetic determinants of oncogenic KRAS-driven lung cancer initiation, overall growth, and exceptional growth. This taxonomy is consistent with changing constraints during the life history of cancer and highlights the value of quantitative in vivo genetic analyses in autochthonous cancer models.This article is highlighted in the In This Issue feature, p. 1601.
Collapse
Affiliation(s)
- Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Su Kit Chew
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Chuan Li
- Department of Biology, Stanford University, Stanford, California
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Christopher W Murray
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Nicholas W Hughes
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | | | - Emily L Ashkin
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - King L Hung
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Leo C Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Shi Ya C Lee
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Maryam Yousefi
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Wen-Yang Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Le Cong
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| |
Collapse
|
35
|
Park Y, Heider D, Hauschild AC. Integrative Analysis of Next-Generation Sequencing for Next-Generation Cancer Research toward Artificial Intelligence. Cancers (Basel) 2021; 13:3148. [PMID: 34202427 PMCID: PMC8269018 DOI: 10.3390/cancers13133148] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022] Open
Abstract
The rapid improvement of next-generation sequencing (NGS) technologies and their application in large-scale cohorts in cancer research led to common challenges of big data. It opened a new research area incorporating systems biology and machine learning. As large-scale NGS data accumulated, sophisticated data analysis methods became indispensable. In addition, NGS data have been integrated with systems biology to build better predictive models to determine the characteristics of tumors and tumor subtypes. Therefore, various machine learning algorithms were introduced to identify underlying biological mechanisms. In this work, we review novel technologies developed for NGS data analysis, and we describe how these computational methodologies integrate systems biology and omics data. Subsequently, we discuss how deep neural networks outperform other approaches, the potential of graph neural networks (GNN) in systems biology, and the limitations in NGS biomedical research. To reflect on the various challenges and corresponding computational solutions, we will discuss the following three topics: (i) molecular characteristics, (ii) tumor heterogeneity, and (iii) drug discovery. We conclude that machine learning and network-based approaches can add valuable insights and build highly accurate models. However, a well-informed choice of learning algorithm and biological network information is crucial for the success of each specific research question.
Collapse
Affiliation(s)
- Youngjun Park
- Department of Mathematics and Computer Science, Philipps-University of Marburg, 35032 Marburg, Germany; (Y.P.); (D.H.)
| | - Dominik Heider
- Department of Mathematics and Computer Science, Philipps-University of Marburg, 35032 Marburg, Germany; (Y.P.); (D.H.)
| | - Anne-Christin Hauschild
- Department of Mathematics and Computer Science, Philipps-University of Marburg, 35032 Marburg, Germany; (Y.P.); (D.H.)
- Department of Medical Informatics, University Medical Center Göttingen, 37075 Göttingen, Germany
| |
Collapse
|
36
|
Takeda H, Jenkins NA, Copeland NG. Identification of cancer driver genes using Sleeping Beauty transposon mutagenesis. Cancer Sci 2021; 112:2089-2096. [PMID: 33783919 PMCID: PMC8177796 DOI: 10.1111/cas.14901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
Cancer genome sequencing studies have identified driver genes for a variety of different cancers and helped to understand the genetic landscape of human cancer. It is still challenging, however, to identify cancer driver genes with confidence simply from genetic data alone. In vivo forward genetic screens using Sleeping Beauty (SB) transposon mutagenesis provides another powerful genetic tool for identifying candidate cancer driver genes in wild-type and sensitized mouse tumors. By comparing cancer driver genes identified in human and mouse tumors, cancer driver genes can be identified with additional confidence based upon comparative oncogenomics. This review describes how SB mutagenesis works in mice and focuses on studies that have identified cancer driver genes in the mouse gastrointestinal tract.
Collapse
Affiliation(s)
- Haruna Takeda
- Laboratory of Molecular Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Nancy A Jenkins
- Laboratory of Molecular Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Neal G Copeland
- Genetics Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
37
|
Narimatsu Y, Büll C, Chen YH, Wandall HH, Yang Z, Clausen H. Genetic glycoengineering in mammalian cells. J Biol Chem 2021; 296:100448. [PMID: 33617880 PMCID: PMC8042171 DOI: 10.1016/j.jbc.2021.100448] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Advances in nuclease-based gene-editing technologies have enabled precise, stable, and systematic genetic engineering of glycosylation capacities in mammalian cells, opening up a plethora of opportunities for studying the glycome and exploiting glycans in biomedicine. Glycoengineering using chemical, enzymatic, and genetic approaches has a long history, and precise gene editing provides a nearly unlimited playground for stable engineering of glycosylation in mammalian cells to explore and dissect the glycome and its many biological functions. Genetic engineering of glycosylation in cells also brings studies of the glycome to the single cell level and opens up wider use and integration of data in traditional omics workflows in cell biology. The last few years have seen new applications of glycoengineering in mammalian cells with perspectives for wider use in basic and applied glycosciences, and these have already led to discoveries of functions of glycans and improved designs of glycoprotein therapeutics. Here, we review the current state of the art of genetic glycoengineering in mammalian cells and highlight emerging opportunities.
Collapse
Affiliation(s)
- Yoshiki Narimatsu
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark.
| | - Christian Büll
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark.
| | | | - Hans H Wandall
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Zhang Yang
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Henrik Clausen
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
38
|
Functional Screening Techniques to Identify Long Non-Coding RNAs as Therapeutic Targets in Cancer. Cancers (Basel) 2020; 12:cancers12123695. [PMID: 33317042 PMCID: PMC7763270 DOI: 10.3390/cancers12123695] [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: 11/19/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Long non-coding RNAs (lncRNAs) are a recently discovered class of molecules in the cell, with potential to be utilized as therapeutic targets in cancer. A number of lncRNAs have been described to play important roles in tumor progression and drive molecular processes involved in cell proliferation, apoptosis or invasion. However, the vast majority of lncRNAs have not been studied in the context of cancer thus far. With the advent of CRISPR/Cas genome editing, high-throughput functional screening approaches to identify lncRNAs that impact cancer growth are becoming more accessible. Here, we review currently available methods to study hundreds to thousands of lncRNAs in parallel to elucidate their role in tumorigenesis and cancer progression. Abstract Recent technological advancements such as CRISPR/Cas-based systems enable multiplexed, high-throughput screening for new therapeutic targets in cancer. While numerous functional screens have been performed on protein-coding genes to date, long non-coding RNAs (lncRNAs) represent an emerging class of potential oncogenes and tumor suppressors, with only a handful of large-scale screens performed thus far. Here, we review in detail currently available screening approaches to identify new lncRNA drivers of tumorigenesis and tumor progression. We discuss the various approaches of genomic and transcriptional targeting using CRISPR/Cas9, as well as methods to post-transcriptionally target lncRNAs via RNA interference (RNAi), antisense oligonucleotides (ASOs) and CRISPR/Cas13. We discuss potential advantages, caveats and future applications of each method to provide an overview and guide on investigating lncRNAs as new therapeutic targets in cancer.
Collapse
|
39
|
Sundara Rajan S, Ludwig KR, Hall KL, Jones TL, Caplen NJ. Cancer biology functional genomics: From small RNAs to big dreams. Mol Carcinog 2020; 59:1343-1361. [PMID: 33043516 PMCID: PMC7702050 DOI: 10.1002/mc.23260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
The year 2021 marks the 20th anniversary of the first publications reporting the discovery of the gene silencing mechanism, RNA interference (RNAi) in mammalian cells. Along with the many studies that delineated the proteins and substrates that form the RNAi pathway, this finding changed our understanding of the posttranscriptional regulation of mammalian gene expression. Furthermore, the development of methods that exploited the RNAi pathway began the technological revolution that eventually enabled the interrogation of mammalian gene function-from a single gene to the whole genome-in only a few days. The needs of the cancer research community have driven much of this progress. In this perspective, we highlight milestones in the development and application of RNAi-based methods to study carcinogenesis. We discuss how RNAi-based functional genetic analysis of exemplar tumor suppressors and oncogenes furthered our understanding of cancer initiation and progression and explore how such studies formed the basis of genome-wide scale efforts to identify cancer or cancer-type specific vulnerabilities, including studies conducted in vivo. Furthermore, we examine how RNAi technologies have revealed new cancer-relevant molecular targets and the implications for cancer of the first RNAi-based drugs. Finally, we discuss the future of functional genetic analysis, highlighting the increasing availability of complementary approaches to analyze cancer gene function.
Collapse
Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katherine L. Hall
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| |
Collapse
|