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Smith DJ, Lunj S, Adamson AD, Nagarajan S, Smith TAD, Reeves KJ, Hoskin PJ, Choudhury A. CRISPR-Cas9 potential for identifying novel therapeutic targets in muscle-invasive bladder cancer. Nat Rev Urol 2024:10.1038/s41585-024-00901-y. [PMID: 38951705 DOI: 10.1038/s41585-024-00901-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2024] [Indexed: 07/03/2024]
Abstract
Gene editing technologies help identify the genetic perturbations driving tumour initiation, growth, metastasis and resistance to therapeutics. This wealth of information highlights tumour complexity and is driving cancer research towards precision medicine approaches based on an individual's tumour genetics. Bladder cancer is the 11th most common cancer in the UK, with high rates of relapse and low survival rates in patients with muscle-invasive bladder cancer (MIBC). MIBC is highly heterogeneous and encompasses multiple molecular subtypes, each with different responses to therapeutics. This evidence highlights the need to identify innovative therapeutic targets to address the challenges posed by this heterogeneity. CRISPR-Cas9 technologies have been used to advance our understanding of MIBC and determine novel drug targets through the identification of drug resistance mechanisms, targetable cell-cycle regulators, and novel tumour suppressor and oncogenes. However, the use of these technologies in the clinic remains a substantial challenge and will require careful consideration of dosage, safety and ethics. CRISPR-Cas9 offers considerable potential for revolutionizing bladder cancer therapies, but substantial research is required for validation before these technologies can be used in the clinical setting.
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Affiliation(s)
- Danielle J Smith
- Division of Cancer Sciences, University of Manchester, Manchester, UK.
| | - Sapna Lunj
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Antony D Adamson
- Faculty of Biology, Medicine and Health Research and Innovation, University of Manchester, Manchester, UK
| | - Sankari Nagarajan
- Division of Molecular and Cellular Function, University of Manchester, Manchester, UK
| | - Tim A D Smith
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- Nuclear Futures Institute, Bangor University, Bangor, UK
| | | | - Peter J Hoskin
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Ananya Choudhury
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
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2
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Li K, Qi L, Tang G, Xu H, Li Z, Fan B, Li Z, Li Y. Epigenetic Regulation in Urothelial Carcinoma. Curr Mol Med 2024; 24:85-97. [PMID: 36545729 DOI: 10.2174/1566524023666221221094432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022]
Abstract
Urothelial carcinoma (UC) is a common malignancy that remains a clinical challenge: Non-muscle-invasive urothelial carcinoma (NMIUC) has a high rate of recurrence and risk of progression, while muscle-invasive urothelial carcinoma (MIUC) has a high mortality. Although some new treatments, such as immunotherapies, have shown potential effects on some patients, most cases of advanced UC remain incurable. While treatments based on epigenetic mechanisms, whether combined with traditional platinum-based chemotherapy or emerging immunotherapy, show therapeutic advantages. With the advancement of sequencing and bioinformatics, the study of epigenomics, containing DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA, is increasingly linked with the occurrence and progression of UC. Since the epigenetics of UC is a constantly developing field of medicine, this review aims to summarize the latest research on epigenetic regulation of UC, generalize the mechanism of epigenetics in UC, and reveal the potential epigenetic therapies in the clinical setting, in order to provide some new clues on the discovery of new drugs based on the epigenetics.
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Affiliation(s)
- Ke Li
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Lin Qi
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Guyu Tang
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Haozhe Xu
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Zhi Li
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Bo Fan
- Department of Urology, Xiangya Hospital of Central South University, Changsha, China
| | - Zhongbei Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Yuan Li
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, China
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3
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Ramal M, Corral S, Kalisz M, Lapi E, Real FX. The urothelial gene regulatory network: understanding biology to improve bladder cancer management. Oncogene 2024; 43:1-21. [PMID: 37996699 DOI: 10.1038/s41388-023-02876-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
The urothelium is a stratified epithelium composed of basal cells, one or more layers of intermediate cells, and an upper layer of differentiated umbrella cells. Most bladder cancers (BLCA) are urothelial carcinomas. Loss of urothelial lineage fidelity results in altered differentiation, highlighted by the taxonomic classification into basal and luminal tumors. There is a need to better understand the urothelial transcriptional networks. To systematically identify transcription factors (TFs) relevant for urothelial identity, we defined highly expressed TFs in normal human bladder using RNA-Seq data and inferred their genomic binding using ATAC-Seq data. To focus on epithelial TFs, we analyzed RNA-Seq data from patient-derived organoids recapitulating features of basal/luminal tumors. We classified TFs as "luminal-enriched", "basal-enriched" or "common" according to expression in organoids. We validated our classification by differential gene expression analysis in Luminal Papillary vs. Basal/Squamous tumors. Genomic analyses revealed well-known TFs associated with luminal (e.g., PPARG, GATA3, FOXA1) and basal (e.g., TP63, TFAP2) phenotypes and novel candidates to play a role in urothelial differentiation or BLCA (e.g., MECOM, TBX3). We also identified TF families (e.g., KLFs, AP1, circadian clock, sex hormone receptors) for which there is suggestive evidence of their involvement in urothelial differentiation and/or BLCA. Genomic alterations in these TFs are associated with BLCA. We uncover a TF network involved in urothelial cell identity and BLCA. We identify novel candidate TFs involved in differentiation and cancer that provide opportunities for a better understanding of the underlying biology and therapeutic intervention.
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Affiliation(s)
- Maria Ramal
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sonia Corral
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark Kalisz
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Eleonora Lapi
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- CIBERONC, Madrid, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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4
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Fadul SM, Arshad A, Mehmood R. CRISPR-based epigenome editing: mechanisms and applications. Epigenomics 2023; 15:1137-1155. [PMID: 37990877 DOI: 10.2217/epi-2023-0281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Epigenomic anomalies contribute significantly to the development of numerous human disorders. The development of epigenetic research tools is essential for understanding how epigenetic marks contribute to gene expression. A gene-editing technique known as CRISPR (clustered regularly interspaced short palindromic repeats) typically targets a particular DNA sequence using a guide RNA (gRNA). CRISPR/Cas9 technology has been remodeled for epigenome editing by generating a 'dead' Cas9 protein (dCas9) that lacks nuclease activity and juxtaposing it with an epigenetic effector domain. Based on fusion partners of dCas9, a specific epigenetic state can be achieved. CRISPR-based epigenome editing has widespread application in drug screening, cancer treatment and regenerative medicine. This paper discusses the tools developed for CRISPR-based epigenome editing and their applications.
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Affiliation(s)
- Shaima M Fadul
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
| | - Aleeza Arshad
- Medical Teaching Insitute, Ayub Teaching Hospital, Abbottabad, 22020, Pakistan
| | - Rashid Mehmood
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
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5
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Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) renaissance was catalysed by the discovery that RNA-guided prokaryotic CRISPR-associated (Cas) proteins can create targeted double-strand breaks in mammalian genomes. This finding led to the development of CRISPR systems that harness natural DNA repair mechanisms to repair deficient genes more easily and precisely than ever before. CRISPR has been used to knock out harmful mutant genes and to fix errors in coding sequences to rescue disease phenotypes in preclinical studies and in several clinical trials. However, most genetic disorders result from combinations of mutations, deletions and duplications in the coding and non-coding regions of the genome and therefore require sophisticated genome engineering strategies beyond simple gene knockout. To overcome this limitation, the toolbox of natural and engineered CRISPR-Cas systems has been dramatically expanded to include diverse tools that function in human cells for precise genome editing and epigenome engineering. The application of CRISPR technology to edit the non-coding genome, modulate gene regulation, make precise genetic changes and target infectious diseases has the potential to lead to curative therapies for many previously untreatable diseases.
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Affiliation(s)
- Michael Chavez
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Paul B Finn
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Selvakumar SC, Preethi KA, Ross K, Tusubira D, Khan MWA, Mani P, Rao TN, Sekar D. CRISPR/Cas9 and next generation sequencing in the personalized treatment of Cancer. Mol Cancer 2022; 21:83. [PMID: 35331236 PMCID: PMC8944095 DOI: 10.1186/s12943-022-01565-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/17/2022] [Indexed: 12/13/2022] Open
Abstract
Background Cancer is caused by a combination of genetic and epigenetic abnormalities. Current cancer therapies are limited due to the complexity of their mechanism, underlining the need for alternative therapeutic approaches. Interestingly, combining the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) system with next-generation sequencing (NGS) has the potential to speed up the identification, validation, and targeting of high-value targets. Main text Personalized or precision medicine combines genetic information with phenotypic and environmental characteristics to produce healthcare tailored to the individual and eliminates the constraints of “one-size-fits-all” therapy. Precision medicine is now possible thanks to cancer genome sequencing. Having advantages over limited sample requirements and the recent development of biomarkers have made the use of NGS a major leap in personalized medicine. Tumor and cell-free DNA profiling using NGS, proteome and RNA analyses, and a better understanding of immunological systems, are all helping to improve cancer treatment choices. Finally, direct targeting of tumor genes in cancer cells with CRISPR/Cas9 may be achievable, allowing for eliminating genetic changes that lead to tumor growth and metastatic capability. Conclusion With NGS and CRISPR/Cas9, the goal is no longer to match the treatment for the diagnosed tumor but rather to build a treatment method that fits the tumor exactly. Hence, in this review, we have discussed the potential role of CRISPR/Cas9 and NGS in advancing personalized medicine.
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Affiliation(s)
- Sushmaa Chandralekha Selvakumar
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 600077, India
| | - K Auxzilia Preethi
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 600077, India
| | - Kehinde Ross
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Deusdedit Tusubira
- Biochemistry Department, Mbarara University of Science and Technology, Mbarara, Uganda.
| | - Mohd Wajid Ali Khan
- Department of Chemistry, College of Sciences, University of Ha'il, Ha'il, 2440, Saudi Arabia
| | - Panagal Mani
- Department of Biotechnology, Annai College of Arts and Science, Kumbakonam, Tamilnadu, India
| | - Tentu Nageswara Rao
- Department of Chemistry, Krishna University, Machilipatnam, Andhra Pradesh, 521001, India
| | - Durairaj Sekar
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 600077, India.
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7
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Rahman MM, Tollefsbol TO. Targeting cancer epigenetics with CRISPR-dCAS9: Principles and prospects. Methods 2021; 187:77-91. [PMID: 32315755 PMCID: PMC7572534 DOI: 10.1016/j.ymeth.2020.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer therapeutics is an ever-evolving field due to incessant demands for effective and precise treatment options. Over the last few decades, cancer treatment strategies have shifted somewhat from surgery to targeted precision medicine. CRISPR-dCas9 is an emerging version of precision cancer therapy that has been adapted from the prokaryotic CRISPR-Cas system. Once ligated to epigenetic effectors (EE), CRISPR-dCas9 can function as an epigenetic editing tool and CRISPR-dCas9-EE complexes could be exploited to alter cancerous epigenetic features associated with different cancer hallmarks. In this article, we discuss the rationale of epigenetic editing as a therapeutic strategy against cancer. We also outline how sgRNA-dCas9 was derived from the CRISPR-Cas system. In addition, the current status of sgRNA-dCas9 use (in vivo and in vitro) in cancer is updated with a molecular illustration of CRISPR-dCas9-mediated epigenetic and transcriptional modulation. As sgRNA-dCas9 is still at the developmental phase, challenges are inherent to its use. We evaluate major challenges in targeting cancer with sgRNA-dCas9 such as off-target effects, lack of sgRNA designing rubrics, target site selection dilemmas and deficient sgRNA-dCas9 delivery systems. Finally, we appraise the sgRNA-dCas9 as a prospective cancer therapeutic by summarizing ongoing improvements of sgRNA-dCas9 methodology.
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Affiliation(s)
- Mohammad Mijanur Rahman
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA; Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA; Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
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8
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Vélot L, Lessard F, Bérubé-Simard FA, Tav C, Neveu B, Teyssier V, Boudaoud I, Dionne U, Lavoie N, Bilodeau S, Pouliot F, Bisson N. Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. Mol Cell Proteomics 2021; 20:100064. [PMID: 33640491 PMCID: PMC8050775 DOI: 10.1016/j.mcpro.2021.100064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer (PCa) is the most frequently diagnosed cancer in men and the third cause of cancer mortality. PCa initiation and growth are driven by the androgen receptor (AR). The AR is activated by androgens such as testosterone and controls prostatic cell proliferation and survival. Here, we report an AR signaling network generated using BioID proximity labeling proteomics in androgen-dependent LAPC4 cells. We identified 31 AR-associated proteins in nonstimulated cells. Strikingly, the AR signaling network increased to 182 and 200 proteins, upon 24 h or 72 h of androgenic stimulation, respectively, for a total of 267 nonredundant AR-associated candidates. Among the latter group, we identified 213 proteins that were not previously reported in databases. Many of these new AR-associated proteins are involved in DNA metabolism, RNA processing, and RNA polymerase II transcription. Moreover, we identified 44 transcription factors, including the Kru¨ppel-like factor 4 (KLF4), which were found interacting in androgen-stimulated cells. Interestingly, KLF4 repressed the well-characterized AR-dependent transcription of the KLK3 (PSA) gene; AR and KLF4 also colocalized genome-wide. Taken together, our data report an expanded high-confidence proximity network for AR, which will be instrumental to further dissect the molecular mechanisms underlying androgen signaling in PCa cells. BioID proteomics identifies 267 androgen receptor (AR)-associated candidates Krüppel-like factor 4 (KLF4) is a new AR interaction partner AR and KLF4 colocalize genome-wide on >4000 genes, including KLK3 (PSA) KLF4 acts as a repressor for the AR target gene KLK3 (PSA)
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Affiliation(s)
- Lauriane Vélot
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Frédéric Lessard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Félix-Antoine Bérubé-Simard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Christophe Tav
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Québec, Canada
| | - Bertrand Neveu
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Valentine Teyssier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Imène Boudaoud
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Ugo Dionne
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Noémie Lavoie
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Steve Bilodeau
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculté de Médecine, Université Laval, Québec, Quebec, Canada
| | - Frédéric Pouliot
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Department of Surgery, Faculté de Médecine, Université Laval, Québec, Quebec, Canada.
| | - Nicolas Bisson
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculté de Médecine, Université Laval, Québec, Quebec, Canada.
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Mohammadinejad R, Biagioni A, Arunkumar G, Shapiro R, Chang KC, Sedeeq M, Taiyab A, Hashemabadi M, Pardakhty A, Mandegary A, Thiery JP, Aref AR, Azimi I. EMT signaling: potential contribution of CRISPR/Cas gene editing. Cell Mol Life Sci 2020; 77:2701-2722. [PMID: 32008085 PMCID: PMC11104910 DOI: 10.1007/s00018-020-03449-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 02/06/2023]
Abstract
Epithelial to mesenchymal transition (EMT) is a complex plastic and reversible cellular process that has critical roles in diverse physiological and pathological phenomena. EMT is involved in embryonic development, organogenesis and tissue repair, as well as in fibrosis, cancer metastasis and drug resistance. In recent years, the ability to edit the genome using the clustered regularly interspaced palindromic repeats (CRISPR) and associated protein (Cas) system has greatly contributed to identify or validate critical genes in pathway signaling. This review delineates the complex EMT networks and discusses recent studies that have used CRISPR/Cas technology to further advance our understanding of the EMT process.
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Affiliation(s)
- Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Alessio Biagioni
- Section of Experimental Pathology and Oncology, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Ganesan Arunkumar
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Kun-Che Chang
- Department of Ophthalmology, School of Medicine, Byers Eye Institute, Stanford University, Palo Alto, CA, 94303, USA
| | - Mohammed Sedeeq
- Division of Pharmacy, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Aftab Taiyab
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Mohammad Hashemabadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University, Kerman, Iran
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abbas Pardakhty
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Mandegary
- Physiology Research Center, Institute of Neuropharmacology and Department of Toxicology & Pharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Jean-Paul Thiery
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Guangzhou, China
| | - Amir Reza Aref
- Department of Medical Oncology, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Iman Azimi
- Division of Pharmacy, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia.
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10
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Breunig CT, Köferle A, Neuner AM, Wiesbeck MF, Baumann V, Stricker SH. CRISPR Tools for Physiology and Cell State Changes: Potential of Transcriptional Engineering and Epigenome Editing. Physiol Rev 2020; 101:177-211. [PMID: 32525760 DOI: 10.1152/physrev.00034.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Given the large amount of genome-wide data that have been collected during the last decades, a good understanding of how and why cells change during development, homeostasis, and disease might be expected. Unfortunately, the opposite is true; triggers that cause cellular state changes remain elusive, and the underlying molecular mechanisms are poorly understood. Although genes with the potential to influence cell states are known, the historic dependency on methods that manipulate gene expression outside the endogenous chromatin context has prevented us from understanding how cells organize, interpret, and protect cellular programs. Fortunately, recent methodological innovations are now providing options to answer these outstanding questions, by allowing to target and manipulate individual genomic and epigenomic loci. In particular, three experimental approaches are now feasible due to DNA targeting tools, namely, activation and/or repression of master transcription factors in their endogenous chromatin context; targeting transcription factors to endogenous, alternative, or inaccessible sites; and finally, functional manipulation of the chromatin context. In this article, we discuss the molecular basis of DNA targeting tools and review the potential of these new technologies before we summarize how these have already been used for the manipulation of cellular states and hypothesize about future applications.
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Affiliation(s)
- Christopher T Breunig
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Anna Köferle
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Andrea M Neuner
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Maximilian F Wiesbeck
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Valentin Baumann
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
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Xie H, Li J, Ying Y, Yan H, Jin K, Ma X, He L, Xu X, Liu B, Wang X, Zheng X, Xie L. METTL3/YTHDF2 m 6 A axis promotes tumorigenesis by degrading SETD7 and KLF4 mRNAs in bladder cancer. J Cell Mol Med 2020; 24:4092-4104. [PMID: 32126149 PMCID: PMC7171394 DOI: 10.1111/jcmm.15063] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/03/2020] [Accepted: 01/19/2020] [Indexed: 01/06/2023] Open
Abstract
N6‐Methyladenosine (m6A) modification, the most prevalent modification of eukaryotic messenger RNA (mRNA), is involved in the progression of various tumours. However, the specific role of m6A in bladder cancer (BCa) is still poorly understood. In this study, we demonstrated the tumour‐promoting function and specific regulatory mechanism of m6A axis, consisting of the core ‘writer’ protein METTL3 and the major reader protein YTHDF2. Depletion of METTL3 impaired cancer proliferation and cancer metastasis in vitro and in vivo. Through transcriptome sequencing, m6A methylated RNA immunoprecipitation (MeRIP) and RIP, we determined that the METTL3/YTHDF2 m6A axis directly degraded the mRNAs of the tumour suppressors SETD7 and KLF4, contributing to the progression of BCa. In addition, overexpression of SETD7 and KLF4 revealed a phenotype consistent with that induced by depletion of the m6A axis. Thus, our findings on the METTL3/YTHDF2/SETD7/KLF4 m6A axis provide the insight into the underlying mechanism of carcinogenesis and highlight potential therapeutic targets for BCa.
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Affiliation(s)
- Haiyun Xie
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jiangfeng Li
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yufan Ying
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Huaqing Yan
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ke Jin
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xueyou Ma
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Liujia He
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xin Xu
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ben Liu
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xiao Wang
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xiangyi Zheng
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Liping Xie
- Department of Urology, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
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12
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Jiang Z, Zhang Y, Chen X, Wu P, Chen D. Long non-coding RNA LINC00673 silencing inhibits proliferation and drug resistance of prostate cancer cells via decreasing KLF4 promoter methylation. J Cell Mol Med 2019; 24:1878-1892. [PMID: 31881124 PMCID: PMC6991650 DOI: 10.1111/jcmm.14883] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/13/2019] [Accepted: 11/21/2019] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer is one of the major causes of cancer‐related mortality in men across the world. Recently, long non‐coding RNAs (lncRNAs) and Kruppel‐like factor 4 (KLF4) have been reported to participate in the biology of multiple cancers including prostate cancer. Here, this study aimed to explore the possible role of LINC00673 in prostate cancer via KLF4 gene promoter methylation. Microarray‐based gene expression profiling of prostate cancer was employed to identify differentially expressed lncRNAs and genes, after which the expression of LINC00673 and KLF4 in prostate cancer tissues was determined using RT‐qPCR. Next, the relationship between LINC00673 and KLF4 was evaluated using in silico analysis. Further, the effect of LINC00673 and KLF4 on cell proliferation and drug resistance of transfected cells was examined with gain‐ and loss‐of‐function experimentation. It was found that LINC00673 was highly expressed, while KLF4 was poorly expressed in prostate cancer tissues. Additionally, LINC00673 could bind to KLF4 gene promoter region and recruit methyltransferase to the KLF4 gene promoter region. Moreover, LINC00673 silencing was demonstrated to reduce methylation of the KLF4 gene promoter to elevate the expression of KLF4, thus suppressing the proliferation and drug resistance of prostate cancer cells. In summary, LINC00673 silencing could drive demethylation of the KLF4 gene promoter and thus inhibit the proliferation and drug resistance of prostate cancer cells, suggesting that silencing of LINC00673 and elevation of KLF4 could serve as tumour suppressors in prostate cancer.
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Affiliation(s)
- Zhenming Jiang
- Department of Urology, The First Hospital of China Medical University, Shenyang, China
| | - Yuxi Zhang
- Department of Urology, The First Hospital of China Medical University, Shenyang, China.,Department of Urology, People's Hospital of Datong Hui and Tu Autonomous County, Xining, China
| | - Xi Chen
- Department of Pharmacy, The First Hospital of China Medical University, Shenyang, China
| | - Pingeng Wu
- Department of Urology, The First Hospital of China Medical University, Shenyang, China
| | - Dong Chen
- Central Lab, The First Hospital of China Medical University, Shenyang, China
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13
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Therapeutic application of the CRISPR system: current issues and new prospects. Hum Genet 2019; 138:563-590. [DOI: 10.1007/s00439-019-02028-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/13/2019] [Indexed: 12/23/2022]
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14
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Monteiro-Reis S, Lobo J, Henrique R, Jerónimo C. Epigenetic Mechanisms Influencing Epithelial to Mesenchymal Transition in Bladder Cancer. Int J Mol Sci 2019; 20:E297. [PMID: 30642115 PMCID: PMC6358899 DOI: 10.3390/ijms20020297] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/02/2019] [Accepted: 01/09/2019] [Indexed: 12/27/2022] Open
Abstract
Bladder cancer is one of the most incident neoplasms worldwide, and its treatment remains a significant challenge, since the mechanisms underlying disease progression are still poorly understood. The epithelial to mesenchymal transition (EMT) has been proven to play an important role in the tumorigenic process, particularly in cancer cell invasiveness and metastatic potential. Several studies have reported the importance of epigenetic mechanisms and enzymes, which orchestrate them in several features of cancer cells and, specifically, in EMT. In this paper, we discuss the epigenetic enzymes, protein-coding and non-coding genes, and mechanisms altered in the EMT process occurring in bladder cancer cells, as well as its implications, which allows for improved understanding of bladder cancer biology and for the development of novel targeted therapies.
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Affiliation(s)
- Sara Monteiro-Reis
- Cancer Biology and Epigenetics Group, Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
| | - João Lobo
- Cancer Biology and Epigenetics Group, Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal.
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal.
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