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Iñiguez-Muñoz S, Llinàs-Arias P, Ensenyat-Mendez M, Bedoya-López AF, Orozco JIJ, Cortés J, Roy A, Forsberg-Nilsson K, DiNome ML, Marzese DM. Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements. Cell Mol Life Sci 2024; 81:274. [PMID: 38902506 DOI: 10.1007/s00018-024-05314-z] [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: 07/06/2023] [Revised: 12/07/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024]
Abstract
Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements involved in gene expression. These gene regulatory elements (GREs) include enhancers, insulators, silencers, and gene promoters. Notably, new evidence shows how mutations within these regions substantially influence gene expression programs, especially in the context of cancer. Advances in high-throughput sequencing technologies have accelerated the identification of somatic and germline single nucleotide mutations in non-coding genomic regions. This review provides an overview of somatic and germline non-coding single nucleotide alterations affecting transcription factor binding sites in GREs, specifically involved in cancer biology. It also summarizes the technologies available for exploring GREs and the challenges associated with studying and characterizing non-coding single nucleotide mutations. Understanding the role of GRE alterations in cancer is essential for improving diagnostic and prognostic capabilities in the precision medicine era, leading to enhanced patient-centered clinical outcomes.
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Affiliation(s)
- Sandra Iñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Andrés F Bedoya-López
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Group, 08017, Barcelona, Spain
- Medica Scientia Innovation Research SL (MEDSIR), 08018, Barcelona, Spain
- Faculty of Biomedical and Health Sciences, Department of Medicine, Universidad Europea de Madrid, 28670, Madrid, Spain
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Maggie L DiNome
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Diego M Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
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Meng H, Nan M, Li Y, Ding Y, Yin Y, Zhang M. Application of CRISPR-Cas9 gene editing technology in basic research, diagnosis and treatment of colon cancer. Front Endocrinol (Lausanne) 2023; 14:1148412. [PMID: 37020597 PMCID: PMC10067930 DOI: 10.3389/fendo.2023.1148412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023] Open
Abstract
Colon cancer is the fourth leading cause of cancer death worldwide, and its progression is accompanied by a complex array of genetic variations. CRISPR/Cas9 can identify new drug-resistant or sensitive mutations in colon cancer, and can use gene editing technology to develop new therapeutic targets and provide personalized treatments, thereby significantly improving the treatment of colon cancer patients. CRISPR/Cas9 systems are driving advances in biotechnology. RNA-directed Cas enzymes have accelerated the pace of basic research and led to clinical breakthroughs. This article reviews the rapid development of CRISPR/Cas in colon cancer, from gene editing to transcription regulation, gene knockout, genome-wide CRISPR tools, therapeutic targets, stem cell genomics, immunotherapy, metabolism-related genes and inflammatory bowel disease. In addition, the limitations and future development of CRISPR/Cas9 in colon cancer studies are reviewed. In conclusion, this article reviews the application of CRISPR-Cas9 gene editing technology in basic research, diagnosis and treatment of colon cancer.
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Affiliation(s)
- Hui Meng
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Mingzhi Zhang, ; Hui Meng,
| | - Manman Nan
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yizhen Li
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yi Ding
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuhui Yin
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mingzhi Zhang
- Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Mingzhi Zhang, ; Hui Meng,
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Sánchez-Roncancio C, García B, Gallardo-Hidalgo J, Yáñez JM. GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to Piscirickettsia salmonis in Rainbow Trout ( Oncorhynchus mykiss). Genes (Basel) 2022; 14:114. [PMID: 36672855 PMCID: PMC9859203 DOI: 10.3390/genes14010114] [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: 11/14/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies (GWAS) allow the identification of associations between genetic variants and important phenotypes in domestic animals, including disease-resistance traits. Whole Genome Sequencing (WGS) data can help increase the resolution and statistical power of association mapping. Here, we conduced GWAS to asses he facultative intracellular bacterium Piscirickettsia salmonis, which affects farmed rainbow trout, Oncorhynchus mykiss, in Chile using imputed genotypes at the sequence level and searched for candidate genes located in genomic regions associated with the trait. A total of 2130 rainbow trout were intraperitoneally challenged with P. salmonis under controlled conditions and genotyped using a 57K single nucleotide polymorphism (SNP) panel. Genotype imputation was performed in all the genotyped animals using WGS data from 102 individuals. A total of 488,979 imputed WGS variants were available in the 2130 individuals after quality control. GWAS revealed genome-wide significant quantitative trait loci (QTL) in Omy02, Omy03, Omy25, Omy26 and Omy27 for time to death and in Omy26 for binary survival. Twenty-four (24) candidate genes associated with P. salmonis resistance were identified, which were mainly related to phagocytosis, innate immune response, inflammation, oxidative response, lipid metabolism and apoptotic process. Our results provide further knowledge on the genetic variants and genes associated with resistance to intracellular bacterial infection in rainbow trout.
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Affiliation(s)
- Charles Sánchez-Roncancio
- Doctorado en Acuicultura, Programa Cooperativo: Universidad de Chile. Universidad Católica del Norte. Pontificia Universidad Católica de Valparaíso, Chile
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
| | - Baltasar García
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile
| | - Jousepth Gallardo-Hidalgo
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile
| | - José M. Yáñez
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile
- Núcleo Milenio de Salmonidos Invasores Australes (INVASAL), Concepcion 4030000, Chile
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Liu Q, Guo L, Lou Z, Xiang X, Shao J. Super-enhancers and novel therapeutic targets in colorectal cancer. Cell Death Dis 2022; 13:228. [PMID: 35277481 PMCID: PMC8917125 DOI: 10.1038/s41419-022-04673-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 12/24/2022]
Abstract
Transcription factors, cofactors, chromatin regulators, and transcription apparatuses interact with transcriptional regulatory elements, including promoters, enhancers, and super-enhancers (SEs), to coordinately regulate the transcription of target genes and thereby control cell behaviors. Among these transcriptional regulatory components and related elements, SEs often play a central role in determining cell identity and tumor initiation and progression. Therefore, oncogenic SEs, which are generated within cancer cells in oncogenes and other genes important in tumor pathogenesis, have emerged as attractive targets for novel cancer therapeutic strategies in recent years. Herein, we review the identification, formation and activation modes, and regulatory mechanisms for downstream genes and pathways of oncogenic SEs. We also review the therapeutic strategies and compounds targeting oncogenic SEs in colorectal cancer and other malignancies.
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Affiliation(s)
- Qian Liu
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijuan Guo
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiyuan Lou
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Xueping Xiang
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jimin Shao
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
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McCarthy MW. Harnessing the potential of CRISPR-based platforms to advance the field of hospital medicine. Expert Rev Anti Infect Ther 2020; 18:799-805. [PMID: 32366131 PMCID: PMC7212535 DOI: 10.1080/14787210.2020.1761333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Clustered regularly interspaced short palindromic repeats (CRISPR) are segments of nucleic acid that play a role in prokaryotic defense and form the basis of a genome editing technology that allows permanent alteration of genetic material. This methodology, known as CRISPR-Cas9, is poised to revolutionize molecular biology, but no literature yet exists on how these advances will affect hospitalists. AREAS COVERED These specialists in inpatient medicine care for a wide variety of hospitalized patients, including those with infectious disease, cancer, cardiovascular disease, autoimmune disease, hematologic disease, and a variety of other conditions that may soon be impacted by advances in gene-modifying technology provided by CRISPR-Cas9. A Literature search was performed using PubMed [1 December 2019-17 April 2020]. EXPERT OPINION This paper reviews the remarkable diagnostic and therapeutic potential of the CRISPR-Cas9 platform and concludes with a look at ethical issues and technical hurdles pertaining to the implementation of permanent gene modification in the practice of Hospital Medicine.
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Affiliation(s)
- Matthew W. McCarthy
- Weill Cornell Medical College, Division of General Internal Medicine, New York-Presbyterian Hospital, New York, NY, USA
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