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Woo SW, Kim M, Kang D, Choe YH, Oh SJ, You AS, Lee SL, Kim J. Genome-Wide Characterization of Somatic Mutation Patterns in Cloned Dogs Reveals Implications for Neuronal Function, Tumorigenesis, and Aging. Genes (Basel) 2024; 15:801. [PMID: 38927737 PMCID: PMC11202621 DOI: 10.3390/genes15060801] [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: 04/25/2024] [Revised: 05/27/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Studies on somatic mutations in cloned animals have revealed slight genetic variances between clones and their originals, but have yet to identify the precise effects of these differences within the organism. Somatic mutations contribute to aging and are implicated in tumor development and other age-related diseases. Thus, we compared whole genome sequencing data from an original dog with that of cloned dogs, identifying candidate somatic mutations that were disproportionately located within genes previously implicated in aging. The substitutional signature of cloning-specific somatic mutations mirrored the uniform distribution characteristic of the signature associated with human aging. Further analysis of genes revealed significant enrichment of traits associated with body size as well as the molecular mechanisms underlying neuronal function and tumorigenesis. Overall, the somatic mutations found in cloned dogs may indicate a conserved mechanism driving aging across species and a broad spectrum of pathway alterations.
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Affiliation(s)
- Seung-Wan Woo
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (S.-W.W.); (D.K.)
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Miju Kim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Dayeon Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (S.-W.W.); (D.K.)
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Yong-ho Choe
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (Y.-h.C.); (S.-J.O.); (S.-L.L.)
| | - Seong-Ju Oh
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (Y.-h.C.); (S.-J.O.); (S.-L.L.)
| | - Are-Sun You
- Division of Animal Diseases & Health, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea;
| | - Sung-Lim Lee
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (Y.-h.C.); (S.-J.O.); (S.-L.L.)
| | - Jaemin Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (S.-W.W.); (D.K.)
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
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2
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Choi Y, Choi SA, Koh EJ, Yun I, Park S, Jeon S, Kim Y, Park S, Woo D, Phi JH, Park SH, Kim DS, Kim SH, Choi JW, Lee JW, Jung TY, Bhak J, Lee S, Kim SK. Comprehensive multiomics analysis reveals distinct differences between pediatric choroid plexus papilloma and carcinoma. Acta Neuropathol Commun 2024; 12:93. [PMID: 38867333 PMCID: PMC11167863 DOI: 10.1186/s40478-024-01814-y] [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: 02/08/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024] Open
Abstract
Choroid plexus tumors (CPTs) are intraventricular tumors derived from the choroid plexus epithelium and occur frequently in children. The aim of this study was to investigate the genomic and epigenomic characteristics of CPT and identify the differences between choroid plexus papilloma (CPP) and choroid plexus carcinoma (CPC). We conducted multiomics analyses of 20 CPT patients including CPP and CPC. Multiomics analysis included whole-genome sequencing, whole-transcriptome sequencing, and methylation sequencing. Mutually exclusive TP53 and EPHA7 point mutations, coupled with the amplification of chromosome 1, were exclusively identified in CPC. In contrast, amplification of chromosome 9 was specific to CPP. Differential gene expression analysis uncovered a significant overexpression of genes related to cell cycle regulation and epithelial-mesenchymal transition pathways in CPC compared to CPP. Overexpression of genes associated with tumor metastasis and progression was observed in the CPC subgroup with leptomeningeal dissemination. Furthermore, methylation profiling unveiled hypomethylation in major repeat regions, including long interspersed nuclear elements, short interspersed nuclear elements, long terminal repeats, and retrotransposons in CPC compared to CPP, implying that the loss of epigenetic silencing of transposable elements may play a role in tumorigenesis of CPC. Finally, the differential expression of AK1, regulated by both genomic and epigenomic factors, emerged as a potential contributing factor to the histological difference of CPP against CPC. Our results suggest pronounced genomic and epigenomic disparities between CPP and CPC, providing insights into the pathogenesis of CPT at the molecular level.
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Affiliation(s)
- Yeonsong Choi
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eun Jung Koh
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ilsun Yun
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Suhyun Park
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | | | | | - Sangbeen Park
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Donggeon Woo
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Ji Hoon Phi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Seok Kim
- Department of Pediatric Neurosurgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Won Choi
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Tae-Young Jung
- Department of Neurosurgery, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Jong Bhak
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
- Clinomics Inc., Ulsan, Republic of Korea
| | - Semin Lee
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea.
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea.
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
- Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea.
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3
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Drzymalla E, Crider KS, Wang A, Marta G, Khoury MJ, Rasooly D. Epigenome-wide association studies of prenatal maternal mental health and infant epigenetic profiles: a systematic review. Transl Psychiatry 2023; 13:377. [PMID: 38062042 PMCID: PMC10703876 DOI: 10.1038/s41398-023-02620-1] [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: 12/12/2022] [Revised: 10/01/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
Prenatal stress and poor maternal mental health are associated with adverse offspring outcomes; however, the biological mechanisms are unknown. Epigenetic modification has linked maternal health with offspring development. Epigenome-wide association studies (EWAS) have examined offspring DNA methylation profiles for association with prenatal maternal mental health to elucidate mechanisms of these complex relationships. The objective of this study is to provide a comprehensive, systematic review of EWASs of infant epigenetic profiles and prenatal maternal anxiety, depression, or depression treatment. We conducted a systematic literature search following PRISMA guidelines for EWAS studies between prenatal maternal mental health and infant epigenetics through May 22, 2023. Of 645 identified articles, 20 fulfilled inclusion criteria. We assessed replication of CpG sites among studies, conducted gene enrichment analysis, and evaluated the articles for quality and risk of bias. We found one repeated CpG site among the maternal depression studies; however, nine pairs of overlapping differentially methylatd regions were reported in at least two maternal depression studies. Gene enrichment analysis found significant pathways for maternal depression but not for any other maternal mental health category. We found evidence that these EWAS present a medium to high risk of bias. Exposure to prenatal maternal depression and anxiety or treatment for such was not consistently associated with epigenetic changes in infants in this systematic review and meta-analysis. Small sample size, potential bias due to exposure misclassification and statistical challenges are critical to address in future efforts to explore epigenetic modification as a potential mechanism by which prenatal exposure to maternal mental health disorders leads to adverse infant outcomes.
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Affiliation(s)
- Emily Drzymalla
- Division of Blood Disorders and Public Health Genomics, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Krista S Crider
- Infant Outcomes Research and Prevention Branch, Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Arick Wang
- Infant Outcomes Research and Prevention Branch, Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Muin J Khoury
- Division of Blood Disorders and Public Health Genomics, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Danielle Rasooly
- Division of Blood Disorders and Public Health Genomics, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Trasierras AM, Luna JM, Ventura S. A contrast set mining based approach for cancer subtype analysis. Artif Intell Med 2023; 143:102590. [PMID: 37673572 DOI: 10.1016/j.artmed.2023.102590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 09/08/2023]
Abstract
The task of detecting common and unique characteristics among different cancer subtypes is an important focus of research that aims to improve personalized therapies. Unlike current approaches mainly based on predictive techniques, our study aims to improve the knowledge about the molecular mechanisms that descriptively led to cancer, thus not requiring previous knowledge to be validated. Here, we propose an approach based on contrast set mining to capture high-order relationships in cancer transcriptomic data. In this way, we were able to extract valuable insights from several cancer subtypes in the form of highly specific genetic relationships related to functional pathways affected by the disease. To this end, we have divided several cancer gene expression databases by the subtype associated with each sample to detect which gene groups are related to each cancer subtype. To demonstrate the potential and usefulness of the proposed approach we have extensively analysed RNA-Seq gene expression data from breast, kidney, and colon cancer subtypes. The possible role of the obtained genetic relationships was further evaluated through extensive literature research, while its prognosis was assessed via survival analysis, finding gene expression patterns related to survival in various cancer subtypes. Some gene associations were described in the literature as potential cancer biomarkers while other results have been not described yet and could be a starting point for future research.
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Affiliation(s)
- A M Trasierras
- Department of Computer Science and Numerical Analysis, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), Spain; Maimonides Biomedical Research Institute of Cordoba, IMIBIC, University of Cordoba, Córdoba, 14071, Spain; Phytoplant Research S.L.U, Departamento Tecnología y Control, Rabanales 21-Parque Científico Tecnológico de Córdoba, Calle Astrónoma Cecilia Payne, Córdoba, Spain
| | - J M Luna
- Department of Computer Science and Numerical Analysis, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), Spain; Maimonides Biomedical Research Institute of Cordoba, IMIBIC, University of Cordoba, Córdoba, 14071, Spain
| | - S Ventura
- Department of Computer Science and Numerical Analysis, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), Spain; Maimonides Biomedical Research Institute of Cordoba, IMIBIC, University of Cordoba, Córdoba, 14071, Spain.
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5
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Giannopoulou N, Constantinou C. Recent Developments in Diagnostic and Prognostic Biomarkers for Colorectal Cancer: A Narrative Review. Oncology 2023; 101:675-684. [PMID: 37364542 DOI: 10.1159/000531474] [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: 01/26/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Colorectal cancer was reported as the second most common cause of cancer death worldwide, in the year 2020. This disease is an important public health problem considering its high incidence and mortality rates. SUMMARY The molecular events that lead to colorectal cancer include genetic and epigenetic abnormalities. Some of the most important molecular mechanisms involved include the APC/β-catenin pathway, the microsatellite pathway, and the CpG island hypermethylation. Evidence in the literature supports a role for the microbiota in the development of colon carcinogenesis, and specific microbes may contribute to or prevent carcinogenesis. Progress in prevention, screening, and management has improved the overall prognosis of the disease when diagnosed at an early stage; yet metastatic disease continues to have a poor long-term prognosis due to late-stage diagnosis and treatment failure. Biomarkers are a key tool for early detection and prognosis and aim to reduce morbidity and mortality associated with colorectal cancer. The main focus of this narrative review is to provide an update on the recent development of diagnostic and prognostic biomarkers in stool, blood, and tumor tissue samples. KEY MESSAGES The review focuses on recent investigations in microRNAs, cadherins, Piwi-interacting RNAs, circulating cell-free DNA, and microbiome biomarkers which can be applied for the diagnosis and prognosis of colorectal cancer.
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Affiliation(s)
- Nefeli Giannopoulou
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus
| | - Constantina Constantinou
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus
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Sun R, Yang Y, Lü W, Yang Y, Li Y, Liu Z, Diao D, Wang Y, Chang S, Lu M, Jiang Q, Dai B, Ma X, Zhao C, Lü M, Zhang J, Ding C, Li N, Zhang J, Xiao Z, Zhou D, Huang C. Single-cell transcriptomic analysis of normal and pathological tissues from the same patient uncovers colon cancer progression. Cell Biosci 2023; 13:62. [PMID: 36944972 PMCID: PMC10031920 DOI: 10.1186/s13578-023-01002-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
The aim of the present study was to elucidate the evolutionary trajectory of colon cells from normal colon mucosa, to adenoma, then to carcinoma in the same microenvironment. Normal colon, adenoma and carcinoma tissues from the same patient were analyzed by single-cell sequencing, which perfectly simulated the process of time-dependent colon cancer due to the same microenvironment. A total of 22 cell types were identified. Results suggest the presence of dominant clones of same cells including C2 goblet cell, epithelial cell subtype 1 (Epi1), enterocyte cell subset 0 (Entero0), and Entero5 in carcinoma. Epi1 and Entero0 were Co-enriched in antibacterial and IL-17 signaling, Entero5 was enriched in immune response and mucin-type O-glycan biosynthesis. We discovered new colon cancer related genes including AC007952.4, NEK8, CHRM3, ANO7, B3GNT6, NEURL1, ODC1 and KCNMA1. The function of TBC1D4, LTB, C2CD4A, AND GBP4/5 in T cells needs to be clarified. We used colon samples from the same person, which provide new information for colon cancer therapy.
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Affiliation(s)
- Ruifang Sun
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yang Yang
- School of Public Health, Shaanxi University of Chinese Medicine, Middle Section of Century Avenue, Xianyang, Shaanxi, People's Republic of China.
| | - Weidong Lü
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yanqi Yang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yulong Li
- Department of Gastroenterology, Shaanxi Provincial People's Hospital, 256 Youyi West Road, Xi'an, Shaanxi, People's Republic of China
| | - Zhigang Liu
- Department of Thoracic Surgery, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Dongmei Diao
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Yang Wang
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Su'e Chang
- Department of Orthopedics, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Qiuyu Jiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Bingling Dai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi, People's Republic of China
| | - Chang'an Zhao
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Moqi Lü
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Juan Zhang
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Caixia Ding
- Department of Pathology, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, 309 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Na Li
- School of Pharmacy, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang, Henan, People's Republic of China
| | - Jian Zhang
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China
| | - Zhengtao Xiao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
| | - Dangxia Zhou
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, 76 Yanta West Road, Xi'an, Shaanxi, People's Republic of China.
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Ilott NE, Neyazi M, Arancibia-Cárcamo CV, Powrie F, Geremia A. Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease. Wellcome Open Res 2022; 6:199. [PMID: 36447600 PMCID: PMC9664024 DOI: 10.12688/wellcomeopenres.16901.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 06/30/2024] Open
Abstract
Background: Patients with primary sclerosing cholangitis (PSC) frequently have co-ocurring ulcerative colitis (UC) and develop colorectal cancer. Colorectal cancer risk in patients with PSC-associated ulcerative colitis (PSC/UC) is elevated relative to patients with ulcerative colitis (UC) alone, reasons for which remain obscure. Understanding the molecular and microbial basis for differences between these two patient groups and how these vary across intestinal sites is important for the development of therapies to prevent colorectal cancer development in at-risk individuals. Methods: We employed ribonucleic acid sequencing (RNA-seq) analysis of biopsy samples across three intestinal tissue locations (ileum, caecum and rectum) in patients with PSC/UC (ileum n = 7, caecum n = 7, rectum n = 7), UC (ileum n = 9, caecum n = 10, rectum n = 10) and healthy controls (ileum n = 11, caecum n = 9, rectum n = 12) to determine tissue-dependent transcriptional alterations in PSC/UC. We also performed 16S ribosomal RNA (rRNA) amplicon sequencing to determine bacterial associations with PSC/UC. Results: Tissue-defining transcriptional signatures revealed that the ileum was enriched for genes involved in lipid and drug metabolism, the caecum for activated immune cells and the rectum for enteric neurogenesis. Transcriptional alterations relative to healthy control samples were largely shared between patients with PSC/UC or UC although were distinct across tissue locations. Nevertheless, we observed reduced expression of gamma-glutamyl transferase 1 ( GGT1) specifically in the ileum and caecum of patients with PSC/UC. Analysis of the bacterial component of the microbiome revealed high inter-individual variability of microbiome composition and little evidence for tissue-dependency. We observed a reduction in Parabacteroides relative abundance in the rectum of patients with PSC/UC. Conclusions: The role of gamma-glutamyl transferase in maintaining the redox environment through the glutathione salvage pathway makes our observed alterations a potential pathway to PSC-associated colorectal cancer.
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Affiliation(s)
- Nicholas E. Ilott
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
| | - Mastura Neyazi
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Oxford Translational Gastroenterology Unit Investigators
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Carolina V. Arancibia-Cárcamo
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Fiona Powrie
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Alessandra Geremia
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
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8
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Ilott NE, Neyazi M, Arancibia-Cárcamo CV, Powrie F, Geremia A. Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease. Wellcome Open Res 2021; 6:199. [PMID: 36447600 PMCID: PMC9664024 DOI: 10.12688/wellcomeopenres.16901.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2021] [Indexed: 06/30/2024] Open
Abstract
Background: Primary sclerosing cholangitis (PSC) is a disease of the bile duct and liver. However, patients frequently have co-morbidities including inflammatory bowel disease (IBD) and colorectal cancer. Colorectal cancer risk in patients with PSC-associated ulcerative colitis (PSC/UC) is elevated relative to patients with ulcerative colitis (UC) alone, reasons for which remain obscure. Further, clinical and immunological features, and involved intestinal sites differ between PSC/UC and UC. Understanding the molecular and microbial basis for differences in cancer risk between these two patient groups and how these differ across intestinal sites is important for the development of therapies to prevent colorectal cancer development in at-risk individuals. Methods: We employed ribonucleic acid sequencing (RNA-seq) analysis of biopsy samples across three intestinal tissue locations (ileum, caecum and rectum) in patients with PSC/UC (n = 8), UC (n = 10) and healthy controls (n = 12) to determine tissue-dependent transcriptional alterations in PSC/UC. We also performed 16S ribosomal RNA (rRNA) amplicon sequencing to determine bacterial associations with PSC/UC and host-microbiome associations. Results: Tissue-defining transcriptional signatures revealed that the ileum was enriched for genes involved in lipid and drug metabolism, the caecum for activated immune cells and the rectum for enteric neurogenesis. Transcriptional alterations relative to healthy control samples were largely shared between patients with PSC/UC or UC although were distinct across tissue locations. Nevertheless, we observed reduced expression of gamma-glutamyl transferase 1 ( GGT1) specifically in the ileum and caecum of patients with PSC/UC. Analysis of the bacterial component of the microbiome revealed high inter-individual variability of microbiome composition and little evidence for tissue-dependency. We observed a reduction in Parabacteroides relative abundance in the rectum of patients with PSC/UC. Conclusions: The role of gamma-glutamyl transferase in maintaining the redox environment through the glutathione salvage pathway makes our observed alterations a potential pathway to PSC-associated colorectal cancer.
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Affiliation(s)
- Nicholas E. Ilott
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
| | - Mastura Neyazi
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Oxford Translational Gastroenterology Unit Investigators
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Carolina V. Arancibia-Cárcamo
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Fiona Powrie
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Alessandra Geremia
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
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9
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Fonseca AS, Ramão A, Bürger MC, de Souza JES, Zanette DL, de Molfetta GA, de Araújo LF, de Barros E Lima Bueno R, Aguiar GM, Plaça JR, Alves CDP, Dos Santos ARD, Vidal DO, Silva GEB, Panepucci RA, Peria FM, Feres O, da Rocha JJR, Zago MA, Silva WA. ETV4 plays a role on the primary events during the adenoma-adenocarcinoma progression in colorectal cancer. BMC Cancer 2021; 21:207. [PMID: 33648461 PMCID: PMC7919324 DOI: 10.1186/s12885-021-07857-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common cancers worldwide; it is the fourth leading cause of death in the world and the third in Brazil. Mutations in the APC, DCC, KRAS and TP53 genes have been associated with the progression of sporadic CRC, occurring at defined pathological stages of the tumor progression and consequently modulating several genes in the corresponding signaling pathways. Therefore, the identification of gene signatures that occur at each stage during the CRC progression is critical and can present an impact on the diagnosis and prognosis of the patient. In this study, our main goal was to determine these signatures, by evaluating the gene expression of paired colorectal adenoma and adenocarcinoma samples to identify novel genetic markers in association to the adenoma-adenocarcinoma stage transition. METHODS Ten paired adenoma and adenocarcinoma colorectal samples were subjected to microarray gene expression analysis. In addition, mutations in APC, KRAS and TP53 genes were investigated by DNA sequencing in paired samples of adenoma, adenocarcinoma, normal tissue, and peripheral blood from ten patients. RESULTS Gene expression analysis revealed a signature of 689 differentially expressed genes (DEG) (fold-change> 2, p< 0.05), between the adenoma and adenocarcinoma paired samples analyzed. Gene pathway analysis using the 689 DEG identified important cancer pathways such as remodeling of the extracellular matrix and epithelial-mesenchymal transition. Among these DEG, the ETV4 stood out as one of the most expressed in the adenocarcinoma samples, further confirmed in the adenocarcinoma set of samples from the TCGA database. Subsequent in vitro siRNA assays against ETV4 resulted in the decrease of cell proliferation, colony formation and cell migration in the HT29 and SW480 colorectal cell lines. DNA sequencing analysis revealed KRAS and TP53 gene pathogenic mutations, exclusively in the adenocarcinomas samples. CONCLUSION Our study identified a set of genes with high potential to be used as biomarkers in CRC, with a special emphasis on the ETV4 gene, which demonstrated involvement in proliferation and migration.
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Affiliation(s)
- Aline Simoneti Fonseca
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil.
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil.
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil.
- Research Institute Pelé Pequeno Príncipe, Av Silva Jardim, 1632, CEP: 80250-060, Água Verde, Curitiba, PR, Brazil.
| | - Anelisa Ramão
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Matheus Carvalho Bürger
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Jorge Estefano Santana de Souza
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Dalila Lucíola Zanette
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil
- Laboratory of Applied Science and Technology in Health (LASTH), Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, PR, Brazil
| | - Greice Andreotti de Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil
| | - Luiza Ferreira de Araújo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil
| | - Rafaela de Barros E Lima Bueno
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Graziela Moura Aguiar
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Jessica Rodrigues Plaça
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Cleidson de Pádua Alves
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Anemari Ramos Dinarte Dos Santos
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Daniel Onofre Vidal
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Gyl Eanes Barros Silva
- Laboratory of Immunofluorescence and Electron Microscopy (LIME), Presidente Dutra University Hospital (HUUFMA), São Luís, MA, Brazil
| | - Rodrigo Alexandre Panepucci
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Fernanda Maris Peria
- Departament of Medical Clinic, Medical School of Ribeirão Preto, University of São Paulo, USP, Ribeirão Preto, SP, Brazil
| | - Omar Feres
- Department of Surgery and Anatomy, School of Medicine of Ribeirão Preto, University of São Paulo, Sao Paulo, Brazil
| | | | - Marco Antonio Zago
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Wilson Araújo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil.
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil.
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil.
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10
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Urh K, Žlajpah M, Zidar N, Boštjančič E. Identification and Validation of New Cancer Stem Cell-Related Genes and Their Regulatory microRNAs in Colorectal Cancerogenesis. Biomedicines 2021; 9:biomedicines9020179. [PMID: 33670246 PMCID: PMC7916981 DOI: 10.3390/biomedicines9020179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/31/2021] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
Significant progress has been made in the last decade in our understanding of the pathogenetic mechanisms of colorectal cancer (CRC). Cancer stem cells (CSC) have gained much attention and are now believed to play a crucial role in the pathogenesis of various cancers, including CRC. In the current study, we validated gene expression of four genes related to CSC, L1TD1, SLITRK6, ST6GALNAC1 and TCEA3, identified in a previous bioinformatics analysis. Using bioinformatics, potential miRNA-target gene correlations were prioritized. In total, 70 formalin-fixed paraffin-embedded biopsy samples from 47 patients with adenoma, adenoma with early carcinoma and CRC without and with lymph node metastases were included. The expression of selected genes and microRNAs (miRNAs) was evaluated using quantitative PCR. Differential expression of all investigated genes and four of six prioritized miRNAs (hsa-miR-199a-3p, hsa-miR-335-5p, hsa-miR-425-5p, hsa-miR-1225-3p, hsa-miR-1233-3p and hsa-miR-1303) was found in at least one group of CRC cancerogenesis. L1TD1, SLITRK6, miR-1233-3p and miR-1225-3p were correlated to the level of malignancy. A negative correlation between miR-199a-3p and its predicted target SLITRK6 was observed, showing potential for further experimental validation in CRC. Our results provide further evidence that CSC-related genes and their regulatory miRNAs are involved in CRC development and progression and suggest that some them, particularly miR-199a-3p and its SLITRK6 target gene, are promising for further validation in CRC.
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