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Deris Zayeri Z, Parsi A, Shahrabi S, Kargar M, Davari N, Saki N. Epigenetic and metabolic reprogramming in inflammatory bowel diseases: diagnostic and prognostic biomarkers in colorectal cancer. Cancer Cell Int 2023; 23:264. [PMID: 37936149 PMCID: PMC10631091 DOI: 10.1186/s12935-023-03117-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND AND AIM "Inflammatory bowel disease" (IBD) is a chronic, relapsing inflammatory disease of the intestinal tract that typically begins at a young age and might transit to colorectal cancer (CRC). In this manuscript, we discussed the epigenetic and metabolic change to present a extensive view of IBDs transition to CRC. This study discusses the possible biomarkers for evaluating the condition of IBDs patients, especially before the transition to CRC. RESEARCH APPROACH We searched "PubMed" and "Google Scholar" using the keywords from 2000 to 2022. DISCUSSION In this manuscript, interesting titles associated with IBD and CRC are discussed to present a broad view regarding the epigenetic and metabolic reprogramming and the biomarkers. CONCLUSION Epigenetics can be the main reason in IBD transition to CRC, and Hypermethylation of several genes, such as VIM, OSM4, SEPT9, GATA4 and GATA5, NDRG4, BMP3, ITGA4 and plus hypomethylation of LINE1 can be used in IBD and CRC management. Epigenetic, metabolisms and microbiome-derived biomarkers, such as Linoleic acid and 12 hydroxy 8,10-octadecadienoic acid, Serum M2-pyruvate kinase and Six metabolic genes (NAT2, XDH, GPX3, AKR1C4, SPHK and ADCY5) expression are valuable biomarkers for early detection and transition to CRC condition. Some miRs, such as miR-31, miR-139-5p, miR -155, miR-17, miR-223, miR-370-3p, miR-31, miR -106a, miR -135b and miR-320 can be used as biomarkers to estimate IBD transition to CRC condition.
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Affiliation(s)
- Zeinab Deris Zayeri
- Golestan Hospital Clinical Research Development Unit, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Abazar Parsi
- Alimentary Tract Research Center, Clinical Sciences Research Inistitute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeid Shahrabi
- Department of Biochemistry and Hematology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Masoud Kargar
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nader Davari
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Yin Y, Wan J, Yu J, Wu K. Molecular Pathogenesis of Colitis-associated Colorectal Cancer: Immunity, Genetics, and Intestinal Microecology. Inflamm Bowel Dis 2023; 29:1648-1657. [PMID: 37202830 DOI: 10.1093/ibd/izad081] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Indexed: 05/20/2023]
Abstract
Patients with inflammatory bowel disease (IBD) have a high risk for colorectal cancer (CRC). This cancer type, which is strongly associated with chronic inflammation, is called colitis-associated CRC (CAC). Understanding the molecular pathogenesis of CAC is crucial to identify biomarkers necessary for early diagnosis and more effective treatment directions. The accumulation of immune cells and inflammatory factors, which constitute a complex chronic inflammatory environment in the intestinal mucosa, may cause oxidative stress or DNA damage to the epithelial cells, leading to CAC development and progression. An important feature of CAC is genetic instability, which includes chromosome instability, microsatellite instability, hypermethylation, and changes in noncoding RNAs. Furthermore, the intestinal microbiota and metabolites have a great impact on IBD and CAC. By clarifying immune, genetic, intestinal microecology, and other related pathogenesis, CAC may be more predictable and treatable.
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Affiliation(s)
- Yue Yin
- Medical School, Fourth Military Medical University, Xi'an, China
| | - Jian Wan
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Jingmin Yu
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Kaichun Wu
- Xijing Hospital of Digestive Diseases, State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Fourth Military Medical University, Xi'an, China
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3
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Shokrollah N, Samadi P, Jalali A, Dalirfardouei R, Afshar S, Pourjafar M. A Systems Biology Approach to Identify Novel Biomarkers in Progression from Crohn's Disease to Colorectal Cancer. Asian Pac J Cancer Prev 2023; 24:1993-2001. [PMID: 37378929 PMCID: PMC10505881 DOI: 10.31557/apjcp.2023.24.6.1993] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
OBJECTIVE This study aimed to find the key genes and miRNAs as potential biomarkers related to the progression of colorectal cancer (CRC) from Crohn's disease (CD). BACKGROUND CD is widely accepted as one of the main risk factors leading to CRC. So, Identifying the novel molecular pathways involved in the development of CRC from CD can provide potential solutions for therapeutic interventions. METHODS By implementing a systematic approach, we have analyzed mRNA and miRNA datasets containing CRC and CD samples to determine differentially expressed genes (DEGs) and miRNAs (DEmiRNA). Then by selecting common genes involved in the progression from CD to CRC, different downstream analyses including mRNA-miRNA network, functional enrichment analysis, gene set enrichment analysis, and survival analysis were performed. Finally, quantitative real-time PCR (RT-PCR) analysis of tissue samples obtained from Normal/CRC samples was used to confirm the differential expression of selected genes and miRNA. RESULTS There were 10 DE miRNA and 181 genes DEGs common between progression from CD to CRC. The genes obtained for each of the 10 miRNAs were considered as the final target for downstream analyzes. In addition, analysis of RT-PCR indicated that miR-195-5p, PHLPP2, and LITAF were downregulated in the cancer group compared to the control group. CONCLUSION This study showed that PHLPP2, LITAF, and miR-195-5p may have key roles in the tumorigenesis of CRC and they can be used as therapeutic targets and diagnostic biomarkers after further in-vitro and in-vivo evaluation.
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Affiliation(s)
- Niloofar Shokrollah
- Department of Molecular Medicine and Genetics, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Pouria Samadi
- Department of Molecular Medicine and Genetics, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Akram Jalali
- Department of Molecular Medicine and Genetics, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Razieh Dalirfardouei
- Department of Molecular Medicine and Genetics, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Saeid Afshar
- Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Mona Pourjafar
- Department of Molecular Medicine and Genetics, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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Zhang X, Jin M, Liu F, Qu H, Chen C. Identification of Key MicroRNAs and Genes between Colorectal Adenoma and Colorectal Cancer via Deep Learning on GEO Databases and Bioinformatics. CONTRAST MEDIA & MOLECULAR IMAGING 2023; 2023:6457152. [PMID: 36793496 PMCID: PMC9922557 DOI: 10.1155/2023/6457152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/10/2022] [Accepted: 11/24/2022] [Indexed: 02/08/2023]
Abstract
Background Deep learning techniques are gaining momentum in medical research. Colorectal adenoma (CRA) is a precancerous lesion that may develop into colorectal cancer (CRC) and its etiology and pathogenesis are unclear. This study aims to identify transcriptome differences between CRA and CRC via deep learning on Gene Expression Omnibus (GEO) databases and bioinformatics in the Chinese population. Methods In this study, three microarray datasets from the GEO database were used to identify the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) in CRA and CRC. The FunRich software was performed to predict the targeted mRNAs of DEMs. The targeted mRNAs were overlapped with DEGs to determine the key DEGs. Molecular mechanisms of CRA and CRC were evaluated using enrichment analysis. Cytoscape was used to construct protein-protein interaction (PPI) and miRNA-mRNA regulatory networks. We analyzed the expression of key DEMs and DEGs, their prognosis, and correlation with immune infiltration based on the Kaplan-Meier plotter, UALCAN, and TIMER databases. Results A total of 38 DEGs are obtained after the intersection, including 11 upregulated genes and 27 downregulated genes. The DEGs were involved in the pathways, including epithelial-to-mesenchymal transition, sphingolipid metabolism, and intrinsic pathway for apoptosis. The expression of has-miR-34c (P = 0.036), hsa-miR-320a (P = 0.045), and has-miR-338 (P = 0.0063) was correlated with the prognosis of CRC patients. The expression levels of BCL2, PPM1L, ARHGAP44, and PRKACB in CRC tissues were significantly lower than normal tissues (P < 0.001), while the expression levels of TPD52L2 and WNK4 in CRC tissues were significantly higher than normal tissues (P < 0.01). These key genes are significantly associated with the immune infiltration of CRC. Conclusion This preliminary study will help identify patients with CRA and early CRC and establish prevention and monitoring strategies to reduce the incidence of CRC.
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Affiliation(s)
- Xin Zhang
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Mingxin Jin
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Fengjun Liu
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Hui Qu
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Cheng Chen
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
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Boros É, Hegedűs Z, Kellermayer Z, Balogh P, Nagy I. Global alteration of colonic microRNAome landscape associated with inflammatory bowel disease. Front Immunol 2022; 13:991346. [PMID: 36177008 PMCID: PMC9513375 DOI: 10.3389/fimmu.2022.991346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Inflammatory Bowel Disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that associates with, among others, increased risk of colorectal cancer. There is a growing evidence that miRNAs have important roles in pathological processes, such as inflammation or carcinogenesis. Understanding the molecular mechanisms such as alterations in microRNAome upon chronic intestinal inflammation is critical for understanding the exact pathomechanism of IBD. Hence, we conducted a genome wide microRNAome analysis by applying miRNA-Seq in a rat model of experimental colitis, validated the data by QPCR, examined the expression of a selection of precursor and mature miRNAs, performed in depth biological interpretation using Ingenuity Pathway Analysis and tested the obtained results on samples derived from human patients. We identified specific, interdependent expression pattern of activator/repressor transcription factors, miRNAs and their direct targets in the inflamed colon samples. Particularly, decreased expression of the miR-200 family members (miR-200a/b/c,-141, and -429) and miR-27b correlates with the reduced level of their enhancers (HNF1B, E2F1), elevated expression of their repressors (ZEB2, NFKB1) and increased expression of their target genes (ZEB2, RUNX1). Moreover, the marked upregulation of six miR-27b target genes (IFI16, GCA, CYP1B1, RUNX1, MEF2C and MMP13) in the inflamed colon tissues is a possible direct consequence of the lack of repression due to the downregulated miRNA-27b expression. Our data indicate that changes in microRNAome are associated with the pathophysiology of IBD, consequently, microRNAs offer potential targets for the diagnosis, prognosis and treatment of IBD.
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Affiliation(s)
- Éva Boros
- Seqomics Biotechnology Ltd., Mórahalom, Hungary
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Zoltán Hegedűs
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
- Department of Biochemistry and Medical Chemistry, Medical School, University of Pécs, Pécs, Hungary
| | - Zoltán Kellermayer
- Department of Immunology and Biotechnology, University of Pécs, Pécs, Hungary
- Lymphoid Organogenesis Research Group, Szentágothai János Research Center, University of Pécs, Pécs, Hungary
| | - Péter Balogh
- Department of Immunology and Biotechnology, University of Pécs, Pécs, Hungary
- Lymphoid Organogenesis Research Group, Szentágothai János Research Center, University of Pécs, Pécs, Hungary
| | - István Nagy
- Seqomics Biotechnology Ltd., Mórahalom, Hungary
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
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Wu J, Wu Y, Feng W, Chen Q, Wang D, Liu M, Yu H, Zhang Y, Wang T. Role of Microbial Metabolites of Histidine in the Development of Colitis. Mol Nutr Food Res 2022; 66:e2101175. [PMID: 35585003 DOI: 10.1002/mnfr.202101175] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/17/2022] [Indexed: 12/31/2022]
Abstract
SCOPE Colitis is a chronic relapsing inflammatory disease of colon. Clinical studies show that meat-rich diet plays a critical role in the relapse of colitis. However, it is unclear whether the microbial metabolites of histidine, which is an amino acid widely found in meat, have an impact on the health of the intestine. METHODS AND RESULTS Six metabolites of histidine are given to IEC-6 cells. The cell activity measurement shows that imidazole propionate (IMP) is the most detrimental metabolite. Then, IMP is injected to mice by rectal administration, with blood and colon tissues collected for the measurement of colitis related parameters. The results show that treatment with IMP significantly increased NF-κB, iNOS, and IL-6, decreased number of goblet cell, and inhibited expressions of miR-146b. However, overexpression of miR-146b in mice rescues the decline of the physical condition. Additionally, Notch receptor 1 (Notch1) is identified as a target gene of miR-146b. Further analysis shows that miR-146b restored the abundance of goblet cells by regulating Notch1 signaling pathway. CONCLUSION IMP is able to induce intestinal inflammation, impairs the intestinal barrier, and affects the proliferation of goblet cells. The underlined mechanism may partially contribute to the dysregulation of miR-146b/Notch1 axis.
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Affiliation(s)
- Jiaqi Wu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Tianjin University of Traditional Chinese Medicine), Ministry of Education, 312 Anshanxi Road, Nankai District, Tianjin, 300193, China
| | - Yuzheng Wu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Tianjin University of Traditional Chinese Medicine), Ministry of Education, 312 Anshanxi Road, Nankai District, Tianjin, 300193, China.,Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China
| | - Wen Feng
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Tianjin University of Traditional Chinese Medicine), Ministry of Education, 312 Anshanxi Road, Nankai District, Tianjin, 300193, China
| | - Qian Chen
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Tianjin University of Traditional Chinese Medicine), Ministry of Education, 312 Anshanxi Road, Nankai District, Tianjin, 300193, China.,Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China
| | - Dan Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Tianjin University of Traditional Chinese Medicine), Ministry of Education, 312 Anshanxi Road, Nankai District, Tianjin, 300193, China.,Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China
| | - Mengyang Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Tianjin University of Traditional Chinese Medicine), Ministry of Education, 312 Anshanxi Road, Nankai District, Tianjin, 300193, China.,Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China
| | - Haiyang Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Tianjin University of Traditional Chinese Medicine), Ministry of Education, 312 Anshanxi Road, Nankai District, Tianjin, 300193, China
| | - Yi Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.,Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China
| | - Tao Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine. 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Tianjin University of Traditional Chinese Medicine), Ministry of Education, 312 Anshanxi Road, Nankai District, Tianjin, 300193, China
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Meng W, Li Z, Zhang Y, Yang A, Wang Y, Zhou Y, Wu W, Qiu Y, Li L. ZhenQi FuZheng formula inhibits the growth of colorectal tumors by modulating intestinal microflora-mediated immune function. Aging (Albany NY) 2022; 14:4769-4785. [PMID: 35680568 PMCID: PMC9217701 DOI: 10.18632/aging.204111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/13/2022] [Indexed: 12/24/2022]
Abstract
Zhenqi Fuzheng formula (ZQFZ), of which the main ingredients are Astragalus membranaceus and Ligustrum lucidum, has immune system regulatory functions and potential anti-tumor bioactivity. The inhibition of colorectal tumor growth by ZQFZ was analyzed in inflammatory cells and B6/JGpt-Apcem1Cin(MinC)/Gpt (ApcMin/+) mice. ZQFZ exhibited anti-inflammatory activity by decreasing the phosphorylation of nuclear factor-kappa B (NF-κB) pathway-related proteins in lipopolysaccharide-induced RAW264.7 cells. After 56 days of treatment, ZQFZ alleviated the progression of colorectal cancer (CRC) and increased the body weight and thymic index values of the ApcMin/+ mice. An analysis of the intestinal microflora showed that ZQFZ affected the abundance of certain immune-related bacteria, which may explain its immunomodulatory effects. Moreover, the percentages of T cells and NK cells in peripheral blood were significantly increased and 15 immune-related cytokines were regulated in serum or the colon or both. ZQFZ upregulated the levels of CD4 and CD8 in the spleen and colorectal tumors and decreased the expression levels of cytotoxic T-lymphocyte-associated protein 4 and programmed death-ligand 1 in colorectal tumors. ZQFZ promoted an anti-tumor immune response and inhibited the occurrence and development of CRC by regulating the immune system. This study provides the experimental basis for the application of ZQFZ as a therapeutic agent for CRC.
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Affiliation(s)
- Weiqi Meng
- School of Life Sciences, Jilin University, Changchun, Jilin, P.R. China
| | - Zhiping Li
- Department of Clinical Pharmacy, The First Hospital of Jilin University, Jilin University, Changchun, Jilin, P.R. China.,School of Life Sciences, Jilin University, Changchun, Jilin, P.R. China
| | - Yiting Zhang
- School of Life Sciences, Jilin University, Changchun, Jilin, P.R. China
| | - Anhui Yang
- School of Life Sciences, Jilin University, Changchun, Jilin, P.R. China
| | - Yanzhen Wang
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai, P.R. China
| | - Yulin Zhou
- School of Life Sciences, Jilin University, Changchun, Jilin, P.R. China
| | - Wanyue Wu
- School of Life Sciences, Jilin University, Changchun, Jilin, P.R. China
| | - Ye Qiu
- Department of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, P.R. China
| | - Lanzhou Li
- School of Life Sciences, Jilin University, Changchun, Jilin, P.R. China.,Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, P.R. China
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Abaach M, Morilla I. Learning models for colorectal cancer signature reconstruction and classification in patients with chronic inflammatory bowel disease. Artif Intell Cancer 2022; 3:27-41. [DOI: 10.35713/aic.v3.i2.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/16/2022] [Accepted: 04/28/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In their everyday life, clinicians face an overabundance of biological indicators potentially helpful during a disease therapy. In this context, to be able to reliably identify a reduced number of those markers showing the ability of optimising the classification of treatment outcomes becomes a factor of vital importance to medical prognosis. In this work, we focus our interest in inflammatory bowel disease (IBD), a long-life threaten with a continuous increasing prevalence worldwide. In particular, IBD can be described as a set of autoimmune conditions affecting the gastrointestinal tract whose two main types are Crohn’s disease and ulcerative colitis.
AIM To identify the minimal signature of microRNA (miRNA) associated with colorectal cancer (CRC) in patients with one chronic IBD.
METHODS We provide a framework of well-established statistical and computational learning methods wisely adapted to reconstructing a CRC network leveraged to stratify these patients.
RESULTS Our strategy resulted in an adjusted signature of 5 miRNAs out of approximately 2600 in Crohn’s Disease (resp. 8 in Ulcerative Colitis) with a percentage of success in patient classification of 82% (resp. 81%).
CONCLUSION Importantly, these two signatures optimally balance the proportion between the number of significant miRNAs and their percentage of success in patients’ stratification.
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Affiliation(s)
- Mariem Abaach
- Mathématiques Appliquées à Paris 5, Unité mixte de Recherche, Centre National de la Recherche Scientifique, Université de Paris, Paris 75006, France
| | - Ian Morilla
- Laboratoire Analyse, Géométrie et Applications, Centre National de la Recherche Scientifique (Unité mixte de Recherche), Université Sorbonne Paris Nord, Villetaneuse, Paris 93430, France
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Li H, Huang B. <em>miR-19a</em> targeting <em>CLCA4</em> to regulate the proliferation, migration, and invasion of colorectal cancer cells. Eur J Histochem 2022; 66. [PMID: 35266369 PMCID: PMC8958453 DOI: 10.4081/ejh.2022.3381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/19/2022] [Indexed: 12/24/2022] Open
Abstract
The role of miR-19a in colorectal cancer (CRC), a devastating disease with high mortality and morbidity, remains controversial. In the present study, we show that the level of miR-19a is significantly higher in clinical CRC tissue samples than in paracancerous tissue samples, and significantly higher in CRC cells lines HT29, SW480, and CaCO2 than in the normal human colon mucosal epithelial cell line NCM460. miR-19a mimics and inhibitors were synthesized and validated. Overexpression of miR-19a mimics significantly promoted, while miR-19a inhibitors inhibited, the proliferation, survival, migration, and invasion of SW480 and CaCO2 CRC cells. Furthermore, mRNA and protein levels of chloride channel accessory 4 (CLCA4) were lower in CRC cells and tissues. Bioinformatics and a luciferase reporter assay confirmed that CLCA4 was a miR-19a target. Further, miR-19a inhibition increased CLCA4 expression. The inhibitory effect of miR-19a on cell growth, survival, migration, and invasion was reversed by knockdown of CLCA4 expression. The data demonstrated that the miR-19a/CLCA4 axis modulates phospho-activation of the PI3K/AKT pathway in CRC cells. In conclusion, our results revealed that miR-19a overexpression decreases CLCA4 levels to promote CRC oncogenesis, suggesting that miR-19a inhibitors have potential applications for future therapeutic of CRC.
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Affiliation(s)
- Huiwen Li
- Department of Pediatrics, the First Affiliated Hospital of Jinan University, Guangzhou; Department of Gastroenterology, Guangzhou Women and Children's Medical Center, Guangzhou.
| | - Bo Huang
- Department of Gastrointestinal Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou.
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