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Al-Rawaf HA, Gabr SA, Iqbal A, Alghadir AH. Circulating microRNAs as potential biomarkers of physical activity in geriatric patients with HCV. BMC Mol Cell Biol 2024; 25:18. [PMID: 39030480 PMCID: PMC11264506 DOI: 10.1186/s12860-024-00514-8] [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: 01/22/2024] [Accepted: 07/09/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Circulating microRNAs have been implicated in a diverse array of biological and pathological phenomena. Their potential utility as noninvasive biomarkers for screening and diagnosing various diseases has been proposed. OBJECTIVE This study aimed to explore the potential role of the miRNAs miR-122 and miR-486 as molecular biomarkers in the pathogenesis of hepatitis C virus (HCV) infection. Thus, miR-122 and miR-486 were detected in the serum of HCV patients and healthy controls. Moreover, the potential correlations of miR-122 and miR-486 with viral complications, such as physical activity, pain, muscle fatigue, and HCV infection, were identified. METHODS A total of 150 subjects aged 30 to 66 years were included in this study. The patients were classified as patients with chronic hepatitis C virus (CHC) (n = 110) or healthy controls (n = 40). Real-time polymerase chain reaction (PCR) analyses were performed to determine miR-122 and miR-486 expression. Physical activity (PA), pain score, HCV genotyping, viral overload, aspartate transaminase (AST), alanine transaminase (ALT), lactic acid dehydrogenase (LDH), creatine kinase (CK), and antioxidant status were also estimated by using prevalidated questionnaires, PCR, and spectrophotometric analyses. RESULTS Compared with those in normal controls, significant increases in the serum levels of miR-122 and miR-486 were reported in patients with CHC. In physically active CHC patients, there was a significant correlation between the expression of miRNAs and increased alanine transaminase (ALT), aspartate transaminase (AST), fibrosis scores, and inflammation activity, but no association was reported for hepatitis C virus (HCV) RNA or viral load. Additionally, significant decreases in LDH, CK, GSSG, and pain scores and increases in TAC, GSH, and the GSH/GSSG ratio were reported. Moreover, the expression of miR-122 and miR-486 was positively correlated with changes in body mass index (BMI) and liver fibrosis stage, as well as negatively correlated with sex, PA, TAC, GSH, GSSG, and the GSH/GSSG ratio. CONCLUSION MiR-122 and miR-486 expression levels were strongly correlated with physical activity, pain perception, and muscle fatigue biomarkers in HCV-infected patients. These miRNA levels were associated with elevated AST, ALT, fibrosis scores, LDH, CK, and antioxidant status, thus suggesting their potential as biomarkers for disease severity and oxidative stress. However, no correlation was observed with viral load or HCV-RNA expression, thus implying that these miRNAs may impact disease progression and symptoms through host factors, rather than directly affecting viral replication. In summary, the results demonstrated that molecular studies of miR-22 and miR-468 and their associations with PA, pain, adiposity, sex differences, and muscle fatigue, as well as routine biomarkers, could be useful as prognostic nanoninvasive biomarkers, thus providing novel therapeutic targets for CHC infection.
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Affiliation(s)
- Hadeel A Al-Rawaf
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, 11433, Saudi Arabia
| | - Sami A Gabr
- Department of Rehabilitation Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh, 11433, Saudi Arabia
| | - Amir Iqbal
- Department of Rehabilitation Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh, 11433, Saudi Arabia.
| | - Ahmad H Alghadir
- Department of Rehabilitation Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh, 11433, Saudi Arabia
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Caserta S, Gangemi S, Murdaca G, Allegra A. Gender Differences and miRNAs Expression in Cancer: Implications on Prognosis and Susceptibility. Int J Mol Sci 2023; 24:11544. [PMID: 37511303 PMCID: PMC10380791 DOI: 10.3390/ijms241411544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
MicroRNAs are small, noncoding molecules of about twenty-two nucleotides with crucial roles in both healthy and pathological cells. Their expression depends not only on genetic factors, but also on epigenetic mechanisms like genomic imprinting and inactivation of X chromosome in females that influence in a sex-dependent manner onset, progression, and response to therapy of different diseases like cancer. There is evidence of a correlation between miRNAs, sex, and cancer both in solid tumors and in hematological malignancies; as an example, in lymphomas, with a prevalence rate higher in men than women, miR-142 is "silenced" because of its hypermethylation by DNA methyltransferase-1 and it is blocked in its normal activity of regulating the migration of the cell. This condition corresponds in clinical practice with a more aggressive tumor. In addition, cancer treatment can have advantages from the evaluation of miRNAs expression; in fact, therapy with estrogens in hepatocellular carcinoma determines an upregulation of the oncosuppressors miR-26a, miR-92, and miR-122 and, consequently, apoptosis. The aim of this review is to present an exhaustive collection of scientific data about the possible role of sex differences on the expression of miRNAs and the mechanisms through which miRNAs influence cancerogenesis, autophagy, and apoptosis of cells from diverse types of tumors.
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Affiliation(s)
- Santino Caserta
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | - Giuseppe Murdaca
- Department of Internal Medicine, University of Genova, Viale Benedetto XV, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, Via Consolare Valeria, 98125 Messina, Italy
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Baraibar I, Ros J, Saoudi N, Salvà F, García A, Castells M, Tabernero J, Élez E. Sex and gender perspectives in colorectal cancer. ESMO Open 2023; 8:101204. [PMID: 37018873 PMCID: PMC10163160 DOI: 10.1016/j.esmoop.2023.101204] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 04/05/2023] Open
Abstract
Historically women were frequently excluded from clinical trials and drug usage to protect unborn babies from potential harm. As a consequence, the impact of sex and gender on both tumour biology and clinical outcomes has been largely underestimated. Although interrelated and often used interchangeably, sex and gender are not equivalent concepts. Sex is a biological attribute that defines species according to their chromosomal makeup and reproductive organ, while gender refers to a chosen sexual identity. Sex dimorphisms are rarely taken into account, in either preclinical or clinical research, with inadequate analysis of differences in outcomes according to sex or gender still widespread, reflecting a gap in our knowledge for a large proportion of the target population. Underestimation of sex-based differences in study design and analyses has invariably led to 'one-drug' treatment regimens for both males and females. For patients with colorectal cancer (CRC), sex also has an impact on the disease incidence, clinicopathological features, therapeutic outcomes, and tolerability to anticancer treatments. Although the global incidence of CRC is higher in male subjects, the proportion of patients presenting right-sided tumours and BRAF mutations is higher among females. Concerning sex-related differences in treatment efficacy and toxicity, drug dosage does not take into account sex-specific differences in pharmacokinetics. Toxicity associated with fluoropyrimidines, targeted therapies, and immunotherapies has been reported to be more extensive for females with CRC than for males, although evidence about differences in efficacy is more controversial. This article aims to provide an overview of the research achieved so far into sex and gender differences in cancer and summarize the growing body of literature illustrating the sex and gender perspective in CRC and their impact in relation to tumour biology and treatment efficacy and toxicity. We propose endorsing research on how biological sex and gender influence CRC as an added value for precision oncology.
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Cheong JK, Rajgor D, Lv Y, Chung KY, Tang YC, Cheng H. Noncoding RNome as Enabling Biomarkers for Precision Health. Int J Mol Sci 2022; 23:10390. [PMID: 36142304 PMCID: PMC9499633 DOI: 10.3390/ijms231810390] [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: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/06/2022] Open
Abstract
Noncoding RNAs (ncRNAs), in the form of structural, catalytic or regulatory RNAs, have emerged to be critical effectors of many biological processes. With the advent of new technologies, we have begun to appreciate how intracellular and circulatory ncRNAs elegantly choreograph the regulation of gene expression and protein function(s) in the cell. Armed with this knowledge, the clinical utility of ncRNAs as biomarkers has been recently tested in a wide range of human diseases. In this review, we examine how critical factors govern the success of interrogating ncRNA biomarker expression in liquid biopsies and tissues to enhance our current clinical management of human diseases, particularly in the context of cancer. We also discuss strategies to overcome key challenges that preclude ncRNAs from becoming standard-of-care clinical biomarkers, including sample pre-analytics standardization, data cross-validation with closer attention to discordant findings, as well as correlation with clinical outcomes. Although harnessing multi-modal information from disease-associated noncoding RNome (ncRNome) in biofluids or in tissues using artificial intelligence or machine learning is at the nascent stage, it will undoubtedly fuel the community adoption of precision population health.
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Affiliation(s)
- Jit Kong Cheong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
- NUS Centre for Cancer Research, Singapore 117599, Singapore
| | | | - Yang Lv
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
| | | | | | - He Cheng
- MiRXES Lab, Singapore 138667, Singapore
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Yang L, Yang S, Ren C, Liu S, Zhang X, Sui A. Deciphering the roles of miR-16-5p in Malignant Solid Tumorsmalignant solid tumors. Pharmacotherapy 2022; 148:112703. [PMID: 35149384 DOI: 10.1016/j.biopha.2022.112703] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 11/02/2022]
Abstract
MiR-16-5p, a member of the miR-16 family, has been reported to be abnormal expression in tumor tissues and blood of tumor patients, and also downregulated in most cancer cell lines. Aberrant expression of miR-16-5p promotes tumor cell proliferation, invasion, metastasis, angiogenesis, and can also affect the treatment sensitivity, such as radiotherapy and chemotherapy. Generally, miR-16-5p plays an anti-tumor role and these diverse functions of miR-16-5p in tumors collectively indicate that miR-16-5p may become an attractive target for novel anticancer therapies and a powerful diagnostic and prognostic biomarker for early tumor detection and population risk screening. Herein we review the role and utilization of miR-16-5p in malignant tumor in detail.
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Affiliation(s)
- Liuyi Yang
- Department of Oncology, Hebei General Hospital, Shijiazhuang, Hebei, China; Graduate School of North China University of Science and Technology, Tangshan, Hebei, China
| | - Sen Yang
- Department of Oncology, Hebei General Hospital, Shijiazhuang, Hebei, China; Graduate School of North China University of Science and Technology, Tangshan, Hebei, China
| | - Congcong Ren
- Department of Oncology, Hebei General Hospital, Shijiazhuang, Hebei, China; Graduate School of Hebei North University, Zhangjiakou, Hebei, China
| | - Shihua Liu
- Department of Oncology, Hebei General Hospital, Shijiazhuang, Hebei, China; Graduate School of Hebei North University, Zhangjiakou, Hebei, China
| | - Xiaopei Zhang
- Department of Oncology, Hebei General Hospital, Shijiazhuang, Hebei, China; Graduate School of Hebei North University, Zhangjiakou, Hebei, China
| | - Aixia Sui
- Department of Oncology, Hebei General Hospital, Shijiazhuang, Hebei, China.
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Chen CC, Chang PY, Chang YS, You JF, Chan EC, Chen JS, Tsai WS, Huang YL, Fan CW, Hsu HC, Chiang JM. MicroRNA-based signature for diagnosis and prognosis of colorectal cancer using residuum of fecal immunochemical test. Biomed J 2022; 46:144-153. [PMID: 35074584 PMCID: PMC10104956 DOI: 10.1016/j.bj.2022.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/28/2021] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is still among the most lethal and prevalent malignancies in the world. Despite continuous efforts, the diagnosis and prognosis of CRC have never been satisfying, especially the non-invasive assays. METHODS Our study comprised three independent cohorts of 835 qualified stool samples. From 46 literature-identified miRNA candidates, four miRNA ratios were selected and developed into a miRNA-based signature after applied to the training and test sets. The clinical performances of this signature were further evaluated in the prospective cohorts. RESULTS Four miRNA ratios with significant alterations and the highest discriminating power between the CRC and control groups in the training set were successfully validated in the test set. In the training dataset, combining these four miRNA ratios using a logistic regression model improved the area under the curve value to 0.821 and obtained a sensitivity of 73.6% and specificity of 78.9%. This miRNA signature showed consistent performances in the other two sample cohorts, with the highest sensitivity of 85.7% in the prospective cohort. Additionally, the higher miRNA signature was associated with worse disease-free survival (hazard ratio = 2.27) and overall survival (hazard ratio = 1.83) of CRC patients. For fecal immunochemical test (FIT)-positive populations, the positive predictive value for CRC detection in miRNA-positive subjects was 3.43-fold higher in the prospective cohort, compared to FIT alone. CONCLUSION This stool miRNA signature is highly associated with poor outcome of CRC and can be added to FIT tests to help identify the most at-risk group to receive prompt colonoscopy examination.
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Lei J, Wang Q, Li G, Li Y, Zhang P, Xu G. β-Caryophyllene from Chilli Pepper Inhibits the Proliferation of Non-Small Cell Lung Cancer Cells by Affecting miR-659-3p-Targeted Sphingosine Kinase 1 (SphK1). Int J Gen Med 2021; 14:9599-9613. [PMID: 34916840 PMCID: PMC8670862 DOI: 10.2147/ijgm.s338513] [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: 09/09/2021] [Accepted: 11/09/2021] [Indexed: 11/25/2022] Open
Abstract
Background β-Caryophyllene is the main ingredient of chilli pepper and used for the prevention of various cancers, while the molecular mechanism for its effects on non-small cell lung cancer (NSCLC) remains unclear. Methods NSCLC cell lines A549 and NCI-H1299 were treated with β-Caryophyllene and miR-659-3p (a potential tumor suppressor) mimic or siRNA. The levels of miR-659-3p, sphingosine kinase 1 (SphK1), apoptotic factors and oxidative stress factors were investigated. Results β-Caryophyllene inhibited NSCLC growth, promoted their apoptotic rate, increased the level of miR-659-3p, apoptotic factors (cleaved caspase-3 and BAX), antioxidant factors (SOD, CAT and GPx) and reduced the level of oxidative stress (ROS and NO) and SphK1. miR-659-3p mimic and siRNA affected NSCLC growth, their apoptosis, and biochemical indices. Conclusion β-Caryophyllene of chilli pepper exerts inhibitory activity in NSCLC cells possibly by affecting miR-659-3p-targeted SphK1.
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Affiliation(s)
- Jiaji Lei
- Department of Second Ward of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 157011, People's Republic of China
| | - Qiushi Wang
- Department of Second Ward of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 157011, People's Republic of China
| | - Guanghua Li
- Department of Second Ward of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 157011, People's Republic of China
| | - Yongchao Li
- Department of Second Ward of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 157011, People's Republic of China
| | - Pengfei Zhang
- Department of Second Ward of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 157011, People's Republic of China
| | - Guangquan Xu
- Department of Second Ward of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 157011, People's Republic of China
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Bizzarri AR, Cannistraro S. Direct Interaction of miRNA and circRNA with the Oncosuppressor p53: An Intriguing Perspective in Cancer Research. Cancers (Basel) 2021; 13:6108. [PMID: 34885216 PMCID: PMC8657023 DOI: 10.3390/cancers13236108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 01/10/2023] Open
Abstract
MicroRNAs (miRNAs) are linear single-stranded non-coding RNAs oligonucleotides, widely distributed in cells, playing a key role as regulators of gene expression at post-transcriptional level. Circular RNAs (circRNAs) are single-stranded RNA oligonucleotides forming a covalently closed continuous loop, which confers them a high structural stability and which may code for proteins or act as gene regulators. Abnormal levels or dysregulation of miRNA or circRNA are linked to several cancerous pathologies, so that they are receiving a large attention as diagnostic and prognostic tools. Some miRNAs and circRNAs are strongly involved in the regulatory networks of the transcription factor p53, which plays a pivotal role as tumor suppressor. Overexpression of miRNAs and/or circRNAs, as registered in a number of cancers, is associated to a concomitant inhibition of the p53 onco-suppressive function. Among other mechanisms, it was recently suggested that a functional inhibition of p53 could arise from a direct interaction between p53 and oncogenic miRNAs or circRNAs; a mechanism that might be reminiscent of the p53 inhibition by some E3 ubiquitin ligase such as MDM2 and COP1. Such evidence might deserve important implications for restoring the p53 anticancer functionality, and pave the way to intriguing perspectives for novel therapeutic strategies. In the present paper, the experimental evidence of the interaction between p53 and miRNAs and/or circRNAs is reviewed and discussed in connection with the development of new anticancer approaches.
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Huang Y, Zou Y, Xiong Q, Zhang C, Sayagués JM, Shelat VG, Wang X. Development of a novel necroptosis-associated miRNA risk signature to evaluate the prognosis of colon cancer patients. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1800. [PMID: 35071494 PMCID: PMC8756225 DOI: 10.21037/atm-21-6576] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/17/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND Necroptosis is a recently discovered caspase-independent form of cell death which plays an important role in the occurrence and development of cancer. As an important regulatory factor in necroptosis, microRNAs (miRNAs) are important for the development of colon cancer. This study established a novel necroptosis-related miRNA risk signature to evaluate the prognosis of patients with colon adenocarcinoma (COAD). METHODS The necroptosis-related miRNAs were selected by assessing the differential expression of miRNAs in 459 COAD patient samples and 8 control samples from The Cancer Genome Atlas (TCGA). Selection operator Cox analyses and survival analyses were used to establish the risk signature of 7 miRNAs related to necroptosis. Functional enrichment analysis and nomograms were used to explore the potential effects of necroptosis-related miRNAs on prognosis and metastasis. The target genes of the necroptosis-related miRNAs were predicted using online databases and the genes related to overall survival (OS) were screened. RESULTS The risk signature was based on 7 necroptosis-related miRNAs. Nomograms showed that the risk signature was effective at predicting the prognosis and TNM stage of COAD patients. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses demonstrated that these miRNAs play an important role in cancer development, metastasis, and prognosis. A total of 38 target genes for these miRNAs were found to be associated with the OS in COAD patients. CONCLUSIONS This study provided novel evidence that necroptosis-related miRNAs are associated with the prognosis of COAD patients. A risk signature established based on these miRNAs could effectively predict the prognosis and metastasis of COAD in patients.
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Affiliation(s)
- Yang Huang
- General Surgery Department, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanyuan Zou
- General Surgery Department, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiru Xiong
- General Surgery Department, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chao Zhang
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - José María Sayagués
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Salamanca e Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Vishal G. Shelat
- Department of General Surgery, Tan Tock Seng Hospital, Singapore, Singapore
| | - Xingyu Wang
- Emergency Surgery Department, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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Fehlmann T, Kern F, Laham O, Backes C, Solomon J, Hirsch P, Volz C, Müller R, Keller A. miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale. Nucleic Acids Res 2021; 49:W397-W408. [PMID: 33872372 PMCID: PMC8262700 DOI: 10.1093/nar/gkab268] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/21/2021] [Accepted: 04/15/2021] [Indexed: 01/19/2023] Open
Abstract
Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Omar Laham
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jeffrey Solomon
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Carsten Volz
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
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Herichova I, Reis R, Hasakova K, Vician M. Downregulation of miR-30c-5p expression in colorectal cancer tissue is sex-dependent. Physiol Res 2020; 69:S479-S487. [PMID: 33476170 DOI: 10.33549/physiolres.934598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We report that decreased expression of miR-30c in tumor compared to adjacent tissue is sex-dependent in colorectal cancer (CRC) patients. High expression of miR-30c was associated with better survival in the whole cohort. When the cohort was split into male and female subcohorts, decreased miR-30c expression in tumor compared to adjacent tissue was observed only in males. Expression of miR-30c was decreased in CRC tumor tissue in male patients with nodes involvement compared to those without metastases in nodes and this difference was not observe in females. Next dependency of miR-30c expression on oestrogen receptor beta (ERbeta) mRNA levels in tumor was tested. In males with low expression of ERbeta, we observed a significant decrease in miR-30c levels in patients with nodes involvement compared to those without nodes involvement. This difference was not observed in males with high ERbeta mRNA levels and in females. Accordingly, males with low expression of ERbeta and high expression of miR-30c showed a better survival that those with low expression ERbeta and low expression of miR-30c. It is possible to conclude that whole cohort survival dependence on miR-30c is mostly generated by a subcohort of males with low expression of ERbeta mRNA in tumor tissue.
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Affiliation(s)
- I Herichova
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University Bratislava, Bratislava, Slovak Republic.
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Abancens M, Bustos V, Harvey H, McBryan J, Harvey BJ. Sexual Dimorphism in Colon Cancer. Front Oncol 2020; 10:607909. [PMID: 33363037 PMCID: PMC7759153 DOI: 10.3389/fonc.2020.607909] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
A higher incidence of colorectal cancer (CRC) is found in males compared to females. Young women (18-44 years) with CRC have a better survival outcome compared to men of the same age or compared to older women (over 50 years), indicating a global incidence of sexual dimorphism in CRC rates and survival. This suggests a protective role for the sex steroid hormone estrogen in CRC development. Key proliferative pathways in CRC tumorigenesis exhibit sexual dimorphism, which confer better survival in females through estrogen regulated genes and cell signaling. Estrogen regulates the activity of a class of Kv channels (KCNQ1:KCNE3), which control fundamental ion transport functions of the colon and epithelial mesenchymal transition through bi-directional interactions with the Wnt/β-catenin signalling pathway. Estrogen also modulates CRC proliferative responses in hypoxia via the novel membrane estrogen receptor GPER and HIF1A and VEGF signaling. Here we critically review recent clinical and molecular insights into sexual dimorphism of CRC biology modulated by the tumor microenvironment, estrogen, Wnt/β-catenin signalling, ion channels, and X-linked genes.
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Affiliation(s)
- Maria Abancens
- Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Beaumont Hospital, Dublin, Ireland
- Department of Surgery, RCSI University of Medicine and Health Sciences, Beaumont Hospital, Dublin, Ireland
| | - Viviana Bustos
- Departamento de Acuicultura y Recursos Agroalimentarios, Programa Fitogen, Universidad de Los Lagos, Osorno, Chile
| | - Harry Harvey
- Department of Medical Oncology, Cork University Hospital, Cork, Ireland
| | - Jean McBryan
- Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Beaumont Hospital, Dublin, Ireland
- Department of Surgery, RCSI University of Medicine and Health Sciences, Beaumont Hospital, Dublin, Ireland
| | - Brian J. Harvey
- Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Beaumont Hospital, Dublin, Ireland
- Centro de Estudios Cientificos CECs, Valdivia, Chile
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Marques D, Ferreira-Costa LR, Ferreira-Costa LL, Bezerra-Oliveira AB, Correa RDS, Ramos CCDO, Vinasco-Sandoval T, Lopes KDP, Vialle RA, Vidal AF, Silbiger VN, Ribeiro-dos-Santos Â. Role of miRNAs in Sigmoid Colon Cancer: A Search for Potential Biomarkers. Cancers (Basel) 2020; 12:cancers12113311. [PMID: 33182525 PMCID: PMC7697997 DOI: 10.3390/cancers12113311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/12/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The aberrant expression of microRNAs in known to play a crucial role in carcinogenesis. Here, we evaluated the miRNA expression profile of sigmoid colon cancer (SCC) compared to adjacent-to-tumor (ADJ) and sigmoid colon healthy (SCH) tissues obtained from colon biopsy extracted from Brazilian patients. Comparisons were performed between each group separately, considering as significant p-values < 0.05 and |Log2(Fold-Change)| > 2. We found 20 differentially expressed miRNAs (DEmiRNAs) in all comparisons, two of which were shared between SCC vs. ADJ and SCC vs. SCH. We used miRTarBase, and miRTargetLink to identify target-genes of the differentially expressed miRNAs, and DAVID and REACTOME databases for gene enrichment analysis. We also used TCGA and GTEx databases to build miRNA-gene regulatory networks and check for the reproducibility in our results. As findings, in addition to previously known miRNAs associated with colorectal cancer, we identified three potential novel biomarkers. We showed that the three types of colon tissue could be clearly distinguished using a panel composed by the 20 DEmiRNAs. Additionally, we found enriched pathways related to the carcinogenic process in which miRNA could be involved, indicating that adjacent-to-tumor tissues may be already altered and cannot be considered as healthy tissues. Overall, we expect that these findings may help in the search for biomarkers to prevent cancer progression or, at least, allow its early detection, however, more studies are needed to confirm our results.
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Affiliation(s)
- Diego Marques
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Av. Augusto Corrêa, 01, Guamá, Belém 66.075-110, Brazil; (D.M.); (T.V.-S.); (K.d.P.L.); (R.A.V.); (A.F.V.)
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Av. Nilo Peçanha, 620, Petrópolis, Natal 59012-300, Brazil; (L.R.F.-C.); (L.L.F.-C.); (A.B.B.-O.)
| | - Layse Raynara Ferreira-Costa
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Av. Nilo Peçanha, 620, Petrópolis, Natal 59012-300, Brazil; (L.R.F.-C.); (L.L.F.-C.); (A.B.B.-O.)
| | - Lorenna Larissa Ferreira-Costa
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Av. Nilo Peçanha, 620, Petrópolis, Natal 59012-300, Brazil; (L.R.F.-C.); (L.L.F.-C.); (A.B.B.-O.)
| | - Ana Beatriz Bezerra-Oliveira
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Av. Nilo Peçanha, 620, Petrópolis, Natal 59012-300, Brazil; (L.R.F.-C.); (L.L.F.-C.); (A.B.B.-O.)
| | - Romualdo da Silva Correa
- Departamento de Cirurgia Oncológica, Liga Norte Riograndense Contra o Câncer, R. Mário Negócio, 2267, Quintas, Natal 59040-000, Brazil;
| | - Carlos Cesar de Oliveira Ramos
- Laboratório de Patologia e Citopatologia, Liga Norte Riograndense Contra o Câncer, R. Mário Negócio, 2267, Quintas, Natal 59040-000, Brazil;
| | - Tatiana Vinasco-Sandoval
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Av. Augusto Corrêa, 01, Guamá, Belém 66.075-110, Brazil; (D.M.); (T.V.-S.); (K.d.P.L.); (R.A.V.); (A.F.V.)
| | - Katia de Paiva Lopes
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Av. Augusto Corrêa, 01, Guamá, Belém 66.075-110, Brazil; (D.M.); (T.V.-S.); (K.d.P.L.); (R.A.V.); (A.F.V.)
| | - Ricardo Assunção Vialle
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Av. Augusto Corrêa, 01, Guamá, Belém 66.075-110, Brazil; (D.M.); (T.V.-S.); (K.d.P.L.); (R.A.V.); (A.F.V.)
| | - Amanda Ferreira Vidal
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Av. Augusto Corrêa, 01, Guamá, Belém 66.075-110, Brazil; (D.M.); (T.V.-S.); (K.d.P.L.); (R.A.V.); (A.F.V.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Av. Augusto Corrêa, 01, Guamá, Belém 66.075-110, Brazil
| | - Vivian Nogueira Silbiger
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Av. Nilo Peçanha, 620, Petrópolis, Natal 59012-300, Brazil; (L.R.F.-C.); (L.L.F.-C.); (A.B.B.-O.)
- Correspondence: (V.N.S.); (Â.R.-d.-S.)
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Av. Augusto Corrêa, 01, Guamá, Belém 66.075-110, Brazil; (D.M.); (T.V.-S.); (K.d.P.L.); (R.A.V.); (A.F.V.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Av. Augusto Corrêa, 01, Guamá, Belém 66.075-110, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, R. dos Mundurucus, 4487, Guamá, Belém 66073-000, Brazil
- Correspondence: (V.N.S.); (Â.R.-d.-S.)
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14
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Wang Q, Sun Q, Wang J, Qiu X, Qi R, Huang J. Identification of differentially expressed miRNAs after Lactobacillus reuteri treatment in the ileum mucosa of piglets. Genes Genomics 2020; 42:1327-1338. [PMID: 32980994 DOI: 10.1007/s13258-020-00998-6] [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: 07/21/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Lactobacillus reuteri I5007 possesses many excellent probiotic characteristics in piglets. miRNA plays important role in host-microbiota interactions, but the mechanism by which L. reuteri I5007 regulates intestinal function through its influence on miRNA expression is unknown. OBJECTIVE This study analyzed the miRNA expression patterns in the ileum mucosa tissue of piglets by L. reuteri I5007 treatment, aim to clarify its molecular mechanism for regulating intestinal function through miRNA. METHODS Neonatal piglets were orally administered L. reuteri I5007 or a placebo daily starting on day 1, and differential expression of ileal miRNAs was analyzed at 10 and 20 days of age by small RNA sequencing. RESULTS 361 known porcine miRNAs were identified, and ten miRNAs were highly expressed in the ileum mucosa in both treatments. Nineteen differentially expressed (DE) miRNAs were identified in response to L. reuteri treatment, and four DE miRNAs (ssc-miR-196a, -196b-5p, -1285 and -10386) were differentially expressed at both time points. The KEGG pathway analyses showed the targets of 19 DE miRNAs were involved in 63 significantly enriched pathways, including the PI3K-Akt and MAPK pathways, which were confirmed to play important roles in probiotic-host communication. L. reuteri I5007 exerted anti-inflammatory effects by influencing the levels of inflammatory cytokines. Suppressor of cytokine signalling 4 gene was the target gene of ssc-miR-196a/-196b-5p, overexpression of ssc-miR-196a/-196b-5p downregulated the mRNA expression of IL-1β and TNFα in IPEC-J2 cells. CONCLUSION Our study provides new insight into the role of miRNAs in the intestinal function of piglets after L. reuteri I5007 treatment.
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Affiliation(s)
- Qi Wang
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing, 402460, China.,Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Rongchang, Chongqing, 402460, China.,Chongqing Key Laboratory of Pig Industry Sciences, Rongchang, Chongqing, 402460, China
| | - Qian Sun
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing, 402460, China
| | - Jing Wang
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing, 402460, China.,Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Rongchang, Chongqing, 402460, China.,Chongqing Key Laboratory of Pig Industry Sciences, Rongchang, Chongqing, 402460, China
| | - Xiaoyu Qiu
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing, 402460, China
| | - Renli Qi
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing, 402460, China.,Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Rongchang, Chongqing, 402460, China.,Chongqing Key Laboratory of Pig Industry Sciences, Rongchang, Chongqing, 402460, China
| | - Jinxiu Huang
- Chongqing Academy of Animal Sciences, Rongchang, Chongqing, 402460, China. .,Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Rongchang, Chongqing, 402460, China. .,Chongqing Key Laboratory of Pig Industry Sciences, Rongchang, Chongqing, 402460, China.
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15
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Pidíkova P, Reis R, Herichova I. miRNA Clusters with Down-Regulated Expression in Human Colorectal Cancer and Their Regulation. Int J Mol Sci 2020; 21:E4633. [PMID: 32610706 PMCID: PMC7369991 DOI: 10.3390/ijms21134633] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/24/2020] [Accepted: 06/27/2020] [Indexed: 02/07/2023] Open
Abstract
Regulation of microRNA (miRNA) expression has been extensively studied with respect to colorectal cancer (CRC), since CRC is one of the leading causes of cancer mortality worldwide. Transcriptional control of miRNAs creating clusters can be, to some extent, estimated from cluster position on a chromosome. Levels of miRNAs are also controlled by miRNAs "sponging" by long non-coding RNAs (ncRNAs). Both types of miRNA regulation strongly influence their function. We focused on clusters of miRNAs found to be down-regulated in CRC, containing miR-1, let-7, miR-15, miR-16, miR-99, miR-100, miR-125, miR-133, miR-143, miR-145, miR-192, miR-194, miR-195, miR-206, miR-215, miR-302, miR-367 and miR-497 and analysed their genome position, regulation and functions. Only evidence provided with the use of CRC in vivo and/or in vitro models was taken into consideration. Comprehensive research revealed that down-regulated miRNA clusters in CRC are mostly located in a gene intron and, in a majority of cases, miRNA clusters possess cluster-specific transcriptional regulation. For all selected clusters, regulation mediated by long ncRNA was experimentally demonstrated in CRC, at least in one cluster member. Oncostatic functions were predominantly linked with the reviewed miRNAs, and their high expression was usually associated with better survival. These findings implicate the potential of down-regulated clusters in CRC to become promising multi-targets for therapeutic manipulation.
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Affiliation(s)
- Paulína Pidíkova
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia;
| | - Richard Reis
- First Surgery Department, University Hospital, Comenius University in Bratislava, 811 07 Bratislava, Slovakia;
| | - Iveta Herichova
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia;
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16
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Farace C, Pisano A, Griñan-Lison C, Solinas G, Jiménez G, Serra M, Carrillo E, Scognamillo F, Attene F, Montella A, Marchal JA, Madeddu R. Deregulation of cancer-stem-cell-associated miRNAs in tissues and sera of colorectal cancer patients. Oncotarget 2020; 11:116-130. [PMID: 32010426 PMCID: PMC6968784 DOI: 10.18632/oncotarget.27411] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/16/2019] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) is a deadly tumour in Western countries characterized by high cellular/molecular heterogeneity. Cancer stem cells (CSC) act in cancer recurrence, drug-resistance and in metastatic epithelial-to-mesenchymal transition. microRNAs (miRNAs) contribute to cancer is increasing, and miRNA roles in CSC phenotype and fate and their utility as CRC biomarkers have also been reported. Here, we investigated miR-21, miR-221, miR-18a, miR-210, miR-31, miR-34a, miR-10b and miR-16 expression in experimental ALDH+ and CD44+/CD326+ colorectal CSCs obtained from the human CRC cell lines HCT-116, HT-29 and T-84. Then, we moved our analysis in cancer tissue (CT), healthy tissue (HT) and serum (S) of adult CRC patients (n=12), determining relationships with clinical parameters (age, sex, metastasis, biochemical serum markers). Specific miRNA patterns were evident in vitro (normal, monolayers and CSCs) and in patients’ samples stratified by TNM stage (LOW vs HIGH) or metastasis (Met vs no-Met). miR-21, miR-210, miR-34a upregulation ad miR-16 dowregulation associated with the CSCs phenotype. miR-31b robustly overexpressed in monolayers and CSCs, and in CT ad S of HIGH grade and Met patients, suggesting a role as marker of CRC progression and metastasis. miR-18a upregulated in all cancer models and associated to CSC phenotype, and to metastasis and age in patients. miR-10b downregulated in CT and S of LOW/HIGH grade and no-Met patients. Our results identify miRNAs useful as colorectal CSC biomarker and that miR-21, miR-210, miR-10b and miR-31b are promising markers of CRC. A specific role of miR-18a as metastatic CRC serum biomarker in adult patients was also highlighted.
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Affiliation(s)
- Cristiano Farace
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
| | - Andrea Pisano
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, Granada, Spain
| | - Carmen Griñan-Lison
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria (ibs.Granada), Granada, Spain
| | - Giuliana Solinas
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Gema Jiménez
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria (ibs.Granada), Granada, Spain.,Bio-Health Research Foundation of Eastern Andalusia - Alejandro Otero (FIBAO), Granada, Spain
| | - Marina Serra
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Esmeralda Carrillo
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria (ibs.Granada), Granada, Spain.,Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, Granada, Spain
| | | | - Federico Attene
- O.U. of Surgery I (Surgical Pathology), A.O.U. Sassari, Sassari, Italy
| | - Andrea Montella
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Juan Antonio Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria (ibs.Granada), Granada, Spain.,Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Roberto Madeddu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
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17
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Zhang X, Cheng Z, Wang L, Jiao B, Yang H, Wang X. MiR-21-3p Centric Regulatory Network in Dairy Cow Mammary Epithelial Cell Proliferation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11137-11147. [PMID: 31532202 DOI: 10.1021/acs.jafc.9b04059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
MicroRNA-mediated gene regulation is important for the development of the mammary gland and the lactating process. A previous study has shown that the expression of microRNA-21 (miR-21) is different in the dry and early lactation period of the dairy cow mammary gland, but the molecular mechanisms underlying the lactation cycle are not fully understood. Here, the function of miR-21-3p on bovine mammary gland epithelial cells (BMECs) was detected by MTT assay and flow cytometry analysis, which showed that miR-21-3p significantly promoted the cell viability and proliferation. Then, the regulating mechanism of miR-21-3p on cell viability and proliferation was elucidated. Dual luciferase assay, RT-qPCR, and Western blot results revealed that IGFBP5 was a target gene of miR-21-3p. It was known that lncRNA could act as a competing endogenous RNA to sequester miRNAs and reduce the regulatory effect of miRNA-targeted genes. Based on our previous lncRNA-seq data and bioinformatics analysis, lncRNA NONBTAT017009.2 was potentially associated with miR-21-3p, and its expression was specifically inhibited with the transfection of miR-21-3p mimic into BMECs. Inversely, the overexpression of NONBTAT017009.2 significantly decreased the expression level of miR-21-3p in BMECs, while the expression of IGFBP5, the target gene of miR-21-3p, was significantly upregulated. In addition, the promoter region of miR-21 contained two STAT3 binding sites, and the dual luciferase reporter assays revealed that the overexpression of STAT3 significantly reduced the promoter activity of miR-21, implying that the transcription factor STAT3 may act as an upstream regulator affecting the regulation process of miR-21-3p. The overexpression of STAT3 significantly inhibited the expression of miR-21-3p, while the mRNA expression of IGFBP5 was significantly increased compared with the control group. Besides, there are no STAT3 binding sites in the promoter region of IGFBP5 as we predicted by gene-regulation and JASPAR software. Therefore, it could infer that STAT3 might regulate the expression of IGFBP5 by miR-21-3p. Taken together, these results established a regulatory network of miR-21-3p to illustrate the regulating mechanism on promoting cow mammary epithelial cell proliferation.
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Affiliation(s)
- Xiaolan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Zixi Cheng
- The Middle School Attached to Northwestern Polytechnical University , Xi'an , Shaanxi 710072 , China
| | - Lixian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Beilei Jiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Hua Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Xin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
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18
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Pardini B, Sabo AA, Birolo G, Calin GA. Noncoding RNAs in Extracellular Fluids as Cancer Biomarkers: The New Frontier of Liquid Biopsies. Cancers (Basel) 2019; 11:E1170. [PMID: 31416190 PMCID: PMC6721601 DOI: 10.3390/cancers11081170] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/04/2019] [Accepted: 08/10/2019] [Indexed: 02/06/2023] Open
Abstract
The last two decades of cancer research have been devoted in two directions: (1) understanding the mechanism of carcinogenesis for an effective treatment, and (2) improving cancer prevention and screening for early detection of the disease. This last aspect has been developed, especially for certain types of cancers, thanks also to the introduction of new concepts such as liquid biopsies and precision medicine. In this context, there is a growing interest in the application of alternative and noninvasive methodologies to search for cancer biomarkers. The new frontiers of the research lead to a search for RNA molecules circulating in body fluids. Searching for biomarkers in extracellular body fluids represents a better option for patients because they are easier to access, less painful, and potentially more economical. Moreover, the possibility for these types of samples to be taken repeatedly, allows a better monitoring of the disease progression or treatment efficacy for a better intervention and dynamic treatment of the patient, which is the fundamental basis of personalized medicine. RNA molecules, freely circulating in body fluids or packed in microvesicles, have all the characteristics of the ideal biomarkers owing to their high stability under storage and handling conditions and being able to be sampled several times for monitoring. Moreover, as demonstrated for many cancers, their plasma/serum levels mirror those in the primary tumor. There are a large variety of RNA species noncoding for proteins that could be used as cancer biomarkers in liquid biopsies. Among them, the most studied are microRNAs, but recently the attention of the researcher has been also directed towards Piwi-interacting RNAs, circular RNAs, and other small noncoding RNAs. Another class of RNA species, the long noncoding RNAs, is larger than microRNAs and represents a very versatile and promising group of molecules which, apart from their use as biomarkers, have also a possible therapeutic role. In this review, we will give an overview of the most common noncoding RNA species detectable in extracellular fluids and will provide an update concerning the situation of the research on these molecules as cancer biomarkers.
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Affiliation(s)
- Barbara Pardini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy.
- Unit of Molecular Epidemiology and Exposome, Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy.
| | - Alexandru Anton Sabo
- Department of Pediatrics, Marie Curie Emergency Clinical Hospital for Children, 077120 Bucharest, Romania
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy
- Unit of Molecular Epidemiology and Exposome, Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy
| | - George Adrian Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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19
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Dehghan F, Boozarpour S, Torabizadeh Z, Alijanpour S. miR-21: a promising biomarker for the early detection of colon cancer. Onco Targets Ther 2019; 12:5601-5607. [PMID: 31371997 PMCID: PMC6628966 DOI: 10.2147/ott.s199508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 05/18/2019] [Indexed: 12/24/2022] Open
Abstract
Purpose The aim of this study was to compare the expression of miR-21 gene in stages II-IV of formalin-fixed paraffin-embedded (FFPE) tissue in patients with colon cancer and introduce miR-21 as a potential molecular marker for detection of colon cancer in the early stages. Introduction Currently, identification of key molecules involved in the pathogenesis of cancer is one of the areas under consideration. miRNAs, are small RNAs which have been identified in many cancers. In this study, we investigated the expression of miR-21 in three pathologic stages in patients with colon cancer in the north of Iran. Patients and methods A total of 40 FFPE samples were obtained from patients with stages II, III, and IV from hospitals in Mazandaran and Golestan provinces. After extraction of RNA, treatment with DNase I and cDNA synthesis was performed and miR-21 expression was assessed by qPCR. Then, the data were analyzed using statistical software R (3.4.3). Results The expression of miR-21 in stage II was significantly different from stage IV. However, no significant difference was observed between the other stages. In stage II, the level of miR-21 expression was higher in men than women. Moreover, in the second pathological stage, miR-21 expression was reduced in patients with adjacent lymphoid tissue engagement. In addition, the expression of miR-21 in grade I was significantly higher than grade II. Conclusion The results of this study suggest that miR-21 can be a diagnostic marker for early stages of colon cancer, especially in men. It can also be considered as a good candidate for targeted treatment of colon cancer in the early stages of the disease. Furthermore, for the first time, we suggested that miR-21 can be a good molecular marker for classification of the stages of colon cancer.
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Affiliation(s)
- Farnaz Dehghan
- Department of Biology, Faculty of Basic Sciences, Gonbad kavous University, Gonbad kavous, Golestan, Iran
| | - Sohrab Boozarpour
- Department of Biology, Faculty of Basic Sciences, Gonbad kavous University, Gonbad kavous, Golestan, Iran
| | - Zhila Torabizadeh
- Department of Medical Pathology, Faculty of Medicine, Sari University of Medical Sciences, Sari, Mazandaran, Iran
| | - Sakineh Alijanpour
- Department of Biology, Faculty of Basic Sciences, Gonbad kavous University, Gonbad kavous, Golestan, Iran
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20
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Upregulated gga-miR-16-5p Inhibits the Proliferation Cycle and Promotes the Apoptosis of MG-Infected DF-1 Cells by Repressing PIK3R1-Mediated the PI3K/Akt/NF-κB Pathway to Exert Anti-Inflammatory Effect. Int J Mol Sci 2019; 20:ijms20051036. [PMID: 30818821 PMCID: PMC6429190 DOI: 10.3390/ijms20051036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 12/11/2022] Open
Abstract
Mycoplasma gallisepticum (MG) mainly infects chickens to initiate chronic respiratory disease (CRD). microRNAs (miRNAs) play vital roles according to previously reported studies. Our previous study showed that gga-miR-16-5p, in MG-infected lungs of chicken embryo, was upregulated by Illumina sequencing. The study aimed to reveal what role gga-miR-16-5p plays in CRD progression. gga-miR-16-5p was upregulated in MG-infected fibroblast cells (DF-1). Phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1) was demonstrated as the target gene of gga-miR-16-5p. Furthermore, PIK3R1 expression was lower in MG-infected groups than it in noninfected controls measured by qPCR. Additionally, overexpressed gga-miR-16-5p could downregulate PIK3R1 and phosphorylated serine/threonine kinase (p-Akt) to express protein, whereas there is an opposite effect on inhibition. Overexpressed gga-miR-16-5p resulted in decreased activity of tumor necrosis factor alpha (TNF-α) and the nuclear factor-kappaB (NF-κB) by qPCR. Furthermore, overexpressed gga-miR-16-5p restricted cell multiplication, cycle progression, and increased apoptosis of MG-infected DF-1 cells, whereas inhibited gga-miR-16-5p led to the opposite effect. Collectively, upregulated gga-miR-16-5p could decrease multiplication, cycle progression, and increase apoptosis of MG-infected DF-1 cells, at least partly through directly targeting PIK3R1 and inhibiting PI3K/Akt/NF-κB pathway to exert an anti-inflammatory effect. Our results will provide more experimental evidence to bring pathogenesis of MG infection to light.
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Neve B, Jonckheere N, Vincent A, Van Seuningen I. Epigenetic Regulation by lncRNAs: An Overview Focused on UCA1 in Colorectal Cancer. Cancers (Basel) 2018; 10:cancers10110440. [PMID: 30441811 PMCID: PMC6266399 DOI: 10.3390/cancers10110440] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancers have become the second leading cause of cancer-related deaths. In particular, acquired chemoresistance and metastatic lesions occurring in colorectal cancer are a major challenge for chemotherapy treatment. Accumulating evidence shows that long non-coding (lncRNAs) are involved in the initiation, progression, and metastasis of cancer. We here discuss the epigenetic mechanisms through which lncRNAs regulate gene expression in cancer cells. In the second part of this review, we focus on the role of lncRNA Urothelial Cancer Associated 1 (UCA1) to integrate research in different types of cancer in order to decipher its putative function and mechanism of regulation in colorectal cancer cells. UCA1 is highly expressed in cancer cells and mediates transcriptional regulation on an epigenetic level through the interaction with chromatin modifiers, by direct regulation via chromatin looping and/or by sponging the action of a diversity of miRNAs. Furthermore, we discuss the role of UCA1 in the regulation of cell cycle progression and its relation to chemoresistance in colorectal cancer cells.
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Affiliation(s)
- Bernadette Neve
- Inserm UMR-S 1172, Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer (JPArc), Team "Mucins, Epithelial Differentiation and Carcinogenesis"; University Lille; CHU Lille,59045, Lille CEDEX, France.
| | - Nicolas Jonckheere
- Inserm UMR-S 1172, Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer (JPArc), Team "Mucins, Epithelial Differentiation and Carcinogenesis"; University Lille; CHU Lille,59045, Lille CEDEX, France.
| | - Audrey Vincent
- Inserm UMR-S 1172, Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer (JPArc), Team "Mucins, Epithelial Differentiation and Carcinogenesis"; University Lille; CHU Lille,59045, Lille CEDEX, France.
| | - Isabelle Van Seuningen
- Inserm UMR-S 1172, Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer (JPArc), Team "Mucins, Epithelial Differentiation and Carcinogenesis"; University Lille; CHU Lille,59045, Lille CEDEX, France.
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Bahreyni A, Rezaei M, Bahrami A, Khazaei M, Fiuji H, Ryzhikov M, Ferns GA, Avan A, Hassanian SM. Diagnostic, prognostic, and therapeutic potency of microRNA 21 in the pathogenesis of colon cancer, current status and prospective. J Cell Physiol 2018; 234:8075-8081. [DOI: 10.1002/jcp.27580] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/18/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Amirhossein Bahreyni
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences Mashhad Iran
| | - Melika Rezaei
- Department of Biology Ferdowsi University of Mashhad Mashhad Iran
| | - Afsane Bahrami
- Cellular and Molecular Research Center, Birjand University of Medical Sciences Birjand Iran
| | - Majid Khazaei
- Department of Medical Physiology Faculty of Medicine, Mashhad University of Medical Sciences Mashhad Iran
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Hamid Fiuji
- Department of Biochemistry Payame‐Noor University Mashhad Iran
| | - Mikhail Ryzhikov
- Division of Pulmonary and Critical Care Medicine Washington University, School of Medicine Saint Louis Missouri
| | - Gordon A. Ferns
- Division of Medical Education Brighton & Sussex Medical School Brighton Sussex UK
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences Mashhad Iran
- Department of Modern Sciences and Technologies School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences Mashhad Iran
- Department of Medical Biochemistry Faculty of Medicine, Mashhad University of Medical Sciences Mashhad Iran
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