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Mohamed AH, Patel AA, Abdulmonem WA, Muzammil K, Shafie A, Ashour AA, Mirdad TMAM, Mallick AK, Alsaiari AA, Almalki AA. The role of miR-765 in human cancers. Int Immunopharmacol 2024; 139:112779. [PMID: 39068750 DOI: 10.1016/j.intimp.2024.112779] [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: 05/10/2024] [Revised: 06/18/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
MicroRNAs, a collection of short noncoding RNAs, are promising biomarkers for identifying cancer in its early stages and tracking the effectiveness of treatment. This is due to their critical role in regulating gene expression and other vital biological functions via cell-level epigenetic mechanisms. This review brings together data on the molecular and clinical effects of miR-765 on different types of cancer. Significant variation in miR-765 levels has been observed in a variety of cancer types, suggesting that it could have an oncogene or tumor suppressor role. A number of pathways, including PLP2/Notch, VEGFA/Akt1, PDX1, KLK4, RUNX2, DPF3, EMP3, APE1, ERK/EMT axis, and others, are impacted by the inclusion of miR-765 in their analysis. MiR-765 is an essential biomarker that shows promise as a diagnostic tool for various types of cancer. The latest research has identified them as reliable predictive markers for detecting tumor development at an early stage. Based on our study, miR-765 shows promising potential as a biomarker for prognosis in multiple types of cancer. Specifically, we suggest that miR-765 could be an early detection marker for tumor development, progression, and metastasis.
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Affiliation(s)
- Asma'a H Mohamed
- Biomedical Engineering Department, College of Engineering and Technologies, Al-Mustaqbal University, Babil 51001, Hilla, Iraq.
| | - Ayyub Ali Patel
- Department of Clinical Biochemistry, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Khursheed Muzammil
- Department of Public Health, College of Applied Medical Sciences, Khamis Mushait Campus, King Khalid University, Abha 62561, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O.Box 11099, Taif 21944, Saudi Arabia
| | - Amal Adnan Ashour
- Department of Oral & Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry. Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | | | - Ayaz Khurram Mallick
- Department of Clinical Biochemistry, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O.Box 11099, Taif 21944, Saudi Arabia
| | - Abdulraheem Ali Almalki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O.Box 11099, Taif 21944, Saudi Arabia
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Zhang Z, Sha W. MicroRNA-513b-5p inhibits epithelial mesenchymal transition of colon cancer stem cells through IL-6/STAT3 signaling pathway. Discov Oncol 2024; 15:267. [PMID: 38967742 PMCID: PMC11226582 DOI: 10.1007/s12672-024-01137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 07/01/2024] [Indexed: 07/06/2024] Open
Abstract
OBJECTIVE To reveal the mechanisms by which miR-513b-5p inhibits metastasis of colon cancer stem cells (CCSCs) through IL-6/STAT3 in HCT116 cells. METHODS Sphere formation media and magnetic cell sorting were used to enrich and screen CCSCs. We used a colony formation assay, cell proliferation and viability assays, and a nude mouse transplantation tumor assay to identify CCSCs. ELISA was performed to identify IL-6 in the cell culture medium, and the growth, viability, wound healing, and transwell migration of distinct cell groups were compared to differentiate them. Dual-luciferase reporter assay, RT-PCR, and/or Western Blot analysis were conducted to determine the correlation between them. RESULTS CD133+CD44+ HCT116 cells were shown to have higher cloning efficiency, greater proliferation ability and viability, and stronger tumorigenicity. A dual-luciferase reporter assay revealed that miR-513b-5p negatively affected STAT3 expression. RT-PCR and/or Western Blot analysis suggested that miR-513b-5p negatively affected STAT3 and Vimentin, while positively affecting E-cadherin expression. The STAT3 overexpression vector + miR-513b-5p inhibitor cell group had the highest efficiency, greatest proliferation ability and viability, and the highest IL-6 level in the experiments. CONCLUSIONS Mir-513b-5p inhibited the epithelial-mesenchymal transition (EMT) of CCSCs through IL-6/STAT3. This potential mechanism may provide a new therapeutic target for colon cancer.
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Affiliation(s)
- Zefeng Zhang
- Department of Gastroenterology and Digestive Endoscopy Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Weihong Sha
- Department of Gastroenterology and Digestive Endoscopy Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China.
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Simiene J, Dabkeviciene D, Stanciute D, Prokarenkaite R, Jablonskiene V, Askinis R, Normantaite K, Cicenas S, Suziedelis K. Potential of miR-181a-5p and miR-630 as clinical biomarkers in NSCLC. BMC Cancer 2023; 23:857. [PMID: 37697308 PMCID: PMC10496384 DOI: 10.1186/s12885-023-11365-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND The development of drug resistance and high mortality rates are the major problems observed in non-small cell lung cancer (NSCLC). Biomarkers indicating and predicting disease development towards these unfavorable directions are therefore on high demand. Many studies have demonstrated that changes in miRNAs expression may be associated with a response to treatment and disease prognosis, thus suggesting its potential biomarker value for a broad spectrum of clinical applications. The aim of the present study was to investigate the expression level of miR-181a-5p, miR-630, and its targets in NSCLC tumor tissue and plasma samples; and to analyze its association with NSCLC patient's response to treatment and disease prognosis. METHODS The study was performed in 89 paired tissue specimens and plasma samples obtained from NSCLC patients who underwent surgical treatment at the Department of Thoracic Surgery and Oncology of the National Cancer Institute. Analysis of miR-181a-5p and miR-630 expression was performed by qRT-PCR using TaqMan miRNA specific primers. Whereas BCL2, LMO3, PTEN, SNAI2, WIF1 expression levels were identified with KAPA SYBR FAST qPCR Kit. Each sample was examined in triplicate and calculated following the 2-ΔΔCt method. When the p-value was less than 0.05, the differences were considered statistically significant. RESULTS It was found that miR-181a-5p and miR-630 expression levels in NSCLC tissue and plasma samples were significantly decreased compared with control samples. Moreover, patients with low miR-181a-5p expression in tumor tissue and plasma had longer PFS rates than those with high miRNA expression. Decreased miR-630 expression in tumor was statistically significantly associated with better NSCLC patients' OS. In addition, the expression of miR-181a-5p, as well as miR-630 in tumor tissue, are the statistically significant variables for NSCLC patients' OS. Moreover, in NSCLC patient plasma samples circulating miR-181a-5p can be evaluated as significant independent prognostic factors for OS and PFS. CONCLUSIONS Our findings indicate the miR-181a-5p and miR-630 expression levels have the potential to prognose and predict and therefore improve the treatment individualization and the outcome of NSCLC patients. Circulating miR-181a-5p has the potential clinical value as a non-invasive biomarker for NSCLC.
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Affiliation(s)
- Julija Simiene
- National Cancer Institute, Vilnius, 08406, Lithuania.
- Vilnius University Life Sciences Center, Vilnius, 10223, Lithuania.
| | - Daiva Dabkeviciene
- National Cancer Institute, Vilnius, 08406, Lithuania
- Vilnius University Life Sciences Center, Vilnius, 10223, Lithuania
| | | | - Rimvile Prokarenkaite
- National Cancer Institute, Vilnius, 08406, Lithuania
- Vilnius University Life Sciences Center, Vilnius, 10223, Lithuania
| | - Valerija Jablonskiene
- Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, 01513, Lithuania
| | | | | | | | - Kestutis Suziedelis
- National Cancer Institute, Vilnius, 08406, Lithuania
- Vilnius University Life Sciences Center, Vilnius, 10223, Lithuania
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Lim SH, Chua W, Ng W, Ip E, Marques TM, Tran NT, Gama-Carvalho M, Asghari R, Henderson C, Ma Y, de Souza P, Spring KJ. Circulating Tumour Cell Associated MicroRNA Profiles Change during Chemoradiation and Are Predictive of Response in Locally Advanced Rectal Cancer. Cancers (Basel) 2023; 15:4184. [PMID: 37627212 PMCID: PMC10452825 DOI: 10.3390/cancers15164184] [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: 06/22/2023] [Revised: 08/08/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Locally advanced rectal cancer (LARC) has traditionally been treated with trimodality therapy consisting of neoadjuvant radiation +/- chemotherapy, surgery, and adjuvant chemotherapy. There is currently a clinical need for biomarkers to predict treatment response and outcomes, especially during neoadjuvant therapy. Liquid biopsies in the form of circulating tumour cells (CTCs) and circulating nucleic acids in particular microRNAs (miRNA) are novel, the latter also being highly stable and clinically relevant regulators of disease. We studied a prospective cohort of 52 patients with LARC, and obtained samples at baseline, during treatment, and post-treatment. We enumerated CTCs during chemoradiation at these three time-points, using the IsofluxTM (Fluxion Biosciences Inc., Alameda, CA, USA) CTC Isolation and detection platform. We then subjected the isolated CTCs to miRNA expression analyses, using a panel of 106 miRNA candidates. We identified CTCs in 73% of patients at baseline; numbers fell and miRNA expression profiles also changed during treatment. Between baseline and during treatment (week 3) time-points, three microRNAs (hsa-miR-95, hsa-miR-10a, and hsa-miR-16-1*) were highly differentially expressed. Importantly, hsa-miR-19b-3p and hsa-miR-483-5p were found to correlate with good response to treatment. The latter (hsa-miR-483-5p) was also found to be differentially expressed between good responders and poor responders. These miRNAs represent potential predictive biomarkers, and thus a potential miRNA-based treatment strategy. In this study, we demonstrate that CTCs are present and can be isolated in the non-metastatic early-stage cancer setting, and their associated miRNA profiles can potentially be utilized to predict treatment response.
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Affiliation(s)
- Stephanie H. Lim
- Medical Oncology Group, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (W.C.); (W.N.); (E.I.); (Y.M.); (P.d.S.)
- Department of Medical Oncology, Macarthur Cancer Therapy Centre, Campbelltown, NSW 2560, Australia
- Liverpool Clinical School, Western Sydney University, Liverpool, NSW 2170, Australia
| | - Wei Chua
- Medical Oncology Group, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (W.C.); (W.N.); (E.I.); (Y.M.); (P.d.S.)
- Liverpool Clinical School, Western Sydney University, Liverpool, NSW 2170, Australia
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Weng Ng
- Medical Oncology Group, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (W.C.); (W.N.); (E.I.); (Y.M.); (P.d.S.)
- Liverpool Clinical School, Western Sydney University, Liverpool, NSW 2170, Australia
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Emilia Ip
- Medical Oncology Group, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (W.C.); (W.N.); (E.I.); (Y.M.); (P.d.S.)
- Liverpool Clinical School, Western Sydney University, Liverpool, NSW 2170, Australia
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Tania M. Marques
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (T.M.M.); (M.G.-C.)
| | - Nham T. Tran
- School Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Margarida Gama-Carvalho
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (T.M.M.); (M.G.-C.)
| | - Ray Asghari
- Department of Medical Oncology, Bankstown Hospital, Bankstown, NSW 2200, Australia;
| | | | - Yafeng Ma
- Medical Oncology Group, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (W.C.); (W.N.); (E.I.); (Y.M.); (P.d.S.)
| | - Paul de Souza
- Medical Oncology Group, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (W.C.); (W.N.); (E.I.); (Y.M.); (P.d.S.)
- Liverpool Clinical School, Western Sydney University, Liverpool, NSW 2170, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW 2522, Australia
- South West Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia
| | - Kevin J. Spring
- Medical Oncology Group, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (W.C.); (W.N.); (E.I.); (Y.M.); (P.d.S.)
- Liverpool Clinical School, Western Sydney University, Liverpool, NSW 2170, Australia
- South West Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia
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Zafari N, Bathaei P, Velayati M, Khojasteh-Leylakoohi F, Khazaei M, Fiuji H, Nassiri M, Hassanian SM, Ferns GA, Nazari E, Avan A. Integrated analysis of multi-omics data for the discovery of biomarkers and therapeutic targets for colorectal cancer. Comput Biol Med 2023; 155:106639. [PMID: 36805214 DOI: 10.1016/j.compbiomed.2023.106639] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/14/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
The considerable burden of colorectal cancer and the rising trend in young adults emphasize the necessity of understanding its underlying mechanisms, providing new diagnostic and prognostic markers, and improving therapeutic approaches. Precision medicine is a new trend all over the world and identification of novel biomarkers and therapeutic targets is a step forward towards this trend. In this context, multi-omics data and integrated analysis are being investigated to develop personalized medicine in the management of colorectal cancer. Given the large amount of data from multi-omics approach, data integration and analysis is a great challenge. In this Review, we summarize how statistical and machine learning techniques are applied to analyze multi-omics data and how it contributes to the discovery of useful diagnostic and prognostic biomarkers and therapeutic targets. Moreover, we discuss the importance of these biomarkers and therapeutic targets in the clinical management of colorectal cancer in the future. Taken together, integrated analysis of multi-omics data has great potential for finding novel diagnostic and prognostic biomarkers and therapeutic targets, however, there are still challenges to overcome in future studies.
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Affiliation(s)
- Nima Zafari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parsa Bathaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahla Velayati
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Khojasteh-Leylakoohi
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Fiuji
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammadreza Nassiri
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex, BN1 9PH, UK
| | - Elham Nazari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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A Novel Strategy for Identifying NSCLC MicroRNA Biomarkers and Their Mechanism Analysis Based on a Brand-New CeRNA-Hub-FFL Network. Int J Mol Sci 2022; 23:ijms231911303. [PMID: 36232605 PMCID: PMC9569765 DOI: 10.3390/ijms231911303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Finding reliable miRNA markers and revealing their potential mechanisms will play an important role in the diagnosis and treatment of NSCLC. Most existing computational methods for identifying miRNA biomarkers only consider the expression variation of miRNAs or rely heavily on training sets. These deficiencies lead to high false-positive rates. The independent regulatory model is an important complement to traditional models of co-regulation and is more impervious to the dataset. In addition, previous studies of miRNA mechanisms in the development of non-small cell lung cancer (NSCLC) have mostly focused on the post-transcriptional level and did not distinguish between NSCLC subtypes. For the above problems, we improved mainly in two areas: miRNA identification based on both the NOG network and biological functions of miRNA target genes; and the construction of a 4-node directed competitive regulatory network to illustrate the mechanisms. NSCLC was classified as lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) in this work. One miRNA biomarker of LUAD (miR-708-5p) and four of LUSC (miR-183-5p, miR-140-5p, miR-766-5p, and miR-766-3p) were obtained. They were validated using literature and external datasets. The ceRNA-hub-FFL involving transcription factors (TFs), microRNAs (miRNAs), mRNAs, and long non-coding RNAs (lncRNAs) was constructed. There were multiple interactions among these components within the net at the transcriptional, post-transcriptional, and protein levels. New regulations were revealed by the network. Meanwhile, the network revealed the reasons for the previous conflicting conclusions on the roles of CD44, ACTB, and ITGB1 in NSCLC, and demonstrated the necessity of typing studies on NSCLC. The novel miRNA markers screening method and the 4-node directed competitive ceRNA-hub-FFL network constructed in this work can provide new ideas for screening tumor markers and understanding tumor development mechanisms in depth.
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Gao J, Lan T, Zong X, Shi G, He S, Na Chen, Cui F, Tu Y. Analysis of circRNA-miRNA-mRNA Regulatory Network in Peripheral Blood of Radiation Workers. Dose Response 2022; 20:15593258221088745. [PMID: 35521437 PMCID: PMC9067054 DOI: 10.1177/15593258221088745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/17/2022] [Indexed: 12/04/2022]
Abstract
The health of radiation workers has always been our focus. Epidemiological investigation shows that long-term exposure to low-dose ionizing radiation can affect human health, especially cancer and cardiovascular disease, and there are many studies on it. However, up to now, there have been few reports on the research of blood and biological samples from radiation workers. In this study, radiation workers and healthy control groups were strictly screened, and the transcriptome of mRNA and circRNA was sequenced by extracting their peripheral venous blood. At the same time, appropriate data sets were selected in the GEO database for bioinformatics analysis, and circRNA-miRNA-mRNA network was constructed. We identified 9 different circular ribonucleic acids, 3 tiny ribonucleic acids, and 2 central genes (NOD 2 and IRF 7). These differentially expressed genes and non-coding RNA are closely related to ionizing radiation damage, and play an important role as biological markers. In conclusion, this study may provide new insights into the role of the circRNA-miRNA-mRNA regulatory network in the health of radiation workers, and provides a new strategy for the future study of radiation biology.
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Affiliation(s)
- Jin Gao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Tinxi Lan
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Xumin Zong
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Gensheng Shi
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Shuqing He
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Na Chen
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Fengmei Cui
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Yu Tu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
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MicroRNA-199b Deregulation Shows Oncogenic Properties and Promising Clinical Value as Circulating Marker in Locally Advanced Rectal Cancer Patients. Int J Mol Sci 2022; 23:ijms23042203. [PMID: 35216319 PMCID: PMC8875596 DOI: 10.3390/ijms23042203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
The identification of robust prognostic markers still represents a need in locally advanced rectal cancer (LARC). MicroRNAs (miRs) have progressively emerged as promising circulating markers, overcoming some limitations that traditional biopsy comprises. Tissue miR-199b deregulation has been reported to predict outcome and response to neoadjuvant chemoradiotherapy (nCRT) in LARC, and was also found to be associated with disease progression in colorectal cancer. However, its biological and clinical relevance remains to be fully clarified. Thus, we observed here that miR-199b regulates cell migration, aggressiveness, and cell growth, and inhibits colonosphere formation and induces caspase-dependent apoptosis. Moreover, miR-199b expression was quantified by real-time PCR in plasma samples from LARC patients and its downregulation was observed in 22.7% of cases. This alteration was found to be associated with higher tumor size (p = 0.002) and pathological stage (p = 0.020) after nCRT. Notably, we observed substantially lower global miR-199b expression associated with patient downstaging (p = 0.009), as well as in non-responders compared to those cases who responded to nCRT in both pre- (p = 0.003) and post-treatment samples (p = 0.038). In concordance, we found that miR-199b served as a predictor marker of response to neoadjuvant therapy in our cohort (p = 0.011). Altogether, our findings here demonstrate the functional relevance of miR-199b in this disease and its potential value as a novel circulating marker in LARC.
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MiR-483 Promotes Colorectal Cancer Cell Biological Progression by Directly Targeting NDRG2 through Regulation of the PI3K/AKT Signaling Pathway and Epithelial-to-Mesenchymal Transition. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:4574027. [PMID: 35126924 PMCID: PMC8813246 DOI: 10.1155/2022/4574027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/10/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND Colorectal cancer is the third frequent tumor in the whole world. MiR-483, located at the 11p15.5 locus, acts as an oncogene in multiple tumors. The purpose of this study is to explore the important roles of miR-483 in colorectal cancer. MATERIALS AND METHODS RT-qPCR and western blot were applied to calculate the mRNA levels of miR-483 and genes. The Kaplan-Meier method was conducted to calculate the survival of patients with colorectal cancer. The proliferation and invasive abilities were measured by Methyl Thiazolyl Tetrazolium (MTT) and transwell assays. RESULTS MiR-483 was upregulated in colorectal cancer tissues, and the upregulation of miR-483 predicted poor prognosis of colorectal cancer patients. NDRG2 was a target gene of miR-483 in colorectal cancer. Furthermore, miR-483 has been reported to promote colorectal cancer cell proliferation and invasion through targeting NDRG2 by the PI3K/AKT pathway and epithelial-to-mesenchymal transition (EMT). In addition, the overexpression of miR-483 promoted xenograft growth of LOVO cells. CONCLUSION MiR-483 promoted cell proliferation through the NDRG2/PI3K/AKT pathway and invasion-mediated EMT in colorectal cancer. In view of the multiple mechanisms of molecular immunotherapy, it is necessary to further study the relationship between miR-483 and colorectal cancer, so as to find a more direct and effective treatment method to prevent colorectal cancer.
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Kaushik P, Kumar A. Emerging role and function of miR-198 in human health and diseases. Pathol Res Pract 2021; 229:153741. [PMID: 34952425 DOI: 10.1016/j.prp.2021.153741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 01/10/2023]
Abstract
Ever since their discovery, microRNAs (miRNAs/miRs) have astonished us by the plethora of processes they regulate, and thus adding another dimension to the gene regulation. They have been implicated in several diseases affecting cardiovascular, neurodegenerative, hepatic, autoimmune and inflammatory functions. A primate specific exonic miRNA, miR-198 has been vastly studied during the past decade, and shown to have a critical role in wound healing. The aberrant expression of miR-198 was first reported in schizophrenia, linking it to neural development. Later, its dysregulation and tumor suppressive role was reported in hepatocellular carcinoma. However, this was just a beginning, and after which there was an explosion of reports linking miR-198 deregulation to cancers and other ailments. The first target to be identified for miR-198 was Cyclin T1 in monocytes affecting HIV1 replication. Depending on the type of cancer, miR-198 has been shown to function either as a tumor suppressor or an oncomir. Interestingly, miR-198 is not only known to regulate multiple targets and pathways, but also is itself regulated by several circular RNAs and long-non-coding RNAs, highlighting a complex regulatory network. This review highlights the currently understood mechanism and regulation of miR-198 in different diseases, and its possible diagnostic and therapeutic potential.
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Affiliation(s)
- Pankhuri Kaushik
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Arun Kumar
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India.
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Li B, Su Y, Xiang N, Qin B, Li G, Wan T, Liu X, Wang D, Jiang C, Wen L, Feng QS. Comparative serum microRNA array analysis of the spleen-stomach dampness-heat syndrome in different diseases: Chronic hepatitis B and chronic gastritis. Anat Rec (Hoboken) 2021; 304:2620-2631. [PMID: 34288535 DOI: 10.1002/ar.24690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/19/2021] [Accepted: 04/24/2021] [Indexed: 12/28/2022]
Abstract
Spleen-stomach dampness-heat syndrome (SSDHS) is the common Traditional Chinese Medicine (TCM) syndrome observed in both chronic hepatitis B (CHB) and chronic gastritis (CG). The specialized TCM prescription for CHB and CG patients with SSDHS is same, but there is limited information about the biological characteristics of this TCM syndrome. This study aimed to identify the serum miRNAs profile for the SSDHS in two different diseases in order to evaluate the miRNA-mediated biological characteristics of this TCM syndrome. We performed comparative microarray analysis of serum miRNA expression profiles in 10 CHB patients with SSDHS (SSDHS-CHB), 10 CG patients with SSDHS (SSDHS-CG), and 10 healthy controls (HC). The selected miRNAs were further validated by qRT-PCR in 13 SSDHS-CHB patients, 13 SSDHS-CG patients, and 13 HC. Moreover, bioinformatics analysis (GO and KEGG pathway enrichment analyses) was applied to identify the involved target genes and pathways for these selected miRNAs. Nine significantly differentially expressed (SDE)-miRNAs in the SSDHS-CHB group and 24 SDE-miRNAs in the SSDHS-CG group were identified, compared with the HC group (fold change >2.0 and p < .05). Among these, upregulated hsa-miR-483-3p and downregulated hsa-miR-223-3p were identified as the common SDE-miRNAs for both SSDHS-CHB and SSDHS-CG groups. Bioinformatics analysis of the common SDE-miRNA's target genes showed their involvement in the regulation of inflammation, immune response, and tumorigenesis. SSDHS-specific hsa-miR-483-3p and hsa-miR-223-3p identified in this study indicated a relevance to the underlying biological basis of SSDHS, and may provide scientific basis for the application of same TCM prescription in CHB and CG.
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Affiliation(s)
- Baixue Li
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yue Su
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ne Xiang
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Bing Qin
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guiyu Li
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tingjun Wan
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiyang Liu
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dong Wang
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Cen Jiang
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Li Wen
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Quan-Sheng Feng
- College of Basic Medical Sciences Chengdu University of Traditional Chinese Medicine, Chengdu, China
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12
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Wu L, Wan S, Li J, Xu Y, Lou X, Sun M, Wang S. Expression and prognostic value of E2F3 transcription factor in non-small cell lung cancer. Oncol Lett 2021; 21:411. [PMID: 33841572 PMCID: PMC8020386 DOI: 10.3892/ol.2021.12672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 01/20/2021] [Indexed: 12/20/2022] Open
Abstract
E2F transcription factor 3 (E2F3) plays a vital role in the development of various types of cancer. To verify whether E2F3 is a suitable biomarker for the prognosis of lung cancer, bioinformatics analysis was performed to determine the differential expression level of E2F3 in lung cancer and the surrounding non-tumor tissues, and the results were confirmed in a NSCLC cell line and a tissue microarray (TMA). The relevance of E2F3 in non-small cell lung cancer (NSCLC) was investigated in 19 studies from the Oncomine database and confirmed in The Cancer Genome Atlas database. In the lung cancer cell line A549, the inhibition of E2F3 mRNA expression level led to decreased tumor cell viability and cell migration, which was determined by a Cell Counting Kit-8 and wound healing assays, respectively. Immunohistochemistry analyses of E2F3, Bcl-2, Bax and caspase-3 were performed in the NSCLC TMA (n=50). The assessment of TMA detected the increase of E2F3 protein expression level in the tumor tissues, as compared with that in the non-tumor tissues, which was also correlated with the increase in expression of Bcl-2 in tumors. Analysis of the clinical data from patients with NSCLC revealed that the overexpression of E2F3 was associated with early lymphatic spreading, and poor patient survival time. The OncomiR website was used to predict the E2F3 upstream microRNAs and determine their prognostic value in patients with NSCLC. The results from the present study revealed that E2F3 was overexpressed at both the transcriptional and translational levels in NSCLC tissues, as compared with that in non-tumor tissues. The overexpression of E2F3 was associated with the upregulation of the anti-apoptotic factor, Bcl-2, which may contribute to uncontrolled tumor growth. Thus, E2F3 was shown to have important oncogenic properties in the development of NSCLC, and it may become a potential biomarker for patients with NSCLC.
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Affiliation(s)
- Lei Wu
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Shan Wan
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Jinfan Li
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China.,Department of Collaborative Innovation Center of Clinical Immunology between Soochow University and Sihong People's Hospital, Sihong, Jiangsu 223900, P.R. China
| | - Yiying Xu
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiaoli Lou
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Maomin Sun
- Laboratory Animal Research Center, Soochow University School of Medicine, Suzhou, Jiangsu 215123, P.R. China
| | - Shouli Wang
- Department of Pathology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China.,Department of Collaborative Innovation Center of Clinical Immunology between Soochow University and Sihong People's Hospital, Sihong, Jiangsu 223900, P.R. China
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13
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Rubio J, Cristóbal I, Santos A, Caramés C, Luque M, Sanz-Alvarez M, Zazo S, Madoz-Gúrpide J, Rojo F, García-Foncillas J. Low MicroRNA-19b Expression Shows a Promising Clinical Impact in Locally Advanced Rectal Cancer. Cancers (Basel) 2021; 13:cancers13061456. [PMID: 33810186 PMCID: PMC8005118 DOI: 10.3390/cancers13061456] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The establishment of molecular markers to predict response to neoadjuvant chemoradiotherapy (CRT) would help to avoid unnecessary toxicities and surgery delays in the clinical management of locally advanced rectal cancer (LARC) patients. Our aim here was to in-vestigate the clinical impact of miR-19b in this disease. Interestingly, our findings highlight the potential usefulness of miR-19b as a predictor of response to neoadjuvant CRT and outcome, and suggest PPP2R5E as a relevant miR-19b target in LARC. Abstract The standard treatment for patients with locally advanced colorectal cancer (LARC) is neoadjuvant 5-fluorouracil (5-FU) based chemoradiotherapy (CRT) followed by surgical mesorectal excision. However, the lack of response to this preoperative treatment strongly compromises patient outcomes and leads to surgical delays and undesired toxicities in those non-responder cases. Thus, the identification of effective and robust biomarkers to predict response to preoperative CRT represents an urgent need in the current clinical management of LARC. The oncomiR microRNA-19b (miR-19b) has been reported to functionally play oncogenic roles in colorectal cancer (CRC) cells as well as regulate 5-FU sensitivity and determine outcome in CRC patients. However, its clinical impact in LARC has not been previously investigated. Here, we show that miR-19b deregulation is a common event in this disease, and its decreased expression significantly associates with lower tumor size after CRT (p = 0.003), early pathological stage (p = 0.003), and absence of recurrence (p = 0.001) in LARC patients. Interestingly, low miR-19b expression shows a predictive value of better response to neoajuvant CRT (p < 0.001), and the subgroup of LARC patients with low miR-19b levels have a markedly longer overall (p = 0.003) and event-free survival (p = 0.023). Finally, multivariate analyses determined that miR-19b independently predicts both patient outcome and response to preoperative CRT, highlighting its potential clinical usefulness in the management of LARC patients.
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Affiliation(s)
- Jaime Rubio
- Cancer Unit for Research on Novel Therapeutic Targets, Oncohealth Institute, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain; (J.R.); (A.S.); (C.C.)
- Translational Oncology Division, Oncohealth Institute, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain
- Medical Oncology Department, University Hospital “Fundación Jiménez Díaz”, UAM, E-28040 Madrid, Spain
| | - Ion Cristóbal
- Cancer Unit for Research on Novel Therapeutic Targets, Oncohealth Institute, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain; (J.R.); (A.S.); (C.C.)
- Translational Oncology Division, Oncohealth Institute, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain
- Correspondence: (I.C.); (J.G.-F.); Tel.: +34-915504800 (I.C. & J.G-F.)
| | - Andrea Santos
- Cancer Unit for Research on Novel Therapeutic Targets, Oncohealth Institute, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain; (J.R.); (A.S.); (C.C.)
- Translational Oncology Division, Oncohealth Institute, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain
| | - Cristina Caramés
- Cancer Unit for Research on Novel Therapeutic Targets, Oncohealth Institute, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain; (J.R.); (A.S.); (C.C.)
- Translational Oncology Division, Oncohealth Institute, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain
- Medical Oncology Department, University Hospital “Fundación Jiménez Díaz”, UAM, E-28040 Madrid, Spain
| | - Melani Luque
- Pathology Department, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain; (M.L.); (M.S.-A.); (S.Z.); (J.M.-G.); (F.R.)
| | - Marta Sanz-Alvarez
- Pathology Department, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain; (M.L.); (M.S.-A.); (S.Z.); (J.M.-G.); (F.R.)
| | - Sandra Zazo
- Pathology Department, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain; (M.L.); (M.S.-A.); (S.Z.); (J.M.-G.); (F.R.)
| | - Juan Madoz-Gúrpide
- Pathology Department, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain; (M.L.); (M.S.-A.); (S.Z.); (J.M.-G.); (F.R.)
| | - Federico Rojo
- Pathology Department, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain; (M.L.); (M.S.-A.); (S.Z.); (J.M.-G.); (F.R.)
| | - Jesús García-Foncillas
- Translational Oncology Division, Oncohealth Institute, IIS- Fundación Jiménez Díaz-UAM, E-28040 Madrid, Spain
- Medical Oncology Department, University Hospital “Fundación Jiménez Díaz”, UAM, E-28040 Madrid, Spain
- Correspondence: (I.C.); (J.G.-F.); Tel.: +34-915504800 (I.C. & J.G-F.)
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14
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Yu C, Qi X, Lin Y, Li Y, Shen B. iODA: An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data. J Biomed Inform 2020; 112:103605. [PMID: 33096244 DOI: 10.1016/j.jbi.2020.103605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/07/2020] [Accepted: 10/15/2020] [Indexed: 02/05/2023]
Abstract
The latest advances in the next generation sequencing technology have greatly facilitated the extensive research of genomics and transcriptomics, thereby promoting the decoding of carcinogenesis with unprecedented resolution. Considering the contribution of analyzing high-throughput multi-omics data to the exploration of cancer molecular mechanisms, an integrated tool for heterogeneous multi-omics data analysis (iODA) is proposed for the systems-level interpretation of multi-omics data, i.e., transcriptomic profiles (mRNA or miRNA expression data) and protein-DNA interactions (ChIP-Seq data). Considering the data heterogeneity, iODA can compare six statistical algorithms in differential analysis for the selected sample data and assist users in choosing the globally optimal one for dysfunctional mRNA or miRNA identification. Since molecular signatures are more consistent at the pathway level than at the gene level, the tool is able to enrich the identified dysfunctional molecules onto the KEGG pathways and extracted the consistent items as key components for further pathogenesis investigation. Compared with other tools, iODA is multi-functional for the systematic analysis of different level of omics data, and its analytical power was demonstrated through case studies of single and cross-level prostate cancer omics data. iODA is open source under GNU GPL and can be downloaded from http://www.sysbio.org.cn/iODA.
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Affiliation(s)
- Chunjiang Yu
- School of Biotechnology, Suzhou Industrial Park Institute of Service Outsourcing, Suzhou, China; Center for Systems Biology, Soochow University, Suzhou, China
| | - Xin Qi
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou, China; Center for Systems Biology, Soochow University, Suzhou, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Yin Li
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
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15
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Yang Y, Meng WJ, Wang ZQ. MicroRNAs in Colon and Rectal Cancer - Novel Biomarkers from Diagnosis to Therapy. Endocr Metab Immune Disord Drug Targets 2020; 20:1211-1226. [PMID: 32370729 DOI: 10.2174/1871530320666200506075219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/31/2020] [Accepted: 02/01/2020] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) is one of the most common cancers and a significant cause of tumor- related deaths worldwide. Traditional biomarkers, such as CEA and CA199, are not sensitive enough to provide useful information for early diagnosis and treatment and are rather used to track the clinical progression of the disease. There is growing evidence that microRNAs (miRNA) are potentially superior to traditional biomarkers as promising non-invasive biomarkers for the timely diagnosis and prediction of prognosis or treatment response in the management of CRC. In this review, the latest studies on the dysregulation of miRNAs expression in CRC and the potential for miRNAs to serve as biomarkers were collected. Given the limitations of miRNA, as discussed in this paper, its clinical applications as a diagnostic biomarker should be limited to use in combination with other biomarkers. Further research is necessary to elucidate the clinical applications of miRNA in therapy for CRC.
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Affiliation(s)
- Ying Yang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wen-Jian Meng
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zi-Qiang Wang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
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16
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Lin Y, Qian F, Shen L, Chen F, Chen J, Shen B. Computer-aided biomarker discovery for precision medicine: data resources, models and applications. Brief Bioinform 2020; 20:952-975. [PMID: 29194464 DOI: 10.1093/bib/bbx158] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Biomarkers are a class of measurable and evaluable indicators with the potential to predict disease initiation and progression. In contrast to disease-associated factors, biomarkers hold the promise to capture the changeable signatures of biological states. With methodological advances, computer-aided biomarker discovery has now become a burgeoning paradigm in the field of biomedical science. In recent years, the 'big data' term has accumulated for the systematical investigation of complex biological phenomena and promoted the flourishing of computational methods for systems-level biomarker screening. Compared with routine wet-lab experiments, bioinformatics approaches are more efficient to decode disease pathogenesis under a holistic framework, which is propitious to identify biomarkers ranging from single molecules to molecular networks for disease diagnosis, prognosis and therapy. In this review, the concept and characteristics of typical biomarker types, e.g. single molecular biomarkers, module/network biomarkers, cross-level biomarkers, etc., are explicated on the guidance of systems biology. Then, publicly available data resources together with some well-constructed biomarker databases and knowledge bases are introduced. Biomarker identification models using mathematical, network and machine learning theories are sequentially discussed. Based on network substructural and functional evidences, a novel bioinformatics model is particularly highlighted for microRNA biomarker discovery. This article aims to give deep insights into the advantages and challenges of current computational approaches for biomarker detection, and to light up the future wisdom toward precision medicine and nation-wide healthcare.
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Affiliation(s)
- Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Fuliang Qian
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Li Shen
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Feifei Chen
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Jiajia Chen
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
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17
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Zhang X, Zhang H, Shen B, Sun XF. Novel MicroRNA Biomarkers for Colorectal Cancer Early Diagnosis and 5-Fluorouracil Chemotherapy Resistance but Not Prognosis: A Study from Databases to AI-Assisted Verifications. Cancers (Basel) 2020; 12:cancers12020341. [PMID: 32028703 PMCID: PMC7073235 DOI: 10.3390/cancers12020341] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/13/2020] [Accepted: 02/01/2020] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the major causes of cancer death worldwide. In general, early diagnosis for CRC and individual therapy have led to better survival for the cancer patients. Accumulating studies concerning biomarkers have provided positive evidence to improve cancer early diagnosis and better therapy. It is, however, still necessary to further investigate the precise biomarkers for cancer early diagnosis and precision therapy and predicting prognosis. In this study, AI-assisted systems with bioinformatics algorithm integrated with microarray and RNA sequencing (RNA-seq) gene expression (GE) data has been approached to predict microRNA (miRNA) biomarkers for early diagnosis of CRC based on the miRNA-messenger RNA (mRNA) interaction network. The relationships between the predicted miRNA biomarkers and other biological components were further analyzed on biological networks. Bayesian meta-analysis of diagnostic test was utilized to verify the diagnostic value of the miRNA candidate biomarkers and the combined multiple biomarkers. Biological function analysis was performed to detect the relationship of candidate miRNA biomarkers and identified biomarkers in pathways. Text mining was used to analyze the relationships of predicted miRNAs and their target genes with 5-fluorouracil (5-FU). Survival analyses were conducted to evaluate the prognostic values of these miRNAs in CRC. According to the number of miRNAs single regulated mRNAs (NSR) and the number of their regulated transcription factor gene percentage (TFP) on the miRNA-mRNA network, there were 12 promising miRNA biomarkers were selected. There were five potential candidate miRNAs (miRNA-186-5p, miRNA-10b-5, miRNA-30e-5p, miRNA-21 and miRNA-30e) were confirmed as CRC diagnostic biomarkers, and two of them (miRNA-21 and miRNA-30e) were previously reported. Furthermore, the combinations of the five candidate miRNAs biomarkers showed better prediction accuracy for CRC early diagnosis than the single miRNA biomarkers. miRNA-10b-5p and miRNA-30e-5p were associated with the 5-FU therapy resistance by targeting the related genes. These miRNAs biomarkers were not statistically associated with CRC prognosis.
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Affiliation(s)
- Xueli Zhang
- School of Medicine, Institute of Medical Sciences, Örebro University, SE-70182 Örebro, Sweden; (X.Z.); (H.Z.)
- Centre for Systems Biology, Soochow University, Suzhou 215006, China
| | - Hong Zhang
- School of Medicine, Institute of Medical Sciences, Örebro University, SE-70182 Örebro, Sweden; (X.Z.); (H.Z.)
| | - Bairong Shen
- Centre for Systems Biology, Soochow University, Suzhou 215006, China
- Correspondence: (B.S.); (X.-F.S.); Tel.: +86-521-6511-0951 (B.S.); +46-101-032-066 (X.-F.S.)
| | - Xiao-Feng Sun
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, SE-58183 Linköping, Sweden
- Correspondence: (B.S.); (X.-F.S.); Tel.: +86-521-6511-0951 (B.S.); +46-101-032-066 (X.-F.S.)
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Matsuoka T, Yashiro M. Precision medicine for gastrointestinal cancer: Recent progress and future perspective. World J Gastrointest Oncol 2020; 12:1-20. [PMID: 31966910 PMCID: PMC6960076 DOI: 10.4251/wjgo.v12.i1.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 10/12/2019] [Accepted: 11/04/2019] [Indexed: 02/05/2023] Open
Abstract
Gastrointestinal (GI) cancer has a high tumor incidence and mortality rate worldwide. Despite significant improvements in radiotherapy, chemotherapy, and targeted therapy for GI cancer over the last decade, GI cancer is characterized by high recurrence rates and a dismal prognosis. There is an urgent need for new diagnostic and therapeutic approaches. Recent technological advances and the accumulation of clinical data are moving toward the use of precision medicine in GI cancer. Here we review the application and status of precision medicine in GI cancer. Analyses of liquid biopsy specimens provide comprehensive real-time data of the tumor-associated changes in an individual GI cancer patient with malignancy. With the introduction of gene panels including next-generation sequencing, it has become possible to identify a variety of mutations and genetic biomarkers in GI cancer. Although the genomic aberration of GI cancer is apparently less actionable compared to other solid tumors, novel informative analyses derived from comprehensive gene profiling may lead to the discovery of precise molecular targeted drugs. These progressions will make it feasible to incorporate clinical, genome-based, and phenotype-based diagnostic and therapeutic approaches and apply them to individual GI cancer patients for precision medicine.
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Affiliation(s)
- Tasuku Matsuoka
- Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
- Oncology Institute of Geriatrics and Medical Science, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
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19
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20
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EBV encoded miRNA BART8-3p promotes radioresistance in nasopharyngeal carcinoma by regulating ATM/ATR signaling pathway. Biosci Rep 2019; 39:BSR20190415. [PMID: 31471531 PMCID: PMC6744588 DOI: 10.1042/bsr20190415] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/17/2019] [Accepted: 08/05/2019] [Indexed: 12/13/2022] Open
Abstract
Resistance to radiotherapy is one of the main causes of treatment failure in patients with nasopharyngeal carcinoma (NPC). Epstein-Barr virus (EBV) infection is an important factor in the pathogenesis of NPC, and EBV-encoded microRNAs (miRNAs) promote NPC progression. However, the role of EBV-encoded miRNAs in the radiosensitivity of NPC remains unclear. Here, we investigated the effects of EBV-miR-BART8-3p on radiotherapy resistance in NPC cells in vitro and in vivo, and explored the underlying molecular mechanisms. Inhibitors of ataxia telangiectasia mutated (ATM)/ataxia telangiectasia mutated and Rad3-related (ATR) (KU60019 and AZD6738, respectively) were used to examine radiotherapy resistance. We proved that EBV-miR-BART8-3p promoted NPC cell proliferation in response to irradiation in vitro and associated with the induction of cell cycle arrest at the G2/M phase, which was a positive factor for the DNA repair after radiation treatment. Besides, EBV-miR-BART8-3p could increase the size of xenograft tumors significantly in nude mice. Treatment with KU60019 or AZD6738 increased the radiosensitivity of NPC by suppressing the expression of p-ATM and p-ATR. The present results indicate that EBV-miR-BART8-3p promotes radioresistance in NPC by modulating the activity of ATM/ATR signaling pathway.
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21
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Alfonso JCL, Berk L. Modeling the effect of intratumoral heterogeneity of radiosensitivity on tumor response over the course of fractionated radiation therapy. Radiat Oncol 2019; 14:88. [PMID: 31146751 PMCID: PMC6543639 DOI: 10.1186/s13014-019-1288-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/06/2019] [Indexed: 01/31/2023] Open
Abstract
Background Standard radiobiology theory of radiation response assumes a uniform innate radiosensitivity of tumors. However, experimental data show that there is significant intratumoral heterogeneity of radiosensitivity. Therefore, a model with heterogeneity was developed and tested using existing experimental data to show the potential effects from the presence of an intratumoral distribution of radiosensitivity on radiation therapy response over a protracted radiation therapy treatment course. Methods The standard radiation response curve was modified to account for a distribution of radiosensitivity, and for variations in the repopulation rates of the tumor cell subpopulations. Experimental data from the literature were incorporated to determine the boundaries of the model. The proposed model was then used to show the changes in radiosensitivity of the tumor during treatment, and the effects of fraction size, α/β ratio and variation of the repopulation rates of tumor cells. Results In the presence of an intratumoral distribution of radiosensitivity, there is rapid selection of radiation-resistant cells over a course of fractionated radiation therapy. Standard treatment fractionation regimes result in the near-complete replacement of the initial population of sensitive cells with a population of more resistant cells. Further, as treatment progresses, the tumor becomes more resistant to further radiation treatment, making each fractional dose less efficacious. A wider initial distribution induces increased radiation resistance. Hypofractionation is more efficient in a heterogeneous tumor, with increased cell kill for biologically equivalent doses, while inducing less resistance. The model also shows that a higher growth rate in resistant cells can account for the accelerated repopulation that is seen during the clinical treatment of patients. Conclusions Modeling of tumor cell survival with radiosensitivity heterogeneity alters the predicted tumor response, and explains the induction of radiation resistance by radiation treatment, the development of accelerated repopulation, and the potential beneficial effects of hypofractionation. Tumor response to treatment may be better predicted by assaying for the distribution of radiosensitivity, or the extreme of the radiosensitivity, rather than measuring the initial, general radiation sensitivity of the untreated tumor.
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Affiliation(s)
- J C L Alfonso
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| | - L Berk
- Division of Radiation Oncology, Department of Radiology, Morsani School of Medicine at the University of South Florida, Tampa, FL, USA
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22
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Spugnini EP, Logozzi M, Di Raimo R, Mizzoni D, Fais S. A Role of Tumor-Released Exosomes in Paracrine Dissemination and Metastasis. Int J Mol Sci 2018; 19:E3968. [PMID: 30544664 PMCID: PMC6321583 DOI: 10.3390/ijms19123968] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 12/13/2022] Open
Abstract
Metastatic diffusion is thought to be a multi-step phenomenon involving the release of cells from the primary tumor and their diffusion through the body. Currently, several hypotheses have been put forward in order to explain the origin of cancer metastasis, including epithelial⁻mesenchymal transition, mutagenesis of stem cells, and a facilitating role of macrophages, involving, for example, transformation or fusion hybridization with neoplastic cells. In this paradigm, tumor-secreted extracellular vesicles (EVs), such as exosomes, play a pivotal role in cell communications, delivering a plethora of biomolecules including proteins, lipids, and nucleic acids. For their natural role in shuttling molecules, EVs have been newly considered a part of the metastatic cascade. They have a prominent role in preparing the so-called "tumor niches" in target organs. However, recent evidence has pointed out an even more interesting role of tumor EVs, consisting in their ability to induce malignant transformation in resident mesenchymal stem cells. All in all, in this review, we discuss the multiple involvements of EVs in the metastatic cascade, and how we can exploit and manipulate EVs in order to reduce the metastatic spread of malignant tumors.
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Affiliation(s)
| | - Mariantonia Logozzi
- Department of Oncology and Molecular Medicine, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Rossella Di Raimo
- Department of Oncology and Molecular Medicine, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Davide Mizzoni
- Department of Oncology and Molecular Medicine, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Stefano Fais
- Department of Oncology and Molecular Medicine, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy.
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23
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Jiang S, Miao D, Wang M, Lv J, Wang Y, Tong J. MiR-30-5p suppresses cell chemoresistance and stemness in colorectal cancer through USP22/Wnt/β-catenin signaling axis. J Cell Mol Med 2018; 23:630-640. [PMID: 30338942 PMCID: PMC6307779 DOI: 10.1111/jcmm.13968] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/06/2018] [Accepted: 09/23/2018] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) remains both common and fatal, and its successful treatment is greatly limited by the development of stem cell‐like characteristics (stemness) and chemoresistance. MiR‐30‐5p has been shown to function as a tumor suppressor by targeting the Wnt/β‐catenin signaling pathway, but its activity in CRC has never been assessed. We hypothesized that miR‐30‐5p exerts anti‐oncogenic effects in CRC by regulating the USP22/Wnt/β‐catenin signaling axis. In the present study, we demonstrate that tissues from CRC patients and human CRC cell lines show significantly decreased miR‐30‐5p family expression. After identifying the 3’UTR of USP22 as a potential binding site of miR‐30‐5p, we constructed a luciferase reporter containing the potential miR‐30‐5p binding site and measured the effects on USP22 expression. Western blot assays showed that miR‐30‐5p decreased USP22 protein expression in HEK293 and Caco2 CRC cells. To evaluate the effects of miR‐30‐5p on CRC cell stemness, we isolated CD133 + CRC cells (Caco2 and HCT15). We then determined that, while miR‐30‐5p is normally decreased in CD133 + CRC cells, miR‐30‐5p overexpression significantly reduces expression of stem cell markers CD133 and Sox2, sphere formation, and cell proliferation. Similarly, we found that miR‐30‐5p expression is normally reduced in 5‐fluorouracil (5‐FU) resistant CRC cells, whereas miR‐30‐5p overexpression in 5‐FU resistant cells reduces sphere formation and cell viability. Inhibition of miR‐30‐5p reversed the process. Finally, we determined that miR‐30‐5p attenuates the expression of Wnt/β‐catenin signaling target genes (Axin2 and MYC), Wnt luciferase activity, and β‐catenin protein levels in CRC stem cells.
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Affiliation(s)
- Shixiong Jiang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dazhuang Miao
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Muhong Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiachen Lv
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yihui Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jinxue Tong
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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24
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Zhang X, Sun XF, Cao Y, Ye B, Peng Q, Liu X, Shen B, Zhang H. CBD: a biomarker database for colorectal cancer. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5010523. [PMID: 29846545 PMCID: PMC6007224 DOI: 10.1093/database/bay046] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/20/2018] [Indexed: 01/05/2023]
Abstract
Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD. Database URL: http://sysbio.suda.edu.cn/CBD/
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Affiliation(s)
- Xueli Zhang
- School of Medicine, Institute of Medical Sciences, Örebro University, SE 70182 Örebro, Sweden.,Centre for Systems Biology, Soochow University, Suzhou 215006, China
| | - Xiao-Feng Sun
- Department of Oncology and Department of Clinical and Experimental Medicine, Linköping University, SE 58183 Linköping, Sweden
| | - Yang Cao
- Clinical Epidemiology and Biostatistics, Institute of Medical Sciences, Örebro University, SE 70182 Örebro, Sweden.,Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institute, SE 17177 Stockholm, Sweden
| | - Benchen Ye
- Centre for Systems Biology, Soochow University, Suzhou 215006, China
| | - Qiliang Peng
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Xingyun Liu
- Centre for Systems Biology, Soochow University, Suzhou 215006, China
| | - Bairong Shen
- Centre for Systems Biology, Soochow University, Suzhou 215006, China
| | - Hong Zhang
- School of Medicine, Institute of Medical Sciences, Örebro University, SE 70182 Örebro, Sweden
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25
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Lhuillier C, Vanpouille-Box C, Galluzzi L, Formenti SC, Demaria S. Emerging biomarkers for the combination of radiotherapy and immune checkpoint blockers. Semin Cancer Biol 2018; 52:125-134. [PMID: 29258856 PMCID: PMC6004231 DOI: 10.1016/j.semcancer.2017.12.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 12/19/2022]
Abstract
Over the past few years, multiple immune checkpoint blockers (ICBs) have achieved unprecedented clinical success and have been approved by regulatory agencies for the treatment of an increasing number of malignancies. However, only a limited fraction of patients responds to ICBs employed as a standalone intervention, calling for the development of combinatorial regimens. Radiation therapy (RT) stands out as a very promising candidate for this purpose. Indeed, RT mediates antineoplastic effects not only by cytotoxic and cytostatic mechanisms, but also by modulating immunological functions, both locally (within the irradiated field) and systemically. As combinatorial regimens involving RT and ICBs are being developed and clinically tested at an accelerating pace, it is paramount to identify biomarkers that reliably predict the likelihood of individual patients to respond. Here, we discuss emerging biomarkers that may potentially predict the response of cancer patients to RT plus ICBs.
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Affiliation(s)
- Claire Lhuillier
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | | | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA
| | - Silvia Chiara Formenti
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA.
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26
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Overcoming stemness and chemoresistance in colorectal cancer through miR-195-5p-modulated inhibition of notch signaling. Int J Biol Macromol 2018; 117:445-453. [DOI: 10.1016/j.ijbiomac.2018.05.151] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 12/31/2022]
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27
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Lin Y, Wu W, Sun Z, Shen L, Shen B. MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. RNA Biol 2018; 15:1093-1105. [PMID: 30081733 DOI: 10.1080/15476286.2018.1502590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with the potential as biomarkers for disease diagnosis, prognosis and therapy. In the era of big data and biomedical informatics, computer-aided biomarker discovery has become the current frontier. However, most of the computational models are highly dependent on specific prior knowledge and training-testing procedures, very few are mechanism-guided or evidence-based. To the best of our knowledge, untill now no general rules have been uncovered and applied to miRNA biomarker screening. In this study, we manually collected literature-reported cancer miRNA biomarkers and analyzed their regulatory patterns, including the regulatory modes, biological functions and evolutionary characteristics of their targets in the human miRNA-mRNA network. Two evidences were statistically detected and used to distinguish biomarker miRNAs from others. Based on these observations, we developed a novel bioinformatics model and software tool for miRNA biomarker discovery ( http://sysbio.suda.edu.cn/MiRNA-BD/ ). In contrast to routine methods that focus on miRNA synergic functions, our method searches for vulnerable sites in the miRNA-mRNA network and considers the independent regulatory power of miRNAs, i.e., single-line regulations between miRNAs and mRNAs. The performance comparison demonstrates the generality and precision of our model, which identifies miRNA biomarkers for cancers as well as other complex diseases without training or specific prior knowledge.
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Affiliation(s)
- Yuxin Lin
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China
| | - Wentao Wu
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China
| | - Zhandong Sun
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China
| | - Li Shen
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China.,b Department of Genetics & Systems Biology Institute , Yale University School of Medicine , West Haven , CT USA
| | - Bairong Shen
- a Center for Systems Biology , Soochow University , Suzhou, Jiangsu , China.,c Center for Translational Biomedical Informatics , Guizhou University School of Medicine , Guiyang , China.,d Institute for Systems Genetics, West China Hospital , Sichuan University , Chengdu , China
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28
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The Glucose-Regulated MiR-483-3p Influences Key Signaling Pathways in Cancer. Cancers (Basel) 2018; 10:cancers10060181. [PMID: 29867024 PMCID: PMC6025222 DOI: 10.3390/cancers10060181] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 02/06/2023] Open
Abstract
The hsa-mir-483 gene, located within the IGF2 locus, transcribes for two mature microRNAs, miR-483-5p and miR-483-3p. This gene, whose regulation is mediated by the the CTNNB1/USF1 complex, shows an independent expression from its host gene IGF2. The miR-483-3p affects the Wnt/β-catenin, the TGF-β, and the TP53 signaling pathways by targeting several genes as CTNNB1, SMAD4, IGF1, and BBC3. Accordingly, miR-483-3p is associated with various tissues specific physiological properties as insulin and melanin production, as well as with cellular physiological functions such as wounding, differentiation, proliferation, and survival. Deregulation of miR-483-3p is observed in different types of cancer, and its overexpression can inhibit the pro-apoptotic pathway induced by the TP53 target effectors. As a result, the oncogenic characteristics of miR-483-3p are linked to the effect of some of the most relevant cancer-related genes, TP53 and CTNNB1, as well as to one of the most important cancer hallmark: the aberrant glucose metabolism of tumor cells. In this review, we summarize the recent findings regarding the miR-483-3p, to elucidate its functional role in physiological and pathological contexts, focusing overall on its involvement in cancer and in the TP53 pathway.
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29
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Tan K, Leong SM, Kee Z, Caramat PV, Teo J, Blanco MVM, Koay ESC, Cheong WK, Soh TIP, Yong WP, Pang A. Longitudinal monitoring reveals dynamic changes in circulating tumor cells (CTCs) and CTC-associated miRNAs in response to chemotherapy in metastatic colorectal cancer patients. Cancer Lett 2018. [PMID: 29518480 DOI: 10.1016/j.canlet.2018.02.039] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We evaluated the changes in CTC count and CTC-associated miRNAs during the course of chemotherapy in patients with metastatic colorectal cancer. Blood samples were collected from 9 metastatic colorectal cancer patients prior to chemotherapy and at every other chemotherapy session during the course of treatment. CTCs were isolated and enumerated using a size-exclusion method (CellSievo, Singapore). CTC-associated miRNAs were isolated using a paper-based, partitioning method, and analyzed using reverse transcription quantitative real-time PCR (MiRXES, Singapore). CTC count trends generally correlated with disease progression defined by radiological measurements and trends in carcinoembryonic antigen (CEA) levels; hence CTC counts may be useful in cases where CEA is not elevated. CTC-associated miRNAs identified were miR-15b, miR-16, miR-19a, miR-21, miR-25, miR-30d, miR-126, miR-185, miR-221, miR-222, and miR-324-5p. The expression of CTC-associated miRNAs did not appear to correlate with CTC count and exhibited inter-individual heterogeneity. This pilot study suggests that analysis of CTC changes during the course of treatment may be useful in monitoring response to therapy in metastatic colorectal cancer.
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Affiliation(s)
- Karen Tan
- Department of Laboratory Medicine, National University Hospital, Singapore.
| | - Sai Mun Leong
- Department of Pathology, National University, Singapore
| | - Zizheng Kee
- Department of Pathology, National University, Singapore
| | | | - James Teo
- Department of Laboratory Medicine, National University Hospital, Singapore
| | | | | | - Wai Kit Cheong
- Department of Surgery, National University Hospital, Singapore
| | | | | | - Angela Pang
- National University Cancer Institute, Singapore.
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30
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Wu QB, Sheng X, Zhang N, Yang MW, Wang F. Role of microRNAs in the resistance of colorectal cancer to chemoradiotherapy. Mol Clin Oncol 2018; 8:523-527. [PMID: 29556386 DOI: 10.3892/mco.2018.1578] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/12/2018] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) is among the main tumor-related causes of death worldwide. The fact that the majority of the patients develop resistance to chemoradiotherapy (CRT) is a major obstacle for the treatment of CRC. In order to develop more effective treatment strategies, it is crucial to elucidate the mechanisms underlying the development of resistance to CRT. Several studies have recently indicated the regulatory effects of microRNAs (miRNAs) in response to antitumor agents. For example, miR-34a attenuates the chemoresistance of colon cancer to 5-FU by inhibiting E2F3 and SIRT1. The miR-34a mimic MRX34 is the first synthetic miRNA to have been entered into clinical trials. miR-21 prevents tumor cell stemness, invasion and drug resistance, which are required for the development of CRC. These findings suggest that miRNAs represent a focus in the research of novel cancer treatments aimed at sensitizing cancer cells to chemotherapeutic drugs. The aim of the present study was to review the functions of miRNAs and investigate the roles of miRNAs in CRC radioresistance or chemoresistance. Furthermore, the potential of including miRNAs in therapeutic strategies and using them as molecular biomarkers for predicting radiosensitivity and chemosensitivity was discussed.
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Affiliation(s)
- Qi-Bing Wu
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xin Sheng
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Ning Zhang
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Ming-Wei Yang
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Fan Wang
- Department of Radiotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
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31
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Liu TL, Liu MN, Xu XL, Liu WX, Shang PJ, Zhai XH, Xu H, Ding Y, Li YW, Wen AD. Differential gene expression profiles between two subtypes of ischemic stroke with blood stasis syndromes. Oncotarget 2017; 8:111608-111622. [PMID: 29340078 PMCID: PMC5762346 DOI: 10.18632/oncotarget.22877] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/17/2017] [Indexed: 12/16/2022] Open
Abstract
Ischemic stroke is a cerebrovascular thrombotic disease with high morbidity and mortality. Qi deficiency blood stasis (QDBS) and Yin deficiency blood stasis (YDBS) are the two major subtypes of ischemic stroke according to the theories of traditional Chinese medicine. This study was conducted to distinguish these two syndromes at transcriptomics level and explore the underlying mechanisms. Male rats were randomly divided into three groups: sham group, QDBS/MCAO group and YDBS/MCAO group. Morphological changes were assessed after 24 h of reperfusion. Microarray analysis with circulating mRNA was then performed to identify differential gene expression profile, gene ontology and pathway enrichment analyses were carried out to predict the gene function, gene co-expression and pathway networks were constructed to identify the hub biomarkers, which were further validated by western blotting and Tunel staining analysis. Three subsets of dysregulated genes were acquired, including 445 QDBS-specific genes, 490 YDBS-specific genes and 1676 blood stasis common genes. Our work reveals for the first time that T cell receptor, MAPK and apoptosis pathway were identified as the hub pathways based on the pathway networks, while Nfκb1, Egfr and Casp3 were recognized as the hub genes by co-expression networks. This research helps contribute to a clearer understanding of the pathological characteristics of ischemic stroke with QDBS and YDBS syndrome, the proposed biomarkers might provide insight into the accurate diagnose and proper treatment for ischemic stroke with blood stasis syndrome.
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Affiliation(s)
- Tian-Long Liu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacy, 25th Hospital of PLA, Jiuquan, China
| | - Min-Na Liu
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, China
| | - Xin-Liang Xu
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, China.,Department of Traumatic Surgery, Jining No.1 Peoples Hospital, Jining, China
| | - Wen-Xing Liu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Pei-Jin Shang
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiao-Hu Zhai
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Hang Xu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yi Ding
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yu-Wen Li
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacy, The First Affiliated Hospital of SooChow University, Suzhou, China
| | - Ai-Dong Wen
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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32
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Screening candidate microRNA-mRNA regulatory pairs for predicting the response to chemoradiotherapy in rectal cancer by a bioinformatics approach. Sci Rep 2017; 7:11312. [PMID: 28900297 PMCID: PMC5595906 DOI: 10.1038/s41598-017-11840-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/30/2017] [Indexed: 01/06/2023] Open
Abstract
Extensive efforts have been undertaken in search of biomarkers for predicting the chemoradiotherapy response in rectal cancer. However, most attention on treatment efficiency prediction in carcinoma is addicted to single or limited molecules. Network biomarkers are considered to outperform single molecules in predictive power. In this study, candidate microRNAs (miRNAs) were identified from the PubMed citations and miRNA expression profiles. Targets of miRNAs were obtained from four experimentally confirmed interactions and three computationally predicted databases. Functional enrichment analysis of all the targets revealed their associations with chemoradiotherapy response, indicating they could be promising biomarkers. Two lists of key target mRNAs of the candidate miRNAs were retrieved from protein–protein interaction (PPI) network and mRNA expression profiles, respectively. Pathway analysis and literature validation revealed that the mRNA lists were highly related to the ionizing radiation. The above miRNAs along with the key miRNA targets provide potential miRNA-mRNA regulatory pairs as network biomarkers in which all the network components may be used for predicting the chemoradiotherapy response. These results demonstrated that the network biomarkers could provide a useful model for predicting the chemoradiotherapy response and help in further understanding the molecular basis of response differences, which should be prioritized for further study.
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33
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Goblirsch M, Richtig G, Slaby O, Berindan-Neagoe I, Gerger A, Pichler M. MicroRNAs as a tool to aid stratification of colorectal cancer patients and to guide therapy. Pharmacogenomics 2017. [PMID: 28639472 DOI: 10.2217/pgs-2017-0004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer is a common type of malignant disease with high rates of morbidity and mortality. Although treatment options have been expanded over the last years, the mainstay of curative treatment remains surgical removal of the tumor-bearing organ. Systemic treatment options include classic cytotoxic drugs as well as some biological agents. Noncoding RNAs are an evolving field in cancer diagnosis, prognosis and possible treatment. Noncoding miRNAs are small molecules with huge impact on gene expression. They have been a substantial part of cancer research for more than a decade. In this review article, the current knowledge of miRNAs and colorectal cancer diagnosis, prognosis and novel or evolving therapeutic concepts are discussed. Examples of how miRNAs might change the management of the disease will be described.
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Affiliation(s)
- Matthew Goblirsch
- College of Science, Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Georg Richtig
- Institute of Experimental & Clinical Pharmacology, Medical University of Graz, 8010 Graz, Austria
| | - Ondrej Slaby
- Molecular Oncology II - Solid Cancers, Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ioana Berindan-Neagoe
- Department of Functional Genomics, The Oncology Institute, Cluj-Napoca, Romania Department of Immunology & Research Center for Functional Genomics, Biomedicine & Translational Medicine University of Medicine & Pharmacy 'I. Hatieganu' 400337 Cluj-Napoca România
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
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34
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Kim SW. [The Role of MicroRNAs in Colorectal Cancer]. THE KOREAN JOURNAL OF GASTROENTEROLOGY = TAEHAN SOHWAGI HAKHOE CHI 2017; 69:206-211. [PMID: 28449421 DOI: 10.4166/kjg.2017.69.4.206] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer related deaths in the world. Many oncogenes and tumor suppressor genes are involved in the development of CRC. MicroRNAs (miRNAs) are a class of small, non-coding, endogenous RNAs in animals and plants. Recent studies have shown that miRNAs are associated with the mediation process of tumorigenesis, including inflammation, cell cycle, stress response, differentiation, apoptosis, migration, and invasion in cancer. These miRNAs have been linked to the development of CRC and recently studied as new potential biomarkers in the diagnosis and treatment for CRC. Specific miRNAs expression patterns help distinguish CRC from other colon-related diseases, and miRNAs can target the oncogenes and regulatory molecular pathways. Recent studies have demonstrated the restoration of tumor suppressive miRNAs and inhibition of oncogenic miRNAs for CRC treatment. Herein, we describe the diagnostic and therapeutic roles of miRNAs in CRC.
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Affiliation(s)
- Sang Wook Kim
- Division of Gastroenterology, Department of Internal Medicine, Chonbuk National University Medical School, Jeonju, Korea
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35
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Gastric Cancer Associated Genes Identified by an Integrative Analysis of Gene Expression Data. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7259097. [PMID: 28232943 PMCID: PMC5292384 DOI: 10.1155/2017/7259097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 01/13/2023]
Abstract
Gastric cancer is one of the most severe complex diseases with high morbidity and mortality in the world. The molecular mechanisms and risk factors for this disease are still not clear since the cancer heterogeneity caused by different genetic and environmental factors. With more and more expression data accumulated nowadays, we can perform integrative analysis for these data to understand the complexity of gastric cancer and to identify consensus players for the heterogeneous cancer. In the present work, we screened the published gene expression data and analyzed them with integrative tool, combined with pathway and gene ontology enrichment investigation. We identified several consensus differentially expressed genes and these genes were further confirmed with literature mining; at last, two genes, that is, immunoglobulin J chain and C-X-C motif chemokine ligand 17, were screened as novel gastric cancer associated genes. Experimental validation is proposed to further confirm this finding.
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36
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Lin Y, Chen J, Shen B. Interactions Between Genetics, Lifestyle, and Environmental Factors for Healthcare. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1005:167-191. [PMID: 28916933 DOI: 10.1007/978-981-10-5717-5_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The occurrence and progression of diseases are strongly associated with a combination of genetic, lifestyle, and environmental factors. Understanding the interplay between genetic and nongenetic components provides deep insights into disease pathogenesis and promotes personalized strategies for people healthcare. Recently, the paradigm of systems medicine, which integrates biomedical data and knowledge at multidimensional levels, is considered to be an optimal way for disease management and clinical decision-making in the era of precision medicine. In this chapter, epigenetic-mediated genetics-lifestyle-environment interactions within specific diseases and different ethnic groups are systematically discussed, and data sources, computational models, and translational platforms for systems medicine research are sequentially presented. Moreover, feasible suggestions on precision healthcare and healthy longevity are kindly proposed based on the comprehensive review of current studies.
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Affiliation(s)
- Yuxin Lin
- Center for Systems Biology, Soochow University, No.1 Shizi Street, Suzhou, Jiangsu, 215006, China
| | - Jiajia Chen
- School of Chemistry, Biology and Materials Engineering, Suzhou University of Science and Technology, No.1 Kerui road, Suzhou, Jiangsu, 215011, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, No.1 Shizi Street, Suzhou, Jiangsu, 215006, China. .,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China. .,Medical College of Guizhou University, Guiyang, 550025, China.
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