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Jarmakiewicz-Czaja S, Gruszecka J, Filip R. The Diagnosis of Intestinal Fibrosis in Crohn's Disease-Present and Future. Int J Mol Sci 2024; 25:6935. [PMID: 39000043 PMCID: PMC11241173 DOI: 10.3390/ijms25136935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Crohn's disease (CD) progresses with periods of remission and exacerbations. During exacerbations, chronic inflammation leads to tissue destruction. As a result, intestinal fibrosis may develop in response to the ongoing inflammatory process. Fibrosis in CD should be considered the result of the response of the intestinal wall (over) to the presence of inflammation in the deep structures of the intestinal wall. In the absence of ideal noninvasive methods, endoscopic evaluation in combination with biopsy, histopathological analysis, stool analysis, and blood analysis remains the gold standard for assessing both inflammation and fibrosis in CD. On the contrary, the ability to identify markers of intestinal fibrosis would help to develop new diagnostic and therapeutic methods to detect early stages of fibrosis. It is speculated that miRNAs may, in the future, become biomarkers for early noninvasive diagnosis in the treatment of intestinal fibrosis. The purpose of this review is to summarise existing diagnostic methods for Crohn's disease and present recent scientific reports on molecular testing.
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Affiliation(s)
| | - Jolanta Gruszecka
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Department of Clinical Microbiology, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
| | - Rafał Filip
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Department of Gastroenterology with IBD Unit, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
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2
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Liu Z, Xu M, Yu Q, Song J, Lin Q, Huang S, Chen Z, Huang Y, Chi P. Fibrosis signature of anastomotic margins for predicting anastomotic stenosis in rectal cancer with neoadjuvant chemoradiotherapy and sphincter-preserving surgery. Gastroenterol Rep (Oxf) 2024; 12:goae012. [PMID: 38510669 PMCID: PMC10950477 DOI: 10.1093/gastro/goae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/27/2023] [Accepted: 12/31/2023] [Indexed: 03/22/2024] Open
Abstract
Background Radiation-induced colorectal fibrosis (RICF) is a common pathological alteration among patients with rectal cancer undergoing neoadjuvant chemoradiotherapy (nCRT). Anastomotic stenosis (AS) causes symptoms and negatively impacts patients' quality of life and long-term survival. In this study, we aimed to evaluate the fibrosis signature of RICF and develop a nomogram to predict the risk of AS in patients with rectal cancer undergoing nCRT. Methods Overall, 335 pairs of proximal and distal margins were collected and randomly assigned at a 7:3 ratio to the training and testing cohorts. The RICF score was established to evaluate the fibrosis signature in the anastomotic margins. A nomogram based on the RICF score for AS was developed and evaluated by using the area under the curve, decision curve analysis, and the DeLong test. Results The training cohort included 235 patients (161 males [68.51%]; mean age, 59.61 years) with an occurrence rate of AS of 17.4%, whereas the testing cohort included 100 patients (72 males [72.00%]; mean age, 57.17 years) with an occurrence rate of AS of 11%. The RICF total score of proximal and distal margins was significantly associated with AS (odds ratio, 3.064; 95% confidence interval [CI], 2.200-4.268; P < 0.001). Multivariable analysis revealed that the RICF total score, neoadjuvant radiotherapy, and surgical approach were independent predictors for AS. The nomogram demonstrated good discrimination in the training cohort (area under the receiver-operating characteristic curve, 0.876; 95% CI, 0.816-0.937), with a sensitivity of 68.3% (95% CI, 51.9%-81.9%) and a specificity of 85.5% (95% CI, 78.7%-89.3%). Similar results were observed in the testing cohort. Conclusions This study results suggest that the RICF total score of anastomotic margins is an independent predictor for AS. The prediction model developed based on the RICF total score may be useful for individualized AS risk prediction in patients with rectal cancer undergoing nCRT and sphincter-preserving surgery.
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Affiliation(s)
- Zhun Liu
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
| | - Meifang Xu
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
| | - Qian Yu
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
| | - Jianyuan Song
- Department of Radiation Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
| | - Qili Lin
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
| | - Shenghui Huang
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
| | - Zhifen Chen
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
| | - Ying Huang
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
| | - Pan Chi
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, P. R. China
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Peng L, Huang L, Su Q, Tian G, Chen M, Han G. LDA-VGHB: identifying potential lncRNA-disease associations with singular value decomposition, variational graph auto-encoder and heterogeneous Newton boosting machine. Brief Bioinform 2023; 25:bbad466. [PMID: 38127089 PMCID: PMC10734633 DOI: 10.1093/bib/bbad466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/05/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) participate in various biological processes and have close linkages with diseases. In vivo and in vitro experiments have validated many associations between lncRNAs and diseases. However, biological experiments are time-consuming and expensive. Here, we introduce LDA-VGHB, an lncRNA-disease association (LDA) identification framework, by incorporating feature extraction based on singular value decomposition and variational graph autoencoder and LDA classification based on heterogeneous Newton boosting machine. LDA-VGHB was compared with four classical LDA prediction methods (i.e. SDLDA, LDNFSGB, IPCARF and LDASR) and four popular boosting models (XGBoost, AdaBoost, CatBoost and LightGBM) under 5-fold cross-validations on lncRNAs, diseases, lncRNA-disease pairs and independent lncRNAs and independent diseases, respectively. It greatly outperformed the other methods with its prominent performance under four different cross-validations on the lncRNADisease and MNDR databases. We further investigated potential lncRNAs for lung cancer, breast cancer, colorectal cancer and kidney neoplasms and inferred the top 20 lncRNAs associated with them among all their unobserved lncRNAs. The results showed that most of the predicted top 20 lncRNAs have been verified by biomedical experiments provided by the Lnc2Cancer 3.0, lncRNADisease v2.0 and RNADisease databases as well as publications. We found that HAR1A, KCNQ1DN, ZFAT-AS1 and HAR1B could associate with lung cancer, breast cancer, colorectal cancer and kidney neoplasms, respectively. The results need further biological experimental validation. We foresee that LDA-VGHB was capable of identifying possible lncRNAs for complex diseases. LDA-VGHB is publicly available at https://github.com/plhhnu/LDA-VGHB.
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
- College of Life Sciences and Chemistry, Hunan University of Technology, 412007, Hunan, China
| | - Liangliang Huang
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
| | - Qiongli Su
- Department of Pharmacy, the Affiliated Zhuzhou Hospital Xiangya Medical College CSU, 412007, Hunan, China
| | - Geng Tian
- Geneis (Beijing) Co. Ltd, China, 100102, Beijing, China
| | - Min Chen
- School of Computer Science, Hunan Institute of Technology, 421002, No. 18 Henghua Road, Zhuhui District, Hengyang, Hunan, China
| | - Guosheng Han
- School of Mathematics and Computational Science, Xiangtan University, 411105, Yuhu District, Xiangtan, Hunan, China
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, 411105, Yuhu District, Xiangtan, Hunan, China
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4
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Lu Q, Liang Y, Meng X, Zhao Y, Fan H, Hou S. The Role of Long Noncoding RNAs in Intestinal Health and Diseases: A Focus on the Intestinal Barrier. Biomolecules 2023; 13:1674. [PMID: 38002356 PMCID: PMC10669616 DOI: 10.3390/biom13111674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/04/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The gut is the body's largest immune organ, and the intestinal barrier prevents harmful substances such as bacteria and toxins from passing through the gastrointestinal mucosa. Intestinal barrier dysfunction is closely associated with various diseases. However, there are currently no FDA-approved therapies targeting the intestinal epithelial barriers. Long noncoding RNAs (lncRNAs), a class of RNA transcripts with a length of more than 200 nucleotides and no coding capacity, are essential for the development and regulation of a variety of biological processes and diseases. lncRNAs are involved in the intestinal barrier function and homeostasis maintenance. This article reviews the emerging role of lncRNAs in the intestinal barrier and highlights the potential applications of lncRNAs in the treatment of various intestinal diseases by reviewing the literature on cells, animal models, and clinical patients. The aim is to explore potential lncRNAs involved in the intestinal barrier and provide new ideas for the diagnosis and treatment of intestinal barrier damage-associated diseases in the clinical setting.
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Affiliation(s)
- Qianying Lu
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Yangfan Liang
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Xiangyan Meng
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Yanmei Zhao
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Haojun Fan
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Shike Hou
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
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Kazmierczak de Camargo JP, Prezia GNDB, Shiokawa N, Sato MT, Rosati R, Beate Winter Boldt A. New Insights on the Regulatory Gene Network Disturbed in Central Areolar Choroidal Dystrophy-Beyond Classical Gene Candidates. Front Genet 2022; 13:886461. [PMID: 35656327 PMCID: PMC9152281 DOI: 10.3389/fgene.2022.886461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Central areolar choroidal dystrophy (CACD) is a rare hereditary disease that mainly affects the macula, resulting in progressive and usually profound visual loss. Being part of congenital retinal dystrophies, it may have an autosomal dominant or recessive inheritance and, until now, has no effective treatment. Given the shortage of genotypic information about the disease, this work systematically reviews the literature for CACD-causing genes. Three independent researchers selected 33 articles after carefully searching and filtering the Scielo, Pubmed, Lilacs, Web of Science, Scopus, and Embase databases. Mutations of six genes (PRPH2, GUCA1A, GUCY2D, CDHR1, ABCA4, and TTLL5) are implicated in the monogenic dominant inheritance of CACD. They are functionally related to photoreceptors (either in the phototransduction process, as in the case of GUCY2D, or the recovery of retinal photodegradation in photoreceptors for GUCA1A, or the formation and maintenance of specific structures within photoreceptors for PRPH2). The identified genetic variants do not explain all observed clinical features, calling for further whole-genome and functional studies for this disease. A network analysis with the CACD-related genes identified in the systematic review resulted in the identification of another 20 genes that may influence CACD onset and symptoms. Furthermore, an enrichment analysis allowed the identification of 13 transcription factors and 4 long noncoding RNAs interacting with the products of the previously mentioned genes. If mutated or dysregulated, they may be directly involved in CACD development and related disorders. More than half of the genes identified by bioinformatic tools do not appear in commercial gene panels, calling for more studies about their role in the maintenance of the retina and phototransduction process, as well as for a timely update of these gene panels.
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Affiliation(s)
| | - Giovanna Nazaré de Barros Prezia
- Post-Graduation Program in Biotechnology Applied to Child and Adolescent Health, Faculdades Pequeno Príncipe and Pelé Pequeno Príncipe Research Institute, Curitiba, Brazil
| | - Naoye Shiokawa
- Retina and Vitreo Consulting Eye Clinic, Curitiba, Brazil
| | - Mario Teruo Sato
- Retina and Vitreo Consulting Eye Clinic, Curitiba, Brazil.,Department of Ophthalmol/Otorhinolaryngology, Federal University of Paraná, Curitiba, Brazil
| | - Roberto Rosati
- Post-Graduation Program in Biotechnology Applied to Child and Adolescent Health, Faculdades Pequeno Príncipe and Pelé Pequeno Príncipe Research Institute, Curitiba, Brazil
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6
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Wang Y, Huang B, Jin T, Ocansey DKW, Jiang J, Mao F. Intestinal Fibrosis in Inflammatory Bowel Disease and the Prospects of Mesenchymal Stem Cell Therapy. Front Immunol 2022; 13:835005. [PMID: 35370998 PMCID: PMC8971815 DOI: 10.3389/fimmu.2022.835005] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/26/2022] [Indexed: 12/12/2022] Open
Abstract
Intestinal fibrosis is an important complication of inflammatory bowel disease (IBD). In the course of the development of fibrosis, certain parts of the intestine become narrowed, significantly destroying the structure and function of the intestine and affecting the quality of life of patients. Chronic inflammation is an important initiating factor of fibrosis. Unfortunately, the existing anti-inflammatory drugs cannot effectively prevent and alleviate fibrosis, and there is no effective anti-fibrotic drug, which makes surgical treatment the mainstream treatment for intestinal fibrosis and stenosis. Mesenchymal stem cells (MSCs) are capable of tissue regeneration and repair through their self-differentiation, secretion of cytokines, and secretion of extracellular vesicles. MSCs have been shown to play an important therapeutic role in the fibrosis of many organs. However, the role of MSC in intestinal fibrosis largely remained unexplored. This review summarizes the mechanism of intestinal fibrosis, including the role of immune cells, TGF-β, and the gut microbiome and metabolites. Available treatment options for fibrosis, particularly, MSCs are also discussed.
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Affiliation(s)
- Yifei Wang
- Aoyang Institute of Cancer, Affiliated Aoyang Hospital of Jiangsu University, Suzhou, China
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Bin Huang
- Aoyang Institute of Cancer, Affiliated Aoyang Hospital of Jiangsu University, Suzhou, China
- General Surgery Department, Affiliated Aoyang Hospital of Jiangsu University, Suzhou, China
| | - Tao Jin
- Department of Gastrointestinal and Endoscopy, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
- Directorate of University Health Services, University of Cape Coast, Cape Coast, Ghana
| | - Jiajia Jiang
- Aoyang Institute of Cancer, Affiliated Aoyang Hospital of Jiangsu University, Suzhou, China
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
- *Correspondence: Jiajia Jiang, ; Fei Mao,
| | - Fei Mao
- Aoyang Institute of Cancer, Affiliated Aoyang Hospital of Jiangsu University, Suzhou, China
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
- *Correspondence: Jiajia Jiang, ; Fei Mao,
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Abstract
PURPOSE This article will briefly review the origins and evolution of functional genomics, first describing the experimental technology, and then some of the approaches applied to data analysis and visualization. It will emphasize application of functional genomics to radiation biology, using examples from the author's work to illustrate several key types of analysis. It concludes with a look at non-coding RNA, alternative reading of the genome, and single-cell transcriptomics, some of the innovative areas that may help to shape future research in radiation biology and oncology. CONCLUSIONS Transcriptomic approaches have provided insight into many areas of radiation biology and medicine, and innovations in technology and data analysis approaches promise continued contributions to radiation science in the future.
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Su F, Duan J, Zhu J, Fu H, Zheng X, Ge C. Long non‑coding RNA nuclear paraspeckle assembly transcript 1 regulates ionizing radiation‑induced pyroptosis via microRNA‑448/gasdermin E in colorectal cancer cells. Int J Oncol 2021; 59:79. [PMID: 34476497 PMCID: PMC8448542 DOI: 10.3892/ijo.2021.5259] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/16/2021] [Indexed: 12/11/2022] Open
Abstract
Pyroptosis is mediated by gasdermins and serves a critical role in ionizing radiation (IR)-induced damage in normal tissues, but its role in cancer radiotherapy and underlying mechanisms remains unclear. Long non-coding (lnc) RNAs serve important roles in regulating the radiosensitivity of cancer cells. The present study aimed to investigate the mechanistic involvement of lncRNAs in IR-induced pyroptosis in human colorectal cancer HCT116 cells. LncRNA, microRNA (miR)-448 and gasdermin E (GSDME) levels were evaluated using reverse transcription-quantitative polymerase chain reaction. Protein expression and activation of gasdermins were measured using western blotting. The binding association between miR-448 and GSDME was assessed using the dual-luciferase reporter assay. Pyroptosis was examined using phase-contrast microscopy, flow cytometry, Cell Counting Kit-8 assay and lactate dehydrogenase release assay. IR dose-dependently induced GSDME-mediated pyroptosis in HCT116 cells. GSDME was identified as a downstream target of miR-448. LncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) was upregulated in response to IR and enhanced GSDME expression by negatively regulating miR-448 expression. Notably, NEAT1 knockdown suppressed IR-induced pyroptosis, full-length GSDME expression and GSDME cleavage compared with that in irradiated cells. In addition, NEAT1 knockdown rescued the IR-induced decrease in cell viability in HCT116 cells. The findings of the present study indicated that lncRNA NEAT1 modulates IR-induced pyroptosis and viability in HCT116 cells via miR-448 by regulating the expression, but not activation of GSDME. The present study provides crucial mechanistic insight into the potential role of lncRNA NEAT1 in IR-induced pyroptosis.
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Affiliation(s)
- Fei Su
- Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Junzhao Duan
- Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Jie Zhu
- Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Hanjiang Fu
- Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Xiaofei Zheng
- Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Changhui Ge
- Department of Experimental Hematology and Biochemistry, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
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May JM, Bylicky M, Chopra S, Coleman CN, Aryankalayil MJ. Long and short non-coding RNA and radiation response: a review. Transl Res 2021; 233:162-179. [PMID: 33582242 PMCID: PMC8475769 DOI: 10.1016/j.trsl.2021.02.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 12/12/2022]
Abstract
Once thought of as arising from "junk DNA," noncoding RNAs (ncRNAs) have emerged as key molecules in cellular processes and response to stress. From diseases such as cancer, coronary artery disease, and diabetes to the effects of ionizing radiation (IR), ncRNAs play important roles in disease progression and as biomarkers of damage. Noncoding RNAs regulate cellular processes by competitively binding DNA, mRNA, proteins, and other ncRNAs. Through these interactions, specific ncRNAs can modulate the radiosensitivity of cells and serve as diagnostic and prognostic biomarkers of radiation damage, whether from incidental exposure in radiotherapy or in accidental exposure scenarios. Analysis of RNA expression after radiation exposure has shown alterations not only in mRNAs, but also in ncRNAs (primarily miRNA, circRNA, and lncRNA), implying an important role in cellular stress response. Due to their abundance and stability in serum and other biofluids, ncRNAs also have great potential as minimally invasive biomarkers with advantages over current biodosimetry methods. Several studies have examined changes in ncRNA expression profiles in response to IR and other forms of oxidative stress. Furthermore, some studies have reported modulation of radiosensitivity by altering expression levels of these ncRNAs. This review discusses the roles of ncRNAs in the radiation response and evaluates prior research on ncRNAs as biomarkers of radiation damage. Future directions and applications of ncRNAs in radiation research are introduced, including the potential for a clinical ncRNA assay for assessing radiation damage and for the therapeutic use of RNA interference (RNAi).
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Affiliation(s)
- Jared M May
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Michelle Bylicky
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sunita Chopra
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - C Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Molykutty J Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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Wu QW, Xia JF, Ni JC, Zheng CH. GAERF: predicting lncRNA-disease associations by graph auto-encoder and random forest. Brief Bioinform 2021; 22:6067881. [PMID: 33415333 DOI: 10.1093/bib/bbaa391] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Predicting disease-related long non-coding RNAs (lncRNAs) is beneficial to finding of new biomarkers for prevention, diagnosis and treatment of complex human diseases. In this paper, we proposed a machine learning techniques-based classification approach to identify disease-related lncRNAs by graph auto-encoder (GAE) and random forest (RF) (GAERF). First, we combined the relationship of lncRNA, miRNA and disease into a heterogeneous network. Then, low-dimensional representation vectors of nodes were learned from the network by GAE, which reduce the dimension and heterogeneity of biological data. Taking these feature vectors as input, we trained a RF classifier to predict new lncRNA-disease associations (LDAs). Related experiment results show that the proposed method for the representation of lncRNA-disease characterizes them accurately. GAERF achieves superior performance owing to the ensemble learning method, outperforming other methods significantly. Moreover, case studies further demonstrated that GAERF is an effective method to predict LDAs.
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Affiliation(s)
- Qing-Wen Wu
- Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, College of Computer Science and Technology, Anhui University, Hefei, China
| | - Jun-Feng Xia
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Jian-Cheng Ni
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, China
| | - Chun-Hou Zheng
- Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, College of Computer Science and Technology, Anhui University, Hefei, China
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Feng Y, Dramani Maman ST, Zhu X, Liu X, Bongolo CC, Liang C, Tu J. Clinical value and potential mechanisms of LINC00221 in hepatocellular carcinoma based on integrated analysis. Epigenomics 2021; 13:299-317. [PMID: 33406920 DOI: 10.2217/epi-2020-0363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aims:This study aimed to unveil the functional roles of LINC00221 in hepatocellular carcinoma (HCC). Materials and methods:A discovery cohort and a validation cohort were respectively used to identify and verify the clinical value of LINC00221 in HCC. Bioinformatics analysis was performed to explore its potential mechanisms. Results:LINC00221 was upregulated in HCC tissues and serum samples. Survival analysis and receiver operating characteristic curve further revealed its prognostic and diagnostic roles. Exploration of the mechanism showed that LINC00221 might exert a pro-cancer role via the lncRNA-miRNA-mRNA network.Conclusions: Our study reveals that upregulated LINC00221 can serve as a potential diagnostic and prognostic biomarker and provides novel clues as to the role of LINC00221 in HCC.
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Affiliation(s)
- Yanlin Feng
- Program & Department of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Souraka Tapara Dramani Maman
- Program & Department of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xinyu Zhu
- Program & Department of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xuefang Liu
- Department of Clinical Laboratory, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Christian Cedric Bongolo
- Program & Department of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Chunzi Liang
- Program & Department of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jiancheng Tu
- Program & Department of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
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12
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Zhou LY, Lin SN, Rieder F, Chen MH, Zhang SH, Mao R. Noncoding RNAs as Promising Diagnostic Biomarkers and Therapeutic Targets in Intestinal Fibrosis of Crohn's Disease: The Path From Bench to Bedside. Inflamm Bowel Dis 2020; 27:971-982. [PMID: 33324986 PMCID: PMC8344842 DOI: 10.1093/ibd/izaa321] [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: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Fibrosis is a major pathway to organ injury and failure, accounting for more than one-third of deaths worldwide. Intestinal fibrosis causes irreversible and serious clinical complications, such as strictures and obstruction, secondary to a complex pathogenesis. Under the stimulation of profibrotic soluble factors, excessive activation of mesenchymal cells causes extracellular matrix deposition via canonical transforming growth factor-β/Smads signaling or other pathways (eg, epithelial-to-mesenchymal transition and endothelial-to-mesenchymal transition) in intestinal fibrogenesis. In recent studies, the importance of noncoding RNAs (ncRNAs) stands out in fibrotic diseases in that ncRNAs exhibit a remarkable variety of biological functions in modulating the aforementioned fibrogenic responses. In this review, we summarize the role of ncRNAs, including the emerging long ncRNAs and circular RNAs, in intestinal fibrogenesis. Notably, the translational potential of ncRNAs as diagnostic biomarkers and therapeutic targets in the management of intestinal fibrosis is discussed based on clinical trials from fibrotic diseases in other organs. The main points of this review include the following: • Characteristics of ncRNAs and mechanisms of intestinal fibrogenesis • Wide participation of ncRNAs (especially the emerging long ncRNAs and circular RNAs) in intestinal fibrosis, including transforming growth factor-β signaling, epithelial-to-mesenchymal transition/endothelial-to-mesenchymal transition, and extracellular matrix remodeling • Translational potential of ncRNAs in the diagnosis and treatment of intestinal fibrosis based on clinical trials from fibrotic diseases in other organs.
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Affiliation(s)
- Long-Yuan Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Si-Nan Lin
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Florian Rieder
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Min-Hu Chen
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Sheng-Hong Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People’s Republic of China,Address correspondence to: Ren Mao, MD, Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan Road 2nd, Guangzhou 510080, People’s Republic of China; Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, OH (); and Sheng-Hong Zhang, MD, Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan Road 2nd, Guangzhou 510080, People’s Republic of China ()
| | - Ren Mao
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People’s Republic of China,Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA,Address correspondence to: Ren Mao, MD, Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan Road 2nd, Guangzhou 510080, People’s Republic of China; Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, OH (); and Sheng-Hong Zhang, MD, Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan Road 2nd, Guangzhou 510080, People’s Republic of China ()
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Guo L, Chen J, Liu D, Liu L. OIP5-AS1/miR-137/ZNF217 Axis Promotes Malignant Behaviors in Epithelial Ovarian Cancer. Cancer Manag Res 2020; 12:6707-6717. [PMID: 32801903 PMCID: PMC7413701 DOI: 10.2147/cmar.s237726] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/08/2020] [Indexed: 01/09/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) have been reported to play crucial regulatory roles in cellular activities and are associated with the carcinogenesis of various diseases. OIP5-AS1, as a novel lncRNA, function in epithelial ovarian cancer (EOC) still remains unclear. Material and Methods qRT-PCR and Western blot analyses were performed to measure relevant expression, as needed. A series of functional experiments were performed to determine the role of OIP5-AS1 in EOC cells. Luciferase report, RNA pull down and RIP assays were performed to testify the interaction between relevant RNAs. Results We found that OIP5-AS1 was significantly overexpressed in EOC. Knockdown of OIP5-AS1 inhibited cell proliferation, migration, invasion and epithelial–mesenchymal transition (EMT) process, yet facilitated apoptosis in vitro. OIP5-AS1 functioned as a competing endogenous RNA (ceRNA) to elevate ZNF217 expression through sponging miR-137. Furthermore, miR-137 inhibition and ZNF217 upregulation can reverse the effects of silencing OIP5-AS1 on the cellular activities of ovarian cancer cells. Also, depleted OIP5-AS1 hindered tumor growth and metastasis in vivo. Conclusion OIP5-AS1 regulated ovarian cancer progression via modulating miR-137/ZNF217 signaling, suggesting that targeting OIP5-AS1 could be conducive to EOC clinical treatment.
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Affiliation(s)
- Linlin Guo
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Jinzhou Medical University, Jinnzhou, Liaoning, People's Republic of China
| | - Jiabao Chen
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Jinzhou Medical University, Jinnzhou, Liaoning, People's Republic of China
| | - Dong Liu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Jinzhou Medical University, Jinnzhou, Liaoning, People's Republic of China
| | - Lili Liu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Jinzhou Medical University, Jinnzhou, Liaoning, People's Republic of China
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MicroRNA-16, via FGF2 Regulation of the ERK/MAPK Pathway, Is Involved in the Magnesium-Promoted Osteogenic Differentiation of Mesenchymal Stem Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3894926. [PMID: 32411326 PMCID: PMC7201663 DOI: 10.1155/2020/3894926] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/16/2020] [Indexed: 12/26/2022]
Abstract
microRNAs (miRNAs) participate in the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). However, few reports have discussed the effect of miRNAs on the magnesium chloride (MgCl2)-induced promotion of osteogenic differentiation of BMSCs, a process involved in the healing of bone tissue. As determined in the present investigation, MgCl2 decreased miR-16 levels; increased levels of fibroblast growth factor 2 (FGF2), p-p38, and p-ERK; and promoted the osteogenic differentiation of BMSCs. Enhancement of miR-16 levels by an miR-16 mimic blocked these MgCl2-induced changes. Moreover, luciferase reporter assays confirmed that miR-16 binds to the 3'UTR region of FGF2 mRNA. Down-regulation of FGF2 blocked the MgCl2-induced increases of p-p38 and p-ERK and the promotion of the osteogenic differentiation of BMSCs. Furthermore, over-expression of miR-16 attenuated the MgCl2-induced overproduction of p-p38 and p-ERK1/2 and the high levels of osteogenic differentiation, effects that were reversed by elevated expression of FGF2. In summary, the present findings provide a mechanism by which miR-16 regulates MgCl2-induced promotion of osteogenic differentiation by targeting FGF2-mediated activation of the ERK/MAPK pathway.
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Chen X, Li Z, Cheng Y, Kardami E, Loh YP. Low and High Molecular Weight FGF-2 Have Differential Effects on Astrocyte Proliferation, but Are Both Protective Against Aβ-Induced Cytotoxicity. Front Mol Neurosci 2020; 12:328. [PMID: 32038161 PMCID: PMC6992557 DOI: 10.3389/fnmol.2019.00328] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022] Open
Abstract
Astrocytes are the most abundant type of glial cells in the brain, and they play a key role in Alzheimer’s disease (AD). Fibroblast Growth Factor-2 (FGF-2) has been implicated as a potential therapeutic agent for treating AD. In the present study, we investigated the protective effects of low molecular weight (LMW; 17 KDa) and high molecular weight (HMW; 23 KDa) forms of FGF-2 on Aβ1–42-induced toxicity, and proliferation in astrocytes. We show that both isoforms of FGF-2 have similar protective effects against Aβ1–42-induced cytotoxicity in primary cultured cortical astrocytes as measured by Lactate Dehydrogenase (LDH) release assay. Additionally, 17 KDa FGF-2 significantly promoted astrocyte proliferation as measured by Trypan Blue, DRAQ5 and 5-ethynyl-2’-deoxyuridine (EdU) staining, but not 23 kDa FGF-2. Furthermore, our results demonstrated that AKT signaling pathway was required for the protective and proliferative effects of FGF-2. Downstream effector studies indicated that 17 kDa FGF-2 promoted astrocyte proliferation by enhanced expression of c-Myc, Cyclin D1, Cyclin E. Furthermore, our data suggested that Cyclin D1 was required for the proliferative effect of LMW FGF2 in astrocytes. Taken together, our findings provide important information for the similarities and differences between 23 kDa and17 kDa isoforms of FGF-2 on astrocyte survival and proliferation.
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Affiliation(s)
- Xi Chen
- Key Laboratory of Ethnomedicine for Ministry of Education, Center on Translational Neuroscience, College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Zhaojin Li
- Section on Cellular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Yong Cheng
- Key Laboratory of Ethnomedicine for Ministry of Education, Center on Translational Neuroscience, College of Life and Environmental Sciences, Minzu University of China, Beijing, China.,Section on Cellular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Elissavet Kardami
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Y Peng Loh
- Section on Cellular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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