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Andrade R, Ribeiro IP, Carreira IM, Tralhão JG. The Diagnostic and Prognostic Potentials of Non-Coding RNA in Cholangiocarcinoma. Int J Mol Sci 2024; 25:6002. [PMID: 38892191 PMCID: PMC11172565 DOI: 10.3390/ijms25116002] [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: 04/17/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Cholangiocarcinoma (CCA) is a rare biliary tract tumor with high malignancy. CCA is the second most common primary hepatobiliary cancer after hepatocarcinoma. Despite its rarity, the incidence of CCA is steadily increasing globally. Most patients with CCA are asymptomatic in the early stages, resulting in a late-stage diagnosis and poor prognosis. Finding reliable biomarkers is essential to improve CCA's early diagnosis and survival rate. Non-coding RNAs (ncRNAs) are non-protein coding RNAs produced by genomic transcription. This includes microRNAs, long non-coding RNAs, and circular RNAs. ncRNAs have multiple functions in regulating gene expression and are crucial for maintaining normal cell function and developing diseases. Many studies have shown that aberrantly expressed ncRNAs can regulate the occurrence and development of CCA. ncRNAs can be easily extracted and detected through tumor tissue and liquid biopsies, representing a potential tool for diagnosing and prognosis CCA. This review will provide a detailed update on the diagnostic and prognostic potentials of lncRNAs and cirRNAs as biomarkers in CCA.
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Affiliation(s)
- Rita Andrade
- Surgery Department, Centro Hospitalar e Universitario de Coimbra EPE (CHUC), 3000-075 Coimbra, Portugal;
- Clinical Academic Center of Coimbra, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Clinical Academic Center of Coimbra, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (CBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Isabel Marques Carreira
- Clinical Academic Center of Coimbra, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (CBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
| | - José Guilherme Tralhão
- Surgery Department, Centro Hospitalar e Universitario de Coimbra EPE (CHUC), 3000-075 Coimbra, Portugal;
- Clinical Academic Center of Coimbra, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (CBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-548 Coimbra, Portugal
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Shobeiri P, Arabzadeh Bahri R, Khadembashiri MM, Khadembashiri MA, Maleki S, Eslami M, Khalili Dehkordi M, Behnoush AH, Rezaei N. Role of long non-coding RNAs in cholangiocarcinoma: A systematic review and meta-analysis. Cancer Rep (Hoboken) 2024; 7:e2029. [PMID: 38517409 PMCID: PMC10959185 DOI: 10.1002/cnr2.2029] [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: 08/04/2023] [Revised: 02/12/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA), as a rare malignancy of the biliary tree, has a poor prognosis most of the time. CCA is highly epigenetically regulated and several long non-coding RNAs (lncRNA) have been investigated to have a diagnostic and prognostic role in CCA. The current study aimed to assess the studies finding relevant lncRNAs in CCA systematically. METHODS International databases, including PubMed, Cochrane Library, and Embase, were comprehensively searched in order to identify studies investigating any lncRNA in CCA. After screening by title/abstract and full-text, necessary data were extracted. Random-effect meta-analysis was performed for pooling the areas under the curve (AUCs), specificity, and sensitivity of lncRNAs for the diagnosis of CCA. RESULTS A total of 33 studies were chosen to be included in the final analysis, comprised of 2677 patients. Meta-analysis of AUCs for evaluation of CCA resulted in pooled AUC of 0.79 (95% CI: 0.75-0.82; I2 = 69.11, p < .01). Additionally, overall sensitivity of 0.80 (95% CI 0.75-0.84) and specificity of 0.77 (95% CI: 0.68-0.84) were observed. Measurement of lncRANs in the assessment of CCA also improved overall survival significantly (effect size 1.61, 95% CI: 1.39-1.82). A similar result was found for progression-free survival (effect size 1.57, 95% CI: 1.20-1.93). CONCLUSION Based on our findings, lncRNAs showed promising results as biomarkers in the diagnosis of CCA since they had acceptable sensitivity and specificity, in addition to the fact that improved survival in this poor prognosis cancer. Further studies might be needed to address this issue and find the best clinically useful lncRNA.
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Affiliation(s)
- Parnian Shobeiri
- School of medicineTehran University of Medical SciencesTehranIran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), TehranIran
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical CenterTehran University of Medical SciencesTehranIran
| | - Razman Arabzadeh Bahri
- School of medicineTehran University of Medical SciencesTehranIran
- Urology Research CenterTehran University of Medical SciencesTehranIran
| | - Mohamad Mehdi Khadembashiri
- Neuromusculoskeletal Research CenterIran University of Medical SciencesTehranIran
- Student Scientific Research Center (SSRC)Tehran University of Medical SciencesTehranIran
| | - Mohamad Amin Khadembashiri
- Neuromusculoskeletal Research CenterIran University of Medical SciencesTehranIran
- Student Scientific Research Center (SSRC)Tehran University of Medical SciencesTehranIran
| | - Saba Maleki
- School of MedicineGuilan University of Medical SciencesRashtIran
| | - Mohammad Eslami
- Student Scientific Research Center (SSRC)Tehran University of Medical SciencesTehranIran
| | | | - Amir Hossein Behnoush
- School of medicineTehran University of Medical SciencesTehranIran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), TehranIran
| | - Nima Rezaei
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), TehranIran
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical CenterTehran University of Medical SciencesTehranIran
- Department of Immunology, School of MedicineTehran University of Medical SciencesTehranIran
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Qian Y, Chen H, Chen L, Ge C, Zhu D, Zhou D. Suppression of hepatocellular carcinoma progression by long noncoding RNA apolipoprotein C1 pseudogene via the regulation of the microRNA-106b-PTEN axis. Transl Cancer Res 2023; 12:3752-3763. [PMID: 38192998 PMCID: PMC10774056 DOI: 10.21037/tcr-23-2189] [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: 11/29/2023] [Accepted: 12/19/2023] [Indexed: 01/10/2024]
Abstract
Background Numerous researches have reported that long noncoding RNAs (lncRNAs) participate in tumor development and progression. LncRNA apolipoprotein C-I pseudogene 1 (APOC1P1), a pseudogene located in 19q13.2 between apolipoprotein C-I and apolipoprotein C-IV, is involved in a variety of diseases. However, the role of lncRNA APOC1P1 in hepatocellular carcinoma (HCC) remains unknown. Methods Quantitative polymerase chain reaction (qPCR) was performed to examine the expression of APOC1P1, miR-106b, and PTEN (phosphatase and TENsin homolog deleted on chromosome 10) in HCC tissues, adjacent normal tissues, and specific cell lines (LO2, Bel-7407, HCCLM3, MHCC-97H, Hep G2, and Huh-7). Upregulation of APOC1P1 and downregulation of miR-106b were conducted via application of vector transfection and microRNA (miRNA) inhibitor. Bioinformatics analysis and luciferase reporter assay were used to verify the binding sites of APOC1P1, miR-106b, and PTEN. Cell proliferation and invasion were determined with Cell Counting Kit-8 (CCK-8) and Transwell experiments. Subcellular location analysis was used to determine the distribution of APOC1P1 in cells, and Western blotting was used to detect the expression of PTEN. Results It was found that the expressions of APOC1P1 and PTEN were downregulated, while that of miR-106b was upregulated in HCC tissues and cells. Subcellular location analysis showed that APOC1P1 was localized in cytoplasm and competitively bound to miR-106b. APOC1P1 overexpression and miR-106b inhibition suppressed HCC cell proliferation and invasion. qPCR indicated the negative correlation between APOC1P1 expression and miR-106b expression in HCC tissues and a positive correlation between APOC1P1 and PTEN. Conclusions Our findings suggested that the lncRNA APOC1P1 inhibits HCC progression by competitively binding to miR-106b, leading to elevated PTEN expression, inhibiting cell proliferation and invasion in HCC cells. These results provide new insights into the diagnosis and therapy of HCC.
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Affiliation(s)
- Yi Qian
- General Surgery Department, The Sixth Affiliated Hospital of Soochow University, Suzhou, China
| | - Hao Chen
- Pathology Department, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Liang Chen
- General Surgery Department, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Chuang Ge
- General Surgery Department, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Dongmei Zhu
- General Surgery Department, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Dinghua Zhou
- General Surgery Department, The Sixth Affiliated Hospital of Soochow University, Suzhou, China
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Huang J, Liu M, Chen H, Zhang J, Xie X, Jiang L, Zhang S, Jiang C, Zhang J, Zhang Q, Yang G, Chi H, Tian G. Elucidating the Influence of MPT-driven necrosis-linked LncRNAs on immunotherapy outcomes, sensitivity to chemotherapy, and mechanisms of cell death in clear cell renal carcinoma. Front Oncol 2023; 13:1276715. [PMID: 38162499 PMCID: PMC10757362 DOI: 10.3389/fonc.2023.1276715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 11/26/2023] [Indexed: 01/03/2024] Open
Abstract
Background Clear cell renal carcinoma (ccRCC) stands as the prevailing subtype among kidney cancers, making it one of the most prevalent malignancies characterized by significant mortality rates. Notably,mitochondrial permeability transition drives necrosis (MPT-Driven Necrosis) emerges as a form of cell death triggered by alterations in the intracellular microenvironment. MPT-Driven Necrosis, recognized as a distinctive type of programmed cell death. Despite the association of MPT-Driven Necrosis programmed-cell-death-related lncRNAs (MPTDNLs) with ccRCC, their precise functions within the tumor microenvironment and prognostic implications remain poorly understood. Therefore, this study aimed to develop a novel prognostic model that enhances prognostic predictions for ccRCC. Methods Employing both univariate Cox proportional hazards and Lasso regression methodologies, this investigation distinguished genes with differential expression that are intimately linked to prognosis.Furthermore, a comprehensive prognostic risk assessment model was established using multiple Cox proportional hazards regression. Additionally, a thorough evaluation was conducted to explore the associations between the characteristics of MPTDNLs and clinicopathological features, tumor microenvironment, and chemotherapy sensitivity, thereby providing insights into their interconnectedness.The model constructed based on the signatures of MPTDNLs was verified to exhibit excellent prediction performance by Cell Culture and Transient Transfection, Transwell and other experiments. Results By analyzing relevant studies, we identified risk scores derived from MPTDNLs as an independent prognostic determinant for ccRCC, and subsequently we developed a Nomogram prediction model that combines clinical features and associated risk assessment. Finally, the application of experimental techniques such as qRT-PCR helped to compare the expression of MPTDNLs in healthy tissues and tumor samples, as well as their role in the proliferation and migration of renal clear cell carcinoma cells. It was found that there was a significant correlation between CDK6-AS1 and ccRCC results, and CDK6-AS1 plays a key role in the proliferation and migration of ccRCC cells. Impressive predictive results were generated using marker constructs based on these MPTDNLs. Conclusions In this research, we formulated a new prognostic framework for ccRCC, integrating mitochondrial permeability transition-induced necrosis. This model holds significant potential for enhancing prognostic predictions in ccRCC patients and establishing a foundation for optimizing therapeutic strategies.
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Affiliation(s)
- Jinbang Huang
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Mengtao Liu
- Pediatric Surgery, Guiyang Matemal and Child Health Care Hospital, Guiyang Children’s Hospital, Guiyang, China
| | - Haiqing Chen
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinhao Zhang
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xixi Xie
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Lai Jiang
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shengke Zhang
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chenglu Jiang
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jieying Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Qinhong Zhang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, GA, United States
| | - Hao Chi
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Gang Tian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, China
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Kozai K, Moreno-Irusta A, Iqbal K, Winchester ML, Scott RL, Simon ME, Muto M, Parrish MR, Soares MJ. The AKT1-FOXO4 axis reciprocally regulates hemochorial placentation. Development 2023; 150:dev201095. [PMID: 36607602 PMCID: PMC10110493 DOI: 10.1242/dev.201095] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023]
Abstract
Hemochorial placentation involves the differentiation of invasive trophoblast cells, specialized cells that possess the capacity to exit the placenta and invade into the uterus where they restructure the vasculature. Invasive trophoblast cells arise from a well-defined compartment within the placenta, referred to as the junctional zone in rat and the extravillous trophoblast cell column in human. In this study, we investigated roles for AKT1, a serine/threonine kinase, in placental development using a genome-edited/loss-of-function rat model. Disruption of AKT1 resulted in placental, fetal and postnatal growth restriction. Forkhead box O4 (Foxo4), which encodes a transcription factor and known AKT substrate, was abundantly expressed in the junctional zone and in invasive trophoblast cells of the rat placentation site. Foxo4 gene disruption using genome editing resulted in placentomegaly, including an enlarged junctional zone. AKT1 and FOXO4 regulate the expression of many of the same transcripts expressed by trophoblast cells, but in opposite directions. In summary, we have identified AKT1 and FOXO4 as part of a regulatory network that reciprocally controls critical indices of hemochorial placenta development.
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Affiliation(s)
- Keisuke Kozai
- Institute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ayelen Moreno-Irusta
- Institute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Mae-Lan Winchester
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Regan L. Scott
- Institute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Mikaela E. Simon
- Institute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Masanaga Muto
- Institute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Marc R. Parrish
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy, Kansas City, MO 64108, USA
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Fang K, Long Q, Liao Z, Zhang C, Jiang Z. Glycoproteomics revealed novel N-glycosylation biomarkers for early diagnosis of lung adenocarcinoma cancers. Clin Proteomics 2022; 19:43. [DOI: 10.1186/s12014-022-09376-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/15/2022] [Indexed: 11/20/2022] Open
Abstract
AbstractCirculating biomarkers play important roles in diagnosis of malignant tumors. N-glycosylation is an important post-translation patter and obviously affect biological behaviors of malignant tumor cells. However, the role of N-glycosylation sites in early diagnosis of tumors still remains further investigation. In this study, plasma from 20 lung adenocarcinoma (LUAD), which were all classified as stage I, as well as 20 normal controls (NL) were labeled and screened by mass spectrometry (MS). Total 39 differential N-glycosylation sites were detected in LUAD, 17 were up-regulated and 22 were down-regulated. In all differential sites, ITGB3-680 showed highest potential in LUAD which showed 99.2% AUC, 95.0% SP and 95.0% SN. Besides, APOB-1523 (AUC: 89.0%, SP: 95.0%, SN: 70.0%), APOB-2982 (AUC: 86.8%, SP: 95.0%, SN: 45.0%) and LPAL2-101 (AUC: 81.1%, SP: 95.0%, SN: 47.4%) also acted as candidate biomarkers in LUAD. Combination analysis was then performed by random forest model, all samples were divided into training group (16 cases) and testing group (4 cases) and conducted by feature selection, machine learning, integrated model of classifier and model evaluation. And the results indicated that combination of differential sites could reach 100% AUC in both training and testing group. Taken together, our study revealed multiple N-glycosylation sites which could be applied as candidate biomarkers for early diagnosis diagnosis of LUAD.
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Wu L, Yang J, Ke RS, Liu Y, Guo P, Feng L, Li Z, Li Z. Impact of lncRNA SOX9-AS1 overexpression on the prognosis and progression of intrahepatic cholangiocarcinoma. Clin Res Hepatol Gastroenterol 2022; 46:101999. [PMID: 35870795 DOI: 10.1016/j.clinre.2022.101999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (ICC) is a latent and malignant tumor with a dismal prognosis. This study was to evaluate the clinical relevance and therapeutic potential of SOX9-AS1 expression in ICC. METHODS The cancerous tissues and adjacent normal tissues were collected from ICC patients. Blood samples from ICC, hepatocellular carcinoma (HCC) group, the extrahepatic cholangiocarcinoma (ECC) group and the healthy controls were collected. SOX9-AS1 levels were evaluated in tissues (versus normal tissues) and plasma samples (versus plasma from HCC and ECC by quantitative real-time RT-PCR. The diagnostic value of SOX9-AS1 for ICC was estimated using receiver operating characteristic (ROC) curves. The relevancy between SOX9-AS1 expression and overall survival or recurrence-free survival was assessed by Kaplan-Meier curves multivariate analyses. The overexpression and knockdown of SOX9-AS1 on cell behavior were assessed by CCK-8 and transwell assay. RESULTS SOX9-AS1 levels were increased in ICC, both in the tissues and the cell lines. The upregulation of SOX9-AS1 showed a highly discriminative profile, distinguishing ICC patients from healthy subjects or HCC or ECC patients. Upregulation of SOX9-AS1 was related to shorter overall survival and recurrence-free survival. Muli-variate analysis revealed that SOX9-AS1 expression was an independent prognostic purpose factor of worst overall survival and recurrence-free survival. CONCLUSIONS SOX9-AS1 drives tumor growth and metastasis in ICC. SOX9-AS1 may be applied as a new diagnostic and prognostic purposed marker, in addition to a promising therapeutic target in ICC.
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Affiliation(s)
- Lupeng Wu
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Jingrui Yang
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Rui-Sheng Ke
- Department of General Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Yujian Liu
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Ping Guo
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Liuxing Feng
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Zhimin Li
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China.
| | - Zhimin Li
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China.
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Su Y, Qi R, Li L, Wang X, Li S, Zhao X, Hou R, Ma W, Liu D, Zheng J, Shi M. An immune-related gene prognostic risk index for pancreatic adenocarcinoma. Front Immunol 2022; 13:945878. [PMID: 35958614 PMCID: PMC9360334 DOI: 10.3389/fimmu.2022.945878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/04/2022] [Indexed: 11/19/2022] Open
Abstract
Objective Our goal is to construct an immune-related gene prognostic risk index (IRGPRI) for pancreatic adenocarcinoma (PAAD), and to clarify the immune and molecular features in IRGPRI-defined PAAD subgroups and the benefit of immune checkpoint inhibitors (ICIs) therapy. Method Through differential gene expression analysis, weighted gene co-expression network analysis (WGCNA), and univariate Cox regression analysis, 16 immune-related hub genes were identified using the Cancer Genome Atlas (TCGA) PAAD dataset (n = 182) and immune gene set. From these genes, we constructed an IRGPRI with the Cox regression method and the IRGPRI was verified based on the Gene Expression Omnibus (GEO) dataset (n = 45). Then, we analyzed the immune and molecular features and the benefit of ICI therapy in IRGPRI-defined subgroups. Results Five genes, including S100A16, CD40, VCAM1, TNFRSF4 and TRAF1 were used to construct IRGPRI. As with the results of the GEO cohort, the overall survival (OS) was more favorable in low IRGPRI patients versus high IRGPRI patients. The composite results pointed out that low IRGPRI was associated with immune response-related pathways, high level of CTLA4, low KRAS and TP53 mutation rate, more infiltration of activated memory CD4+ T cells, CD8+ T cells, and more benefits from ICIs therapy. In comparison, high IRGPRI was associated with cancer-related pathways, low expression of CTLA4, high KRAS and TP53 mutation rate, more infiltration of M2 macrophages, and less benefit from ICIs therapies. Conclusion This IRGPRI is an encouraging biomarker to define the prognosis, immune and molecular features, and benefits from ICIs treatments in PAAD.
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Affiliation(s)
- Yang Su
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Ruoshan Qi
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Lanying Li
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Xu Wang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Sijin Li
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Xuan Zhao
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Rui Hou
- College of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Wen Ma
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Dan Liu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Ming Shi, ; Junnian Zheng, ; Dan Liu,
| | - Junnian Zheng
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Ming Shi, ; Junnian Zheng, ; Dan Liu,
| | - Ming Shi
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Ming Shi, ; Junnian Zheng, ; Dan Liu,
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Wu Y, Hayat K, Hu Y, Yang J. Long Non-Coding RNAs as Molecular Biomarkers in Cholangiocarcinoma. Front Cell Dev Biol 2022; 10:890605. [PMID: 35573683 PMCID: PMC9093656 DOI: 10.3389/fcell.2022.890605] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/10/2022] [Indexed: 11/13/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a biliary system cancer that has the characteristics of strong invasiveness, poor prognosis, and few therapy choices. Furthermore, the absence of precise biomarkers for early identification and prognosis makes it hard to intervene in the early phase of initial diagnosis or recurring cholangiocarcinoma following surgery. Encouragingly, previous studies found that long non-coding RNA (lncRNA), a subgroup of RNA that is more than 200 nucleotides long, can affect cell proliferation, migration, apoptosis, and even drug resistance by altering numerous signaling pathways, thus reaching pro-cancer or anti-cancer outcomes. This review will take a retrospective view of the recent investigations on the work of lncRNAs in cholangiocarcinoma progression and the potential of lncRNAs serving as promising clinical biomarkers and therapeutic targets for CCA.
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Affiliation(s)
- Yanhua Wu
- Department of Gastroenterology, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Khizar Hayat
- Department of Gastroenterology, International Education College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Yufei Hu
- Department of Gastroenterology, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianfeng Yang
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, China
- *Correspondence: Jianfeng Yang,
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Sun Q, Gong X, Wu J, Hu Z, Zhang Q, Gong J, Zhu X. Effect of lncRNA PVT1/miR186/KLF5 Axis on the Occurrence and Progression of Cholangiocarcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8893652. [PMID: 34337058 PMCID: PMC8286192 DOI: 10.1155/2021/8893652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/03/2020] [Accepted: 01/28/2021] [Indexed: 01/16/2023]
Abstract
This study primarily focused on the effect of the long noncoding RNA (lncRNA) PVT1/miR186/KLF5 axis on the occurrence and progression of cholangiocarcinoma (CCA). miR186 was found both in the lncRNA PVT1 targeting miRNAs and KLF5 targeting miRNAs using bioinformatic analysis. The expression of lncRNA PVT1 and KLF5 in the TFK-1, QBC939, and HuCCT1 cell lines and normal biliary epithelial HIBEpiC cells was detected by RT-qPCR. The significance of lncRNA PVT1 and KLF5 on cell proliferation was analyzed using the MTT assay and clone formation assay in lncRNA PVT1 and KLF5 silencing HuCCT1 cell lines and lncRNA PVT1and KLF5 overexpressing TFK-1 and QBC939 cell lines, respectively. The potential role of lncRNA PVT1 and KLF5 in cell migration was detected using the transwell invasion assay in CCA cell lines and tumor formation assay. Additionally, lncRNA PVT1 and KLF5 were proved to be highly expressed in CCA tissues and cell lines. Silencing and overexpressing of lncRNA PVT1 or KLF5 markedly inhibited or increased the cell proliferation and cell invasion in CCA cell lines, respectively. Silencing and overexpressing of lncRNA PVT1 significantly inhibited and increased the expression of KLF5 in CCA cell lines, respectively. Silencing of lncRNA PVT1 increased the expression of miR186, and silencing of miR186 increased the expression of KLF5 in CCA cell lines. Cotransfection of lncRNA PVT1 and miR186 increased the expression of KLF5 compared with controls. Overall, these results demonstrated that the lncRNA PVT1/miR186/KLF5 axis might exert a key role in the occurrence and progression of CCA, and this axis might provide a new target for treating CCA.
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Affiliation(s)
- Qiang Sun
- General Surgery Department, Zhongshan Hospital, Sun Yat-Sen University, Zhongshan, China
| | - Xueyi Gong
- General Surgery Department, Zhongshan Hospital, Sun Yat-Sen University, Zhongshan, China
| | - Jianlong Wu
- General Surgery Department, Zhongshan Hospital, Sun Yat-Sen University, Zhongshan, China
| | - Zhipeng Hu
- General Surgery Department, Zhongshan Hospital, Sun Yat-Sen University, Zhongshan, China
| | - Qiao Zhang
- General Surgery Department, Zhongshan Hospital, Sun Yat-Sen University, Zhongshan, China
| | - Jingling Gong
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xiaofeng Zhu
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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SOX2 knockdown slows cholangiocarcinoma progression through inhibition of transcriptional activation of lncRNA PVT1. Biochem J 2021; 477:3527-3540. [PMID: 32812642 DOI: 10.1042/bcj20200219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/26/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022]
Abstract
Cholangiocarcinoma (CCA) has accounted for a high rate of mortality and morbidity in the recent years. Long non-coding RNAs (lncRNAs) play an important role in different cellular environments, including cancer. As such, they have been used as potential targets during CCA therapy. The objective of this study was to investigate the effects of lncRNA PVT1 on CCA and its mechanisms behind lncRNA PVT1 regulation. The interactions among SOX2, lncRNA PVT1, miR-186 and SEMA4D were verified by chromatin immunoprecipitation, RNA immunoprecipitation and dual luciferase reporter gene assay. Gain- and loss-of-function experiments were conducted to explore the modulatory effects of SOX2, lncRNA PVT1, miR-186 and SEMA4D on cell viability, migration and invasion of CCA by CCK-8 and Transwell assays. In vivo effects of lncRNA PVT1 or SEMA4D were studied in a nude mouse model. MiR-186 was poorly expressed while SOX2, lncRNA PVT1 and SEMA4D were highly expressed in CCA cells. SOX2 induced the transcriptional activation of lncRNA PVT1 expression to promote proliferation, migration and invasion of CCA cells. LncRNA PVT1 bound to miR-186 and miR-186 was found to target SEMA4D. The overexpression of lncRNA PVT1 and SEMA4D, as well as the inhibition of miR-186 led to elevated CCA cell proliferation, migration and invasion. In vivo experiments confirmed the inhibitory role of lncRNA PVT1 knockdown or SEMA4D knockdown in CCA. All in all, SOX2 down-regulated miR-186 through the transcriptional activation of lncRNA PVT1, whereas elevating SEMA4D expression, thus promoting the progression of CCA.
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Zengin T, Önal-Süzek T. Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. J Pers Med 2021; 11:154. [PMID: 33672117 PMCID: PMC7926392 DOI: 10.3390/jpm11020154] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Lung cancer is the second most frequently diagnosed cancer type and responsible for the highest number of cancer deaths worldwide. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are subtypes of non-small-cell lung cancer which has the highest frequency of lung cancer cases. We aimed to analyze genomic and transcriptomic variations including simple nucleotide variations (SNVs), copy number variations (CNVs) and differential expressed genes (DEGs) in order to find key genes and pathways for diagnostic and prognostic prediction for lung adenocarcinoma and lung squamous cell carcinoma. We performed a univariate Cox model and then lasso-regularized Cox model with leave-one-out cross-validation using The Cancer Genome Atlas (TCGA) gene expression data in tumor samples. We generated 35- and 33-gene signatures for prognostic risk prediction based on the overall survival time of the patients with LUAD and LUSC, respectively. When we clustered patients into high- and low-risk groups, the survival analysis showed highly significant results with high prediction power for both training and test datasets. Then, we characterized the differences including significant SNVs, CNVs, DEGs, active subnetworks, and the pathways. We described the results for the risk groups and cancer subtypes separately to identify specific genomic alterations between both high-risk groups and cancer subtypes. Both LUAD and LUSC high-risk groups have more downregulated immune pathways and upregulated metabolic pathways. On the other hand, low-risk groups have both up- and downregulated genes on cancer-related pathways. Both LUAD and LUSC have important gene alterations such as CDKN2A and CDKN2B deletions with different frequencies. SOX2 amplification occurs in LUSC and PSMD4 amplification in LUAD. EGFR and KRAS mutations are mutually exclusive in LUAD samples. EGFR, MGA, SMARCA4, ATM, RBM10, and KDM5C genes are mutated only in LUAD but not in LUSC. CDKN2A, PTEN, and HRAS genes are mutated only in LUSC samples. The low-risk groups of both LUAD and LUSC tend to have a higher number of SNVs, CNVs, and DEGs. The signature genes and altered genes have the potential to be used as diagnostic and prognostic biomarkers for personalized oncology.
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Affiliation(s)
- Talip Zengin
- Department of Molecular Biology and Genetics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey;
- Department of Bioinformatics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
| | - Tuğba Önal-Süzek
- Department of Bioinformatics, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
- Department of Computer Engineering, Muğla Sıtkı Koçman University, 48000 Muğla, Turkey
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13
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Comprehensive analysis of lncRNA and mRNA based on expression microarray profiling reveals different characteristics of osteoarthritis between Tibetan and Han patients. J Orthop Surg Res 2021; 16:133. [PMID: 33579305 PMCID: PMC7879695 DOI: 10.1186/s13018-021-02213-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Background Osteoarthritis (OA) is thought to be the most prevalent chronic joint disease, especially in Tibet of China. Here, we aimed to explore the integrative lncRNA and mRNA landscape between the OA patients of Tibet and Han. Methods The lncRNA and mRNA expression microarray profiling was performed by SurePrint G3 Human Gene Expression 8x60K v2 Microarray in articular cartilage samples from OA patients of Han nationality and Tibetans, followed by GO, KEGG, and trans-regulation and cis-regulation analysis of lncRNA and mRNA. Results We found a total of 117 lncRNAs and 297 mRNAs differently expressed in the cartilage tissues of Tibetans (n = 5) comparing with those of Chinese Han (n = 3), in which 49 lncRNAs and 158 mRNAs were upregulated, and 68 lncRNAs and 139 mRNAs were downregulated. GO and KEGG analysis showed that several unreported biological processes and signaling pathways were particularly identified. LncRNA-mRNA co-expression analysis revealed a remarkable lncRNA-mRNA relationship, in which OTOA may play a critical role in the different mechanisms of the OA progression between Tibetans and Chinese Han. Conclusion This study identified different lncRNA/mRNA expression profiling between OA patients of Tibetans and Han, which were involved in many characteristic biological processes and signaling pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-021-02213-y.
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14
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Li Y, Yan J, Wang Y, Wang C, Zhang C, Li G. LINC00240 promotes gastric cancer cell proliferation, migration and EMT via the miR-124-3p / DNMT3B axis. Cell Biochem Funct 2020; 38:1079-1088. [PMID: 32526811 DOI: 10.1002/cbf.3551] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/02/2020] [Accepted: 05/03/2020] [Indexed: 01/17/2023]
Abstract
Gastric cancer (GC) remains one of prevalent causes of cancer-related deaths worldwide. Long noncoding RNA is related to various cancers. Our study was conducted to explore the biological effects of LINC00240 on the tumorigenesis of GC and uncover its possible mechanisms. LINC00240 expression was determined in GC cell lines and samples through quantitative Real-time Polymerase Chain Reaction (qRT-PCR). The functional effects of LINC00240 were validated using in vitro and in vivo assays. Targets were assessed by AGO2-dependent RNA immunoprecipitation assay and dual-luciferase report assays. Our findings suggested higher LINC00240 expression in GC tissues and cells. Through downregulating LINC00240, cell proliferation, invasion and migration were retarded in vitro, and tumorigenesis of GC cells was notably suppressed in vivo. Further research showed that LINC00240 was a cytoplasmic lncRNA that shared miRNA response elements of microRNA (miR)-124-3p with DNMT3B, thus forming a LINC00240/miR-124-3p/DNMT3B axis explaining the functions of LINC00240. In a word, our study reveals that LINC00240 promotes GC tumorigenesis via a LINC00240/miR-124-3p/DNMT3B axis as an oncogene. These findings objectivise that LINC00240 may be a potential diagnostic biomarker for GC. SIGNIFICANCE OF THE STUDY: Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-related death across the world. Then we analysed lncRNA microarray of GC and selected LINC00240 as the study object. Therefore, the potential molecular mechanism as well as physiological function of LINC00240 in GC was discussed. Then we reveal that LINC00240 acts as an oncogene in GC progression via the miR-99a-5p/IGF1R axis. This study is the first to demonstrate the roles of LINC00240 in GC.
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Affiliation(s)
- Yuanyuan Li
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jing Yan
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yiting Wang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Caifeng Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Guohua Li
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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15
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Yang Y, Deng X, Li Q, Wang F, Miao L, Jiang Q. Emerging roles of long noncoding RNAs in cholangiocarcinoma: Advances and challenges. Cancer Commun (Lond) 2020; 40:655-680. [PMID: 33142045 PMCID: PMC7743012 DOI: 10.1002/cac2.12109] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/10/2020] [Accepted: 10/21/2020] [Indexed: 12/19/2022] Open
Abstract
Cholangiocarcinoma (CCA), a cancer with a relatively low incidence rate, is usually associated with poor prognosis. Current modalities for the diagnosis and treatment of CCA patients are still far from satisfactory. In recent years, numerous long noncoding RNAs (lncRNAs) have been identified as crucial players in the development of various cancers, including CCA. Abnormally expressed lncRNAs in CCA, regulated by some upstream molecules, significantly influence the biological behavior of tumor cells and are involved in tumor development through various mechanisms, including interactions with functional proteins, participation in competing for endogenous RNA (ceRNA) regulatory networks, activation of cancer‐related signaling pathways and epigenetic modification of gene expression. Furthermore, several lncRNAs are closely associated with the clinicopathological features of CCA patients, and are promising biomarkers for diagnosing and prognostication of CCA. Some of these lncRNAs play an important role in chemotherapy drug resistance. In addition, lncRNAs have also been shown to be involved in the inflammation microenvironment of CCA and malignant outcome of CCA risk factors, such as cholestatic liver diseases. In view of the difficulty of diagnosing CCA, more attention should be paid to detectable lncRNAs in the serum or bile. This review summarizes the recent knowledge on lncRNAs in CCA and provides a new outlook on the molecular mechanisms of CCA development from the perspective of lncRNAs. Moreover, we also discussed the limitations of the current studies and differential expression of lncRNAs in different types of CCA.
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Affiliation(s)
- Yang Yang
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Xueting Deng
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Quanpeng Li
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Fei Wang
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Lin Miao
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Qi Jiang
- Department of Gastroenterology, Dongtai People's Hospital, Yancheng, Jiangsu, 224000, P. R. China
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Ahn JW, Park Y, Kang SJ, Hwang SJ, Cho KG, Lim J, Kwack K. CeRNA Network Analysis Representing Characteristics of Different Tumor Environments Based on 1p/19q Codeletion in Oligodendrogliomas. Cancers (Basel) 2020; 12:cancers12092543. [PMID: 32906679 PMCID: PMC7564449 DOI: 10.3390/cancers12092543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Oligodendroglioma (OD) is a subtype of glioma occurring in the central nervous system. The 1p/19q codeletion is a prognostic marker of OD with an isocitrate dehydrogenase (IDH) mutation and is associated with a clinically favorable overall survival (OS). The long non-coding RNAs (lncRNAs) protects the mRNA from degradation by binding with the same miRNA by acting as a competitive endogenous RNA (ceRNA). Recently, although there is an increasing interest in lncRNAs on glioma studies, however, studies regarding their effects on OD and the 1p/19q codeletion remain limited. In our study, we performed in silico analyses using low-grade gliomas from datasets obtained from The Cancer Genome Atlas to investigate the effects of ceRNA with 1p/19q codeletion on ODs. We constructed 16 coding RNA–miRNA–lncRNA networks and the ceRNA network participated in ion channel activity, insulin secretion, and collagen network and extracellular matrix (ECM) changes. In conclusion, our results can provide insights into the possibility in the different tumor microenvironments and OS following 1p/19q codeletion through changes in the ceRNA network. Abstract Oligodendroglioma (OD) is a subtype of glioma occurring in the central nervous system. The 1p/19q codeletion is a prognostic marker of OD with an isocitrate dehydrogenase (IDH) mutation and is associated with a clinically favorable overall survival (OS); however, the exact underlying mechanism remains unclear. Long non-coding RNAs (lncRNAs) have recently been suggested to regulate carcinogenesis and prognosis in cancer patients. Here, we performed in silico analyses using low-grade gliomas from datasets obtained from The Cancer Genome Atlas to investigate the effects of ceRNA with 1p/19q codeletion on ODs. Thus, we selected modules of differentially expressed genes that were closely related to 1p/19q codeletion traits using weighted gene co-expression network analysis and constructed 16 coding RNA–miRNA–lncRNA networks. The ceRNA network participated in ion channel activity, insulin secretion, and collagen network and extracellular matrix (ECM) changes. In conclusion, ceRNAs with a 1p/19q codeletion can create different tumor microenvironments via potassium ion channels and ECM composition changes; furthermore, differences in OS may occur. Moreover, if extrapolated to gliomas, our results can provide insights into the consequences of identical gene expression, indicating the possibility of tracking different biological processes in different subtypes of glioma.
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Affiliation(s)
- Ju Won Ahn
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - YoungJoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - Su Jung Kang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - So Jung Hwang
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
| | - Kyung Gi Cho
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
| | - JaeJoon Lim
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
- Correspondence: (J.L.); (K.K.); Tel.: +82-031-780-5688 (J.L.); +82-031-725-7141 (K.K.)
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
- Correspondence: (J.L.); (K.K.); Tel.: +82-031-780-5688 (J.L.); +82-031-725-7141 (K.K.)
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Darwiche N. Epigenetic mechanisms and the hallmarks of cancer: an intimate affair. Am J Cancer Res 2020; 10:1954-1978. [PMID: 32774995 PMCID: PMC7407342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023] Open
Abstract
Epigenetic mechanisms comprising DNA methylation, histone modifications, and noncoding RNAs affect chromatin structure and regulate gene expression. These mechanisms control normal embryonic development and adult life and their deregulation contributes to several diseases including cancer. The process of tumorigenesis is complex and results from the evolution of different "hallmarks of cancer". Hanahan and Weinberg presented in 2000 and 2011 seminal contributions in the cancer field, first the six hallmarks of cancer and a decade later two additional hallmarks and two enabling characteristics were added. Here, we surmise that epigenetic mechanisms regulate and contribute to every single hallmark in cancer, and thus represent the hallmark of hallmarks in tumorigenesis. Focusing on epigenetics as a major hallmark in cancer formation has profound preventive, therapeutic, and clinical implications.
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Affiliation(s)
- Nadine Darwiche
- Department of Biochemistry and Molecular Genetics, American University of Beirut Beirut, Lebanon
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Extracellular Vesicle lincRNA-p21 Expression in Tumor-Draining Pulmonary Vein Defines Prognosis in NSCLC and Modulates Endothelial Cell Behavior. Cancers (Basel) 2020; 12:cancers12030734. [PMID: 32244977 PMCID: PMC7140053 DOI: 10.3390/cancers12030734] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 12/21/2022] Open
Abstract
Hypoxia-induced upregulation of lincRNA-p21 in tumor tissue was previously shown by our group to be related to poor prognosis in resected non-small cell lung cancer (NSCLC) patients. In the present study, we have evaluated the presence of lincRNA-p21 in extracellular vesicles (EVs) from NSCLC patients and assessed its potential as a prognostic biomarker. High EV lincRNA-p21 levels in blood from the tumor-draining vein were associated with shorter time to relapse and shorter overall survival. Moreover, the multivariate analysis identified high lincRNA-p21 levels as an independent prognostic marker. In addition, lincRNA-p21 was overexpressed in H23 and HCC44 NSCLC cell lines and their derived EVs under hypoxic conditions. Functional assays using human umbilical vein endothelial cells (HUVECs) showed that tumor-derived EVs enriched in lincRNA-p21 affected endothelial cells by promoting tube formation and enhancing tumor cell adhesion to endothelial cells. Additionally, the analysis of selected EV microRNAs related to angiogenesis and metastasis showed that the microRNAs correlated with EV lincRNA-p21 levels in both patients and cell lines. Finally, EV co-culture with HUVEC cells increased the expression of microRNAs and genes related to endothelial cell activation. In conclusion, EV lincRNA-p21 acts as a novel prognosis marker in resected NSCLC patients, promoting angiogenesis and metastasis.
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Fuior EV, Gafencu AV. Apolipoprotein C1: Its Pleiotropic Effects in Lipid Metabolism and Beyond. Int J Mol Sci 2019; 20:ijms20235939. [PMID: 31779116 PMCID: PMC6928722 DOI: 10.3390/ijms20235939] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/20/2022] Open
Abstract
Apolipoprotein C1 (apoC1), the smallest of all apolipoproteins, participates in lipid transport and metabolism. In humans, APOC1 gene is in linkage disequilibrium with APOE gene on chromosome 19, a proximity that spurred its investigation. Apolipoprotein C1 associates with triglyceride-rich lipoproteins and HDL and exchanges between lipoprotein classes. These interactions occur via amphipathic helix motifs, as demonstrated by biophysical studies on the wild-type polypeptide and representative mutants. Apolipoprotein C1 acts on lipoprotein receptors by inhibiting binding mediated by apolipoprotein E, and modulating the activities of several enzymes. Thus, apoC1 downregulates lipoprotein lipase, hepatic lipase, phospholipase A2, cholesterylester transfer protein, and activates lecithin-cholesterol acyl transferase. By controlling the plasma levels of lipids, apoC1 relates directly to cardiovascular physiology, but its activity extends beyond, to inflammation and immunity, sepsis, diabetes, cancer, viral infectivity, and-not last-to cognition. Such correlations were established based on studies using transgenic mice, associated in the recent years with GWAS, transcriptomic and proteomic analyses. The presence of a duplicate gene, pseudogene APOC1P, stimulated evolutionary studies and more recently, the regulatory properties of the corresponding non-coding RNA are steadily emerging. Nonetheless, this prototypical apolipoprotein is still underexplored and deserves further research for understanding its physiology and exploiting its therapeutic potential.
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Affiliation(s)
- Elena V. Fuior
- Institute of Cellular Biology and Pathology “N. Simionescu”, 050568 Bucharest, Romania;
| | - Anca V. Gafencu
- Institute of Cellular Biology and Pathology “N. Simionescu”, 050568 Bucharest, Romania;
- Correspondence:
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Gao J, Qin W, Kang P, Xu Y, Leng K, Li Z, Huang L, Cui Y, Zhong X. Up-regulated LINC00261 predicts a poor prognosis and promotes a metastasis by EMT process in cholangiocarcinoma. Pathol Res Pract 2019; 216:152733. [PMID: 31812439 DOI: 10.1016/j.prp.2019.152733] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/24/2019] [Accepted: 11/10/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVE LINC00261 plays a vital role in tumorigenesis and metastasis of digestive system cancer. However, an influence of LINC00261 on cholangiocarcinoma has a little research. There, we investigated clinical role and molecular mechanisms of LINC00261 in cholangiocarcinoma. METHODS The qRT-PCR was performed for the detection of LINC00261 level in 50 paired specimens from CCA patients and six cell lines. Cell proliferation were explored by CCK-8 and colony formation assays in QBC939 and RBE cells after transfected with si-LINC00261 or si-NC. Then, AO/EB double fluorescence staining and flow cytometric assays were performed to assess cell apoptosis. Transwell and wound healing assays were selected to evaluate migratory and invasive property of cells. Protein levels, such as PCNA, Bax, Bcl-2, and several epithelial-to-mesenchymal transition markers, including E-cadherin, N-cadherin and Vimentin, were detected by western blot assays. Furthermore, we use a R2 platform to evaluate the correlation between LINC00261 and EMT makers and predict the overall survival and relapse-free survival for CCA patients by the expression of LINC00261/ EMT makers. RESULTS LINC00261 was overexpressed in cancerous tissues and CCA cell lines compared with adjacent tissues and HIBEC, respectively. Up-regulation of LINC00261 was related to larger tumor size (p = 0.009), positive lymph node metastasis (p = 0.021), advanced TNM stages (p = 0.017) and higher postoperative recurrence (p = 0.009) for CCA patients. Additionally, univariate and multivariate analysis displayed that LINC00261 an independent prognostic factor in CCA patients. Knockdown of LINC00261 expression in RBE and QBC939 cell lines inhibited cell proliferation, migration and invasion property and increased cell apoptosis and the EMT progression. Moreover, there was a strong correlation between LINC00261 and E-cadherin (CDH1) (p < 0.05), and low expression of E-cadherin (CDH1) has a poor overall survival and relapse-free survival in CCA patients (p < 0.05). CONCLUSION Overall, high level of LINC00261 in CCA predicts a poor prognosis, and promotes a metastasis via EMT process. Thus, LINC00261 could be a promising biomarker and therapeutic target for CCA, and in the high level of LINC00261 in CCA, E-cadherin or CDH1 might be an effective factor for tumor metastasis or poor prognosis.
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Affiliation(s)
- Jianjun Gao
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei Qin
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Pengcheng Kang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yi Xu
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China; The Key Laboratory of Myocardial Ischemia, Harbin Medical University, Ministry of Education, Heilongjiang Province, China
| | - Kaiming Leng
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China; The Key Laboratory of Myocardial Ischemia, Harbin Medical University, Ministry of Education, Heilongjiang Province, China
| | - Zhenglong Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China; The Key Laboratory of Myocardial Ischemia, Harbin Medical University, Ministry of Education, Heilongjiang Province, China
| | - Lining Huang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Xiangyu Zhong
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China.
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21
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Lin X, Qiu L, Song X, Hou J, Chen W, Zhao J. A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples. BMC Genomics 2019; 20:831. [PMID: 31703614 PMCID: PMC6842158 DOI: 10.1186/s12864-019-6166-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023] Open
Abstract
Background Formalin-fixed and paraffin-embedded (FFPE) blocks held in clinical laboratories are an invaluable resource for clinical research, especially in the era of personalized medicine. It is important to accurately quantitate gene expression with degraded and small amounts of total RNA from FFPE materials. Results High concordance in transcript quantifications were shown between FF and FFPE samples using the same kit. The gene expression using the TaKaRa kit showed a difference with other kits, which may be due to the different principle of rRNA depletion or the amount of input total RNA. For seriously degraded RNA from FFPE samples, libraries could be constructed with as low as 50 ng of total RNA, although there was residual rRNA in the libraries. Data analysis with HISAT demonstrated that the unique mapping ratio, percentage of exons in unique mapping reads and number of detected genes decreased along with the decreasing quality of input RNA. Conclusions The method of RNA library construction with rRNA depletion can be used for clinical FFPE samples. For degraded and low-input RNA samples, it is still possible to obtain repeatable RNA expression profiling but with a low unique mapping ratio and high residual rRNA.
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Affiliation(s)
- Xiaojing Lin
- Department of Thoracic Surgery, Cancer Hospital Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lihong Qiu
- Department of Thoracic Surgery, Cancer Hospital Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xue Song
- Department of Thoracic Surgery, Cancer Hospital Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Junyan Hou
- Department of Thoracic Surgery, Cancer Hospital Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Weizhi Chen
- Department of Thoracic Surgery, Cancer Hospital Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jun Zhao
- Genecast Precision Medicine Technology Institute, Room 903-908, Health work, Huayuan North Road 35, Haidian District, Beijing, 100191, China.
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22
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Angenard G, Merdrignac A, Louis C, Edeline J, Coulouarn C. Expression of long non-coding RNA ANRIL predicts a poor prognosis in intrahepatic cholangiocarcinoma. Dig Liver Dis 2019; 51:1337-1343. [PMID: 31040073 DOI: 10.1016/j.dld.2019.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/05/2019] [Accepted: 03/22/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (iCCA) is a deadly cancer worldwide associated with an increased incidence, limited therapeutic options and absence of reliable prognostic biomarkers. Long non-coding RNAs (lncRNA) emerge as relevant biomarkers in cancer being associated with tumor progression. However, lncRNA have been poorly investigated in iCCA. AIM To identify lncRNA significantly associated with the survival of patients with iCCA after tumor resection for curative intent. METHODS Gene expression profiling and Q-RT-PCR were performed from a cohort of 39 clinically well-annotated iCCA. Univariate Cox proportional hazards model with Wald Statistic was used to identify lncRNA significantly associated with overall (OS) and/or disease-free (DFS) survival. RESULTS A signature made of 9 lncRNA was identified to be significantly (P < 0.05) associated with OS and DFS, including 4 lncRNA (lnc-CDK9-1, XLOC_l2_009441, CDKN2B-AS1, HOXC13-AS) highly expressed in poor prognosis iCCA and 5 lncRNA (lnc-CCHCR1-1, lnc-AF131215.3.1, lnc-CBLB-5, COL18A1-AS2, lnc-RELL2-1) highly expressed in better prognosis iCCA. We further validated CDKN2B-AS1 (ANRIL) as a poor prognosis biomarker, not only in iCCA, but also in hepatocellular carcinoma, kidney renal clear cell carcinoma and uterine corpus endometrial carcinoma. CONCLUSIONS We report a prognosis lncRNA signature in iCCA and the clinical relevance of CDKN2B-AS1 (ANRIL) overexpression in several cancers.
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Affiliation(s)
- Gaëlle Angenard
- Inserm, Univ Rennes, Inra, Institut NuMeCan (Nutrition Metabolisms and Cancer), CHU Rennes, Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Aude Merdrignac
- Inserm, Univ Rennes, Inra, Institut NuMeCan (Nutrition Metabolisms and Cancer), CHU Rennes, Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Corentin Louis
- Inserm, Univ Rennes, Inra, Institut NuMeCan (Nutrition Metabolisms and Cancer), CHU Rennes, Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Julien Edeline
- Inserm, Univ Rennes, Inra, Institut NuMeCan (Nutrition Metabolisms and Cancer), CHU Rennes, Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Cédric Coulouarn
- Inserm, Univ Rennes, Inra, Institut NuMeCan (Nutrition Metabolisms and Cancer), CHU Rennes, Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France.
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23
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Li J, Huang L, Li Z, Zhong X, Tai S, Jiang X, Cui Y. Functions and roles of long noncoding RNA in cholangiocarcinoma. J Cell Physiol 2019; 234:17113-17126. [PMID: 30888066 DOI: 10.1002/jcp.28470] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/20/2019] [Indexed: 02/06/2023]
Abstract
Cholangiocarcinoma (CCA) is one of the most fatal cancers in humans, with a gradually increasing incidence worldwide. The efficient diagnostic and therapeutic measures for CCA to reduce mortality are urgently needed. Long noncoding RNAs (lncRNAs) may provide the potential diagnostic and therapeutic option for suppressing the CCA development. LncRNAs are a type of non-protein-coding RNAs, which are larger than 200 nucleotides in length. Increasing evidence reveals that lncRNAs exhibit critical roles in the carcinogenesis and development of CCA. Deregulation of lncRNAs impacts the proliferation, migration, invasion, and antiapoptosis of CCA cells by multiple sophisticated mechanisms. Consequently, lncRNAs likely represent promising biomarkers or intervention targets of CCA. In this review, we summarize current studies regarding the biological functions and regulatory mechanisms of diverse lncRNAs in CCA.
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Affiliation(s)
- Jinglin Li
- Department of HPB Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Lining Huang
- Department of HPB Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhenglong Li
- Department of HPB Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiangyu Zhong
- Department of HPB Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Sheng Tai
- Department of HPB Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xingming Jiang
- Department of HPB Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yunfu Cui
- Department of HPB Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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