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Batiste M, Joy B, Yee CK, Cho L, Christensen A, Abed I, Nguyen K, Yanumula A, Chang H, Cho ED, Wang W, Chou E, Chang EH, Shyu YL, Abram A, Alcaide J, Zhou J, Gillespie B, Senderovich M, Cusick GA, Le AV, Hoang F, Shi Y, Mohamed E, Cusick JK. RELT Is Upregulated in Breast Cancer and Induces Death in Breast Cancer Cells. Biomedicines 2024; 12:2667. [PMID: 39767574 PMCID: PMC11727564 DOI: 10.3390/biomedicines12122667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Revised: 11/02/2024] [Accepted: 11/08/2024] [Indexed: 01/16/2025] Open
Abstract
BACKGROUND Receptor Expressed in Lymphoid Tissues (RELT) is a TNFRSF member that has two paralogs, RELL1 and RELL2; the three proteins are collectively referred to as RELT family members (RELTfms). METHODS We sought to evaluate RELT expression in cancerous cells by using real-time PCR, western blotting, flow cytometry, and immunohistochemistry (IHC). The mechanism of RELT-induced cell death was assessed by western blotting, flow cytometry, luciferase assays, and morphology staining. RELT localization was detected through immunofluorescence and western blotting, and co-immunoprecipitation was used to test whether a mutated RELT interacts with the OXSR1 kinase. RESULTS RELT and RELL1 protein expression was significantly elevated in cell lines representing breast and lung cancer, whereas RELL2 protein expression was relatively consistent across different cell lines. The surface expression of RELT was highest in monocytes. IHC staining revealed increased RELT expression in malignant breast cancer biopsies compared to patient-matched benign tissue. RELTfm overexpression induced death in MDA-MB-231 (231) breast cancer cells, accompanied by increased phosphatidylserine externalization and Caspase-3/7 activation. The co-transfection of plasmids predicted to block the phosphorylation of RELT by the OXSR1 kinase did not abrogate RELT-induced apoptosis, indicating that the activation of p38 by RELT through the OXSR1 kinase is not required for RELT-induced cell death. Interestingly, nuclear localization of RELT was detected in 231 and HEK-293 cells. CONCLUSIONS These results demonstrate that RELT induces death in breast cancer cells through an apoptotic pathway that does not require OXSR1 phosphorylation and that RELT possesses the ability to translocate to the nucleus, a novel finding that warrants further investigation.
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Affiliation(s)
- Maryann Batiste
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Bethany Joy
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Cara K. Yee
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Luke Cho
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Ashley Christensen
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Ihab Abed
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Kailey Nguyen
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Anusri Yanumula
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Hannah Chang
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Evan D. Cho
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Wenjia Wang
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Emily Chou
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Esther H. Chang
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Yennie L. Shyu
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Alyssa Abram
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Jessa Alcaide
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - James Zhou
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Brittany Gillespie
- Masters of Pharmaceutical Sciences Department, College of Graduate Studies, California Northstate University, Elk Grove, CA 95757, USA
| | - Michelle Senderovich
- Masters of Pharmaceutical Sciences Department, College of Graduate Studies, California Northstate University, Elk Grove, CA 95757, USA
| | - Gianne Almeida Cusick
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Ai-Vy Le
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Frank Hoang
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
| | - Yihui Shi
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Eslam Mohamed
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
- Masters of Pharmaceutical Sciences Department, College of Graduate Studies, California Northstate University, Elk Grove, CA 95757, USA
| | - John K. Cusick
- Department of Basic Science, College of Medicine, California Northstate University, Elk Grove, CA 95757, USA (B.J.); (A.C.); (H.C.); (E.D.C.); (E.H.C.); (Y.L.S.); (A.-V.L.); (Y.S.); (E.M.)
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Yang S, Song J, Deng M, Cheng S. Comprehensive analysis of aging-related gene expression patterns and identification of potential intervention targets. Postgrad Med J 2024:qgae131. [PMID: 39357883 DOI: 10.1093/postmj/qgae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/17/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024]
Abstract
PURPOSE This study aims to understand the molecular mechanisms underlying the aging process and identify potential interventions to mitigate age-related decline and diseases. METHODS This study utilized the GSE168753 dataset to conduct comprehensive differential gene expression analysis and co-expression module analysis. Machine learning and Mendelian randomization analyses were employed to identify core aging-associated genes and potential drug targets. Molecular docking simulations and mediation analysis were also performed to explore potential compounds and mediators involved in the aging process. RESULTS The analysis identified 4164 differentially expressed genes, with 1893 upregulated and 2271 downregulated genes. Co-expression analysis revealed 21 modules, including both positively and negatively correlated modules between older age and younger age groups. Further exploration identified 509 aging-related genes with distinct biological functions. Machine learning and Mendelian randomization analyses identified eight core genes associated with aging, including DPP9, GNAZ, and RELL2. Molecular docking simulations suggested resveratrol, folic acid, and ethinyl estradiol as potential compounds capable of attenuating aging through modulation of RELL2 expression. Mediation analysis indicated that eosinophil counts and neutrophil count might act as mediators in the causal relationship between genes and aging-related indicators. CONCLUSION This comprehensive study provides valuable insights into the molecular mechanisms of aging and offers important implications for the development of anti-aging therapeutics. Key Messages What is already known on this topic - Prior research outlines aging's complexity, necessitating precise molecular targets for intervention. What this study adds - This study identifies novel aging-related genes, potential drug targets, and therapeutic compounds, advancing our understanding of aging mechanisms. How this study might affect research, practice, or policy - Findings may inform targeted therapies for age-related conditions, influencing future research and clinical practices.
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Affiliation(s)
- Sha Yang
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China
| | - Jianning Song
- Interventional Department, GuiQian International General Hospital, Guiyang, China
| | - Min Deng
- The First Affiliated Hospital of Chongqing Medical and Pharmaceutical College, Chongqing 400000, China
| | - Si Cheng
- Department of Orthopedics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
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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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Cusick JK, Alcaide J, Shi Y. The RELT Family of Proteins: An Increasing Awareness of Their Importance for Cancer, the Immune System, and Development. Biomedicines 2023; 11:2695. [PMID: 37893069 PMCID: PMC10603948 DOI: 10.3390/biomedicines11102695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
This review highlights Receptor Expressed in Lymphoid Tissues (RELT), a Tumor Necrosis Factor Superfamily member, and its two paralogs, RELL1 and RELL2. Collectively, these three proteins are referred to as RELTfms and have gained much interest in recent years due to their association with cancer and other human diseases. A thorough knowledge of their physiological functions, including the ligand for RELT, is lacking, yet emerging evidence implicates RELTfms in a variety of processes including cytokine signaling and pathways that either promote cell death or survival. T cells from mice lacking RELT exhibit increased responses against tumors and increased inflammatory cytokine production, and multiple lines of evidence indicate that RELT may promote an immunosuppressive environment for tumors. The relationship of individual RELTfms in different cancers is not universal however, as evidence indicates that individual RELTfms may be risk factors in certain cancers yet appear to be protective in other cancers. RELTfms are important for a variety of additional processes related to human health including microbial pathogenesis, inflammation, behavior, reproduction, and development. All three proteins have been strongly conserved in all vertebrates, and this review aims to provide a clearer understanding of the current knowledge regarding these interesting proteins.
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Affiliation(s)
- John K. Cusick
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA
| | - Jessa Alcaide
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA
| | - Yihui Shi
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA
- California Pacific Medical Center Research Institute, Sutter Bay Hospitals, San Francisco, CA 94107, USA
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Moldogazieva NT, Zavadskiy SP, Astakhov DV, Sologova SS, Margaryan AG, Safrygina AA, Smolyarchuk EA. Differentially expressed non-coding RNAs and their regulatory networks in liver cancer. Heliyon 2023; 9:e19223. [PMID: 37662778 PMCID: PMC10474437 DOI: 10.1016/j.heliyon.2023.e19223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
The vast majority of human transcriptome is represented by various types of small RNAs with little or no protein-coding capability referred to as non-coding RNAs (ncRNAs). Functional ncRNAs include microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), which are expressed at very low, but stable and reproducible levels in a variety of cell types. ncRNAs regulate gene expression due to miRNA capability of complementary base pairing with mRNAs, whereas lncRNAs and circRNAs can sponge miRNAs off their target mRNAs to act as competitive endogenous RNAs (ceRNAs). Each miRNA can target multiple mRNAs and a single mRNA can interact with several miRNAs, thereby creating miRNA-mRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA regulatory networks. Over the past few years, a variety of differentially expressed miRNAs, lncRNAs, and circRNAs (DEMs, DELs, and DECs, respectively) have been linked to cancer pathogenesis. They can exert both oncogenic and tumor suppressor roles. In this review, we discuss the recent advancements in uncovering the roles of DEMs, DELs, and DECs and their networks in aberrant cell signaling, cell cycle, transcription, angiogenesis, and apoptosis, as well as tumor microenvironment remodeling and metabolic reprogramming during hepatocarcinogenesis. We highlight the potential and challenges in the use of differentially expressed ncRNAs as biomarkers for liver cancer diagnosis and prognosis.
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Affiliation(s)
- Nurbubu T. Moldogazieva
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Sergey P. Zavadskiy
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Dmitry V. Astakhov
- Department of Biochemistry, Institute of Biodesign and Complex Systems Modelling, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Susanna S. Sologova
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Arus G. Margaryan
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Anastasiya A. Safrygina
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Elena A. Smolyarchuk
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
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Sanchez A, Lhuillier J, Grosjean G, Ayadi L, Maenner S. The Long Non-Coding RNA ANRIL in Cancers. Cancers (Basel) 2023; 15:4160. [PMID: 37627188 PMCID: PMC10453084 DOI: 10.3390/cancers15164160] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
ANRIL (Antisense Noncoding RNA in the INK4 Locus), a long non-coding RNA encoded in the human chromosome 9p21 region, is a critical factor for regulating gene expression by interacting with multiple proteins and miRNAs. It has been found to play important roles in various cellular processes, including cell cycle control and proliferation. Dysregulation of ANRIL has been associated with several diseases like cancers and cardiovascular diseases, for instance. Understanding the oncogenic role of ANRIL and its potential as a diagnostic and prognostic biomarker in cancer is crucial. This review provides insights into the regulatory mechanisms and oncogenic significance of the 9p21 locus and ANRIL in cancer.
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Affiliation(s)
| | | | | | - Lilia Ayadi
- CNRS, Université de Lorraine, IMoPA, F-54000 Nancy, France
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Bohosova J, Kozelkova K, Al Tukmachi D, Trachtova K, Naar O, Ruckova M, Kolarikova E, Stanik M, Poprach A, Slaby O. Long non-coding RNAs enable precise diagnosis and prediction of early relapse after nephrectomy in patients with renal cell carcinoma. J Cancer Res Clin Oncol 2023; 149:7587-7600. [PMID: 36988708 PMCID: PMC10374689 DOI: 10.1007/s00432-023-04700-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
PURPOSE Renal cell carcinoma belongs among the deadliest malignancies despite great progress in therapy and accessibility of primary care. One of the main unmet medical needs remains the possibility of early diagnosis before the tumor dissemination and prediction of early relapse and disease progression after a successful nephrectomy. In our study, we aimed to identify novel diagnostic and prognostic biomarkers using next-generation sequencing on a novel cohort of RCC patients. METHODS Global expression profiles have been obtained using next-generation sequencing of paired tumor and non-tumor tissue of 48 RCC patients. Twenty candidate lncRNA have been selected for further validation on an independent cohort of paired tumor and non-tumor tissue of 198 RCC patients. RESULTS Sequencing data analysis showed significant dysregulation of more than 2800 lncRNAs. Out of 20 candidate lncRNAs selected for validation, we confirmed that 14 of them are statistically significantly dysregulated. In order to yield better discriminatory results, we combined several best performing lncRNAs into diagnostic and prognostic models. A diagnostic model consisting of AZGP1P1, CDKN2B-AS1, COL18A1, and RMST achieved AUC 0.9808, sensitivity 95.96%, and specificity 90.4%. The model for prediction of early relapse after nephrectomy consists of COLCA1, RMST, SNHG3, and ZNF667-AS1 and achieved AUC 0.9241 with sensitivity 93.75% and specificity 71.07%. Notably, no combination has outperformed COLCA1 alone. Lastly, a model for stage consists of ZNF667-AS1, PVT1, RMST, LINC00955, and TCL6 and achieves AUC 0.812, sensitivity 85.71%, and specificity 69.41%. CONCLUSION In our work, we identified several lncRNAs as potential biomarkers and developed models for diagnosis and prognostication in relation to stage and early relapse after nephrectomy.
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Affiliation(s)
- Julia Bohosova
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Katerina Kozelkova
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Dagmar Al Tukmachi
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Karolina Trachtova
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Ondrej Naar
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Michaela Ruckova
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Eva Kolarikova
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk University, Zluty Kopec 543/7, 602 00, Brno, Czech Republic
| | - Michal Stanik
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk University, Zluty Kopec 543/7, 602 00, Brno, Czech Republic
| | - Alexandr Poprach
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk University, Zluty Kopec 543/7, 602 00, Brno, Czech Republic
| | - Ondrej Slaby
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic.
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
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Gao H, Gao P, Ye N. Prelnc2: A prediction tool for lncRNAs with enhanced multi-level features of RNAs. PLoS One 2023; 18:e0286377. [PMID: 37262050 DOI: 10.1371/journal.pone.0286377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been widely studied for their important biological significance. In general, we need to distinguish them from protein coding RNAs (pcRNAs) with similar functions. Based on various strategies, algorithms and tools have been designed and developed to train and validate such classification capabilities. However, many of them lack certain scalability, versatility, and rely heavily on genome annotation. In this paper, we design a convenient and biologically meaningful classification tool "Prelnc2" using multi-scale position and frequency information of wavelet transform spectrum and generalizes the frequency statistics method. Finally, we used the extracted features and auxiliary features together to train the model and verify it with test data. PreLnc2 achieved 93.2% accuracy for animal and plant transcripts, outperforming PreLnc by 2.1% improvement and our method provides an effective alternative to the prediction of lncRNAs.
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Affiliation(s)
- Hua Gao
- College of Forestry, Nanjing Forestry University, Nanjing, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Peng Gao
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ning Ye
- College of Forestry, Nanjing Forestry University, Nanjing, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, China
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Zhang L, Piipponen M, Liu Z, Li D, Bian X, Niu G, Geara J, Toma MA, Sommar P, Xu Landén N. Human skin specific long noncoding RNA HOXC13-AS regulates epidermal differentiation by interfering with Golgi-ER retrograde transport. Cell Death Differ 2023; 30:1334-1348. [PMID: 36869179 PMCID: PMC10154349 DOI: 10.1038/s41418-023-01142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
After a skin injury, keratinocytes switch from a state of homeostasis to one of regeneration leading to the reconstruction of the epidermal barrier. The regulatory mechanism of gene expression underpinning this key switch during human skin wound healing is enigmatic. Long noncoding RNAs (lncRNAs) constitute a new horizon in the understanding of the regulatory programs encoded in the mammalian genome. By comparing the transcriptome of an acute human wound and skin from the same donor as well as keratinocytes isolated from these paired tissue samples, we generated a list of lncRNAs showing changed expression in keratinocytes during wound repair. Our study focused on HOXC13-AS, a recently evolved human lncRNA specifically expressed in epidermal keratinocytes, and we found that its expression was temporally downregulated during wound healing. In line with its enrichment in suprabasal keratinocytes, HOXC13-AS was found to be increasingly expressed during keratinocyte differentiation, but its expression was reduced by EGFR signaling. After HOXC13-AS knockdown or overexpression in human primary keratinocytes undergoing differentiation induced by cell suspension or calcium treatment and in organotypic epidermis, we found that HOXC13-AS promoted keratinocyte differentiation. Moreover, RNA pull-down assays followed by mass spectrometry and RNA immunoprecipitation analysis revealed that mechanistically HOXC13-AS sequestered the coat complex subunit alpha (COPA) protein and interfered with Golgi-to-endoplasmic reticulum (ER) molecular transport, resulting in ER stress and enhanced keratinocyte differentiation. In summary, we identified HOXC13-AS as a crucial regulator of human epidermal differentiation.
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Affiliation(s)
- Letian Zhang
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Minna Piipponen
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Zhuang Liu
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Dongqing Li
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden.,Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Xiaowei Bian
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Guanglin Niu
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Jennifer Geara
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Maria A Toma
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Pehr Sommar
- Department of Plastic and Reconstructive Surgery, Karolinska University Hospital, Stockholm, Sweden
| | - Ning Xu Landén
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, 17176, Stockholm, Sweden. .,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17176, Stockholm, Sweden.
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10
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Liu Y, Zhu L, Zhao W, Zhou Y, Shao S. High expression of ANRIL correlated with the poor prognosis in patients with cancer: A meta-analysis. Medicine (Baltimore) 2022; 101:e30531. [PMID: 36086708 PMCID: PMC10980395 DOI: 10.1097/md.0000000000030531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND ANRIL, also called CDKN2B antisense RNA 1, is an important genetic susceptibility locus for cardiovascular diseases and associated with numerous pathologies, including several human cancers. OBJECTIVE The relationship between ANRIL and the clinical outcome or prognosis of cancer patients was analyzed in this meta-analysis. METHODS One thousand seven hundred eight cancer patients were selected in 23 studies from 3 databases (Pubmed, Cochrane Library, and EMBASE). RESULTS A fixed-effects model indicated that the high expression of ANRIL is obviously linked to poor overall survival (OS) (Hazard ratio [HR] = 1.77, 95% confidence interval [CI] = 1.57-2.00, P < .00001); the random-effects model revealed poor disease-free survival (DFS) (HR = 1.86, 95% CI: 1.46-2.37, P < .00001). A high level of ANRIL expression was also associated with the tumor size (small vs large, odds ratio [OR] = 0.57, 95% CI: 0.39-0.83, P = .003), TNM stage (I + II vs III + IV; OR = 0.40, 95% CI: 0.24-0.69, P = .0008), and lymph node metastasis (LNM) (Yes vs No, OR = 3.66, 95% CI: 1.46-9.17, P = .006). ANRIL was not related significantly to histologic differentiation compared to poor with moderate + well; the OR value is 0.74, 95% CI: 0.26-2.12, P = .58. In addition, evidence suggested that a high level of ANRIL was positively associated with human cancer type, follow-up time, and sample size. CONCLUSION This meta-analysis demonstrated that ANRIL may be a valuable biomarker for predicting poor prognosis in cancer patients.
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Affiliation(s)
- Yun Liu
- Department of Digestive, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, Jiangsu, China
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Linqi Zhu
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wenjun Zhao
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yong Zhou
- Department of Digestive, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shihe Shao
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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11
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Significance of lncRNA CDKN2B-AS1 in Interventional Therapy of Liver Cancer and the Mechanism under Its Participation in Tumour Cell Growth via miR-199a-5p. JOURNAL OF ONCOLOGY 2022; 2022:2313416. [PMID: 36081669 PMCID: PMC9448535 DOI: 10.1155/2022/2313416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022]
Abstract
Methods Totally 34 LC patients admitted to our hospital between January 2020 and March 2021 (Obs group) and 32 healthy individuals over the same time span (Con group) were enrolled. CDKN2B-AS1 and miR-199a-5p in the two groups were PCR quantified, and their association and value for the diagnosis and therapy of LC were analyzed. In addition, purchased LC cells were adopted for in vitro assays, and the influences of CDKN2B-AS1 and miR-199a-5p on biological behaviours of LC cells were assessed through CCK-8, Transwell, and flow cytometry experiment, and their regulatory association was verified by the dual luciferase reporter (DLR) assay and rescue assay. And the autophagic protein expression was tested by the western blot to confirm the effect of both on the autophagic capacity of LC cells. Results CDKN2B-AS1 in LC cases presented high expression and dropped after therapy (P < 0.05), and the opposite situation of miR-199a-5p was found in the LC cases (P < 0.05). In vitro assays, after silencing of CDKN2B-AS1 and upregulation of miR-199a-5p, LC cells presented weaker viability, invasion and migration activities, and stronger apoptotic activity (all P < 0.05). The DLR assay revealed suppressed fluorescence activity of CDKN2B-AS1-WT by miR-199a-5p (P < 0.05). Moreover, according to the rescue assay, the impacts of silencing CDKN2B-AS1 on LC cells could be completely offset by silencing miR-199a-5p (P < 0.05). According to the clone formation and WB assay, the growth and autophagy of LC cells were under the regulation of CDKN2B-AS1 targeting miR-199a-5p (P < 0.05). Conclusion With high expression in LC cases, CDKN2B-AS1 is implicated in the development and progression of LC by suppressing cell autophagy through targeting miR-199a-5p.
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12
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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: 1.3] [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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13
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Biomarkers and Genetic Markers of Hepatocellular Carcinoma and Cholangiocarcinoma-What Do We Already Know. Cancers (Basel) 2022; 14:cancers14061493. [PMID: 35326644 PMCID: PMC8946081 DOI: 10.3390/cancers14061493] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/09/2022] [Accepted: 03/13/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Hepatocellular carcinoma and cholangiocarcinoma continue to remain a serious threat. In this review, we describe the most common biomarkers and genetic markers currently used in the diagnosis of hepatocellular carcinoma and cholangiocarcinoma. It can be observed that biomarkers and genetic markers might be applied in various parts of diagnosis including screening tests in a high-risk group, non-invasive detection, control of therapy, treatment selection, and control of recurrence. Also, it can be seen that nowadays there is a need for more specific markers that would improve the detection in early or very early stages of both types of cancers and further research should be focused on it. Abstract Hepatocellular carcinoma (HCC) is the most common primary liver cancer with an increasing worldwide mortality rate. Cholangiocarcinoma (CCA) is the second most common primary liver cancer. In both types of cancers, early detection is very important. Biomarkers are a relevant part of diagnosis, enabling non-invasive detection and control of cancer recurrence, as well as in the application of screening tests in high-risk groups. Furthermore, some of these biomarkers are useful in controlling therapy and treatment selection. Detection of some markers presents higher sensitivity and specificity in combination with other markers when compared with a single detection. Some gene aberrations are also prognostic markers in the two types of cancers. In the following review, we discuss the most common biomarkers and genetic markers currently being used in the diagnosis of hepatocellular carcinoma and cholangiocarcinoma.
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14
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Shan B, Qu S, Lv S, Fan D, Wang S. YY1-induced long non-coding RNA small nucleolar RNA host gene 8 promotes the tumorigenesis of melanoma via the microRNA-656-3p/SERPINE1 mRNA binding protein 1 axis. Bioengineered 2022; 13:4832-4843. [PMID: 35156513 PMCID: PMC8973976 DOI: 10.1080/21655979.2022.2034586] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Long non-coding (lnc) RNA serves a vital role in the cellular processes of carcinoma. This study aimed to explore the accurate mechanism underlying lncRNA small nucleolar RNA host gene 8 (SNHG8) in melanoma. In this study, lncRNA SNHG8 expression were upregulated in melanoma tissues and cells, and lncRNA SNHG8 knockdown reduced melanoma cell viability, migration and invasion. Moreover, lncRNA SNHG8 expression could be induced by transcription factor YY1. In addition, we found that miR-656 could directly bind to lncRNA SNHG8 and SERPINE1 mRNA binding protein 1 (SERBP1). Rescue assays indicated that miR-656 overexpression inhibited the aforementioned cellular activities in melanoma cells, which were reversed by SERBP1 overexpression. In conclusion, this work elucidated that YY1-induced upregulation of lncRNA SNHG8 boosted the development of melanoma via the miR-656-3p/SERBP1 axis, providing a novel therapeutic strategy for melanoma treatment.
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Affiliation(s)
- Baihui Shan
- Department of Dermatology, The Second Hospital of Jilin University, China
| | - Shengming Qu
- Department of Dermatology, The Second Hospital of Jilin University, China
| | - Sha Lv
- Department of Dermatology, The Second Hospital of Jilin University, China
| | - Dandan Fan
- Department of Dermatology, Jilin Province People’s Hospital, China
| | - Shu Wang
- Department of Radio Therapy, The Second Hospital of Jilin University, China
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15
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Li J, Kong M, Wang D, Yang Z, Hao X. Prediction of lncRNA-Disease Associations via Closest Node Weight Graphs of the Spatial Neighborhood Based on the Edge Attention Graph Convolutional Network. Front Genet 2022; 12:808962. [PMID: 35058974 PMCID: PMC8763691 DOI: 10.3389/fgene.2021.808962] [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: 11/04/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022] Open
Abstract
Accumulated evidence of biological clinical trials has shown that long non-coding RNAs (lncRNAs) are closely related to the occurrence and development of various complex human diseases. Research works on lncRNA–disease relations will benefit to further understand the pathogenesis of human complex diseases at the molecular level, but only a small proportion of lncRNA–disease associations has been confirmed. Considering the high cost of biological experiments, exploring potential lncRNA–disease associations with computational approaches has become very urgent. In this study, a model based on closest node weight graph of the spatial neighborhood (CNWGSN) and edge attention graph convolutional network (EAGCN), LDA-EAGCN, was developed to uncover potential lncRNA–disease associations by integrating disease semantic similarity, lncRNA functional similarity, and known lncRNA–disease associations. Inspired by the great success of the EAGCN method on the chemical molecule property recognition problem, the prediction of lncRNA–disease associations could be regarded as a component recognition problem of lncRNA–disease characteristic graphs. The CNWGSN features of lncRNA–disease associations combined with known lncRNA–disease associations were introduced to train EAGCN, and correlation scores of input data were predicted with EAGCN for judging whether the input lncRNAs would be associated with the input diseases. LDA-EAGCN achieved a reliable AUC value of 0.9853 in the ten-fold cross-over experiments, which was the highest among five state-of-the-art models. Furthermore, case studies of renal cancer, laryngeal carcinoma, and liver cancer were implemented, and most of the top-ranking lncRNA–disease associations have been proven by recently published experimental literature works. It can be seen that LDA-EAGCN is an effective model for predicting potential lncRNA–disease associations. Its source code and experimental data are available at https://github.com/HGDKMF/LDA-EAGCN.
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Affiliation(s)
- Jianwei Li
- Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin, China.,Hebei Province Key Laboratory of Big Data Calculation, Hebei University of Technology, Tianjin, China
| | - Mengfan Kong
- Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Duanyang Wang
- Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Zhenwu Yang
- Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Xiaoke Hao
- Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
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16
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A Minimal Subset of Seven Genes Associated with Tumor Hepatocyte Differentiation Predicts a Poor Prognosis in Human Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13225624. [PMID: 34830779 PMCID: PMC8616205 DOI: 10.3390/cancers13225624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022] Open
Abstract
Simple Summary Liver cancer is one of the most commonly diagnosed cancers worldwide and the fourth leading cause of cancer-related deaths. Hepatocellular carcinoma (HCC) accounts for at least 80% of all malignant liver primary tumors. A better characterization of molecular mechanisms underlying HCC onset and progression may lead to discover new therapeutic targets and biomarkers. In this study, we performed an integrative transcriptomics analysis to evaluate the clinical relevance of genes associated with hepatocyte differentiation in human HCC. The HepaRG cell line model was used to define a gene expression signature reflecting the status of tumor hepatocyte differentiation. This signature was able to stratify HCC patients into clinically relevant molecular subtypes. Then, a minimal subset of seven differentiation-associated genes was identified to predict a poor prognosis in several cancer datasets. Abstract Hepatocellular carcinoma (HCC) is a deadly cancer worldwide as a result of a frequent late diagnosis which limits the therapeutic options. Tumor progression in HCC is closely correlated with the dedifferentiation of hepatocytes, the main parenchymal cells in the liver. Here, we hypothesized that the expression level of genes reflecting the differentiation status of tumor hepatocytes could be clinically relevant in defining subsets of patients with different clinical outcomes. To test this hypothesis, an integrative transcriptomics approach was used to stratify a cohort of 139 HCC patients based on a gene expression signature established in vitro in the HepaRG cell line using well-controlled culture conditions recapitulating tumor hepatocyte differentiation. The HepaRG model was first validated by identifying a robust gene expression signature associated with hepatocyte differentiation and liver metabolism. In addition, the signature was able to distinguish specific developmental stages in mice. More importantly, the signature identified a subset of human HCC associated with a poor prognosis and cancer stem cell features. By using an independent HCC dataset (TCGA consortium), a minimal subset of seven differentiation-related genes was shown to predict a reduced overall survival, not only in patients with HCC but also in other types of cancers (e.g., kidney, pancreas, skin). In conclusion, the study identified a minimal subset of seven genes reflecting the differentiation status of tumor hepatocytes and clinically relevant for predicting the prognosis of HCC patients.
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Huang GH, Zhang YH, Chen L, Li Y, Huang T, Cai YD. Identifying Lung Cancer Cell Markers with Machine Learning Methods and Single-Cell RNA-Seq Data. Life (Basel) 2021; 11:life11090940. [PMID: 34575089 PMCID: PMC8467493 DOI: 10.3390/life11090940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/21/2022] Open
Abstract
Non-small cell lung cancer is a major lethal subtype of epithelial lung cancer, with high morbidity and mortality. The single-cell sequencing technique plays a key role in exploring the pathogenesis of non-small cell lung cancer. We proposed a computational method for distinguishing cell subtypes from the different pathological regions of non-small cell lung cancer on the basis of transcriptomic profiles, including a group of qualitative classification criteria (biomarkers) and various rules. The random forest classifier reached a Matthew’s correlation coefficient (MCC) of 0.922 by using 720 features, and the decision tree reached an MCC of 0.786 by using 1880 features. The obtained biomarkers and rules were analyzed in the end of this study.
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Affiliation(s)
- Guo-Hua Huang
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Department of Mechanical and Energy Engineering, Shaoyang University, Shaoyang 422000, China;
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Lei Chen
- Department of College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China;
| | - You Li
- Department of Mechanical and Energy Engineering, Shaoyang University, Shaoyang 422000, China;
| | - Tao Huang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (T.H.); (Y.-D.C.); Tel.: +86-21-54923269 (T.H.); +86-21-66136132 (Y.-D.C.)
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Correspondence: (T.H.); (Y.-D.C.); Tel.: +86-21-54923269 (T.H.); +86-21-66136132 (Y.-D.C.)
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Zhang S, Zhang F, Niu Y, Yu S. Aberration of lncRNA LINC00460 is a Promising Prognosis Factor and Associated with Progression of Clear Cell Renal Cell Carcinoma. Cancer Manag Res 2021; 13:6489-6497. [PMID: 34429655 PMCID: PMC8379393 DOI: 10.2147/cmar.s322747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/26/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Long noncoding RNAs have been studied more and more as potential prognostic markers. However, the prognostic of LINC00460 in clear cell renal cell carcinoma (ccRCC) has not been explored. In this study, the potential role of LINC00460 was investigated in ccRCC. Patients and Methods One hundred thirteen pairs of ccRCC tissues and para-normal tissues were collected. The expressions of LINC00460 in these tissues and ccRCC cells were evaluated via qRT-PCR. The prognostic value of LINC00460 was accessed with the use of Kaplan–Meier analysis and Cox proportional hazards model analysis. The influence of LINC00460 on ccRCC cell proliferation, migration, and invasion was determined via cell counting kit-8 (CCK-8) and Transwell assays. Results The results revealed that LINC00460 was significantly enhanced in ccRCC tissues, as well as in ccRCC cell lines. The overexpression of LINC00460 was significantly associated with lymph node metastasis and TNM stage, and lead to poor overall survival. Knockdown of LINC00460 reduces the cell ability of proliferation, migration, and invasion. LINC00460 could sponge to miR-149-5p. Conclusion LINC00460 may be developed as a prognostic biomarker and molecular therapy target for ccRCC.
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Affiliation(s)
- Shijie Zhang
- General Surgery, The Second Affiliated Hospital of Mudanjiang Medical University, Mudanjiang, Heilongjiang, 157011, People's Republic of China
| | - Fengyun Zhang
- Hematology and Rheumatology, The Second Affiliated Hospital of Mudanjiang Medical University, Mudanjiang, Heilongjiang, 157011, People's Republic of China
| | - Yingdong Niu
- Supply Room, The Second Affiliated Hospital of Mudanjiang Medical University, Mudanjiang, Heilongjiang, 157011, People's Republic of China
| | - Shenglong Yu
- Urology Surgery, The Second Affiliated Hospital of Mudanjiang Medical University, Mudanjiang, Heilongjiang, 157011, People's Republic of China
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Sun L, Cui Y, Jiang K, Li J. Down-regulation of long non-coding RNA antisense non-coding RNA in the INK4 locus suppresses OVCAR-3 cells proliferation and induction of apoptosis by Wnt/β -catenin. J Pharm Pharmacol 2021; 73:1212-1217. [PMID: 33772549 DOI: 10.1093/jpp/rgab042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/20/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Ovarian cancer is a lethal gynecological malignancy. Long non-coding RNA antisense non-coding RNA in the INK4 locus (lncRNA ANRIL) was reported to have a critical role in cancer advancement. The ANRIL-mediated oncogenic underlying molecular mechanisms are not fully understood in ovarian cancer. We aimed to study ANRIL silencing effects on the proliferation and apoptosis of OVCAR-3 cells. METHODS The ANRIL was Knockdown by transfection of OVCAR-3 cells with si-RNA against ANRIL. MTT assay and cell death ELISA kit were used to evaluate cellular proliferation and apoptosis. The expression levels of ANRIL, pro-and anti-apoptotic genes were assessed using q-RT-PCR. Western blotting was used to assess Wnt/β-catenin signalling pathway. KEY FINDINGS ANRIL down-regulating in OVCAR-3 cell lines resulted in significant inhibition of cellular proliferation, apoptosis induction, as well as suppression of cellular invasion. Besides, knockdown of ANRIL led to pro-apoptotic genes up-regulation, Bad and Bax and anti-apoptotic genes down-regulation, Bid and Bcl-2. More importantly, we observed that ANRIL inhibition suppressed the vital components expression of the Wnt/β-catenin cascade. CONCLUSION Our findings showed that down-regulation of lncRNA ANRIL resulted in the effective suppression of OVCAR-3 cell proliferation and invasion and induction of apoptosis by preventing Wnt/β-catenin signal transduction.
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Affiliation(s)
- Lingna Sun
- Department of Gynecology, Maternal and Child Health Care Hospital of Shandong Province, Jinan City, Shandong Province, China
| | - Yuping Cui
- Department of Obstetrics and Gynecology, Huantai County People's Hospital, Zibo City, Shandong Province, China
| | - Kongdi Jiang
- Department of Obstetrics and Gynecology, Huantai County People's Hospital, Zibo City, Shandong Province, China
| | - Juan Li
- Department of Gynecology, Maternal and Child Health Care Hospital of Shandong Province, Jinan City, Shandong Province, China
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20
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Merdrignac A, Papoutsoglou P, Coulouarn C. Long Noncoding RNAs in Cholangiocarcinoma. Hepatology 2021; 73:1213-1226. [PMID: 32865244 DOI: 10.1002/hep.31534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/30/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Aude Merdrignac
- InsermUniv RennesNuMeCan (Nutrition Metabolisms and Cancer)UMR_S 1241CHU Rennes, F-35000RennesFrance
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21
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Sun JR, Kong CF, Xiao KM, Yang JL, Qu XK, Sun JH. Integrated Analysis of lncRNA-Mediated ceRNA Network Reveals a Prognostic Signature for Hepatocellular Carcinoma. Front Genet 2021; 11:602542. [PMID: 33381151 PMCID: PMC7767998 DOI: 10.3389/fgene.2020.602542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common types of malignancy and is associated with high mortality. Prior research suggests that long non-coding RNAs (lncRNAs) play a crucial role in the development of HCC. Therefore, it is necessary to identify lncRNA-associated therapeutic biomarkers to improve the accuracy of HCC prognosis. Transcriptomic data of HCC obtained from The Cancer Genome Atlas (TCGA) database were used in the present study. Differentially expressed RNAs (DERNAs), including 74 lncRNAs, 16 miRNAs, and 35 mRNAs, were identified using bioinformatics analysis. The DERNAs were subsequently used to reconstruct a competing endogenous RNA (ceRNA) network. A lncRNA signature was revealed using Cox regression analysis, including LINC00200, MIR137HG, LINC00462, AP002478.1, and HTR2A-AS1. Kaplan-Meier plot demonstrated that the lncRNA signature is highly accurate in discriminating high- and low-risk patients (P < 0.05). The area under curve (AUC) value exceeded 0.7 in both training and validation cohort, suggesting a high prognostic potential of the signature. Furthermore, multivariate Cox regression analysis indicated that both the TNM stage and the lncRNA signature could serve as independent prognostic factors for HCC (P < 0.05). Then, a nomogram comprising the TNM stage and the lncRNA signature was determined to raise the accuracy in predicting the survival of HCC patients. In the present study, we have introduced a ceRNA network that could contribute to provide a new insight into the identification of potential regulation mechanisms for the development of HCC. The five-lncRNA signature could serve as a reliable biosignature for HCC prognosis, while the nomogram possesses strong potential in clinical applications.
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Affiliation(s)
- Jian-Rong Sun
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China.,Oncology Department of Integrated Traditional Chinese and Western Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Chen-Fan Kong
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China.,Gastroenterology Department, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Kun-Min Xiao
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jia-Lu Yang
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China.,Gastroenterology Department, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xiang-Ke Qu
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jing-Hui Sun
- Gastroenterology Department, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
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22
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Ahn KS, Kang KJ. Molecular heterogeneity in intrahepatic cholangiocarcinoma. World J Hepatol 2020; 12:1148-1157. [PMID: 33442444 PMCID: PMC7772740 DOI: 10.4254/wjh.v12.i12.1148] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/01/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023] Open
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a heterogeneous primary liver cancer, and currently there exist only a few options of targeted therapy. Histopathologically, iCCA is sub-classified according to morphology (mass forming type, periductal infiltrating type, and intraductal growing type) and histology (small duct type and large duct type). According to different histopathological types, clinical features such as risk factors and prognosis vary. Recent developments in genomic profiling have revealed several molecular markers for poor prognosis and activation of oncogenic pathways. Exploration of molecular characteristics of iCCA in each patient is a major challenge in a clinical setting, and there is no effective molecular-based targeted therapy. However, several recent studies suggested molecular-based subtypes with corresponding clinical and pathological features. Even though the subtypes have not yet been validated, it is possible that molecular features can be predicted based on clinicopathological characteristics and that this could be used for a more rational approach to integrative clinical and molecular subclassification and targeted therapy. In this review, we explored the genomic landscape of iCCA and attempted to find relevance between clinicopathologic and molecular features in molecular subtypes in several published studies. The results reveal future directions that may lead to a rational approach to the targeted therapy.
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Affiliation(s)
- Keun Soo Ahn
- Department of Surgery, Keimyung University Dongsan Hospital, Keimyung University School of Medicine, Daegu 42601, South Korea
| | - Koo Jeong Kang
- Department of Surgery, Keimyung University Dongsan Hospital, Keimyung University School of Medicine, Daegu 42601, South Korea
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23
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Rizzo A, Ricci AD, Bonucci C, Tober N, Palloni A, Frega G, Brandi G. Experimental HER2- targeted therapies for biliary tract cancer. Expert Opin Investig Drugs 2020; 30:389-399. [PMID: 33218269 DOI: 10.1080/13543784.2021.1854724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Biliary tract cancers (BTCs) constitute a heterogeneous group of poor-prognosis solid tumors with limited treatment options. In the last decade, global efforts have tried to identify therapeutic targets by genomic profiling of BTC, unveiling several genetic aberrations that could play a prognostic and/or a predictive role in these malignancies.Areas covered: In this review, we will present an overview regarding the role of HER2 targeted therapies in BTC, with a particular focus on clinical studies carried out in this field to date and ongoing trials. A literature search was conducted in August 2020 of Pubmed/Medline, Cochrane library and Scopus databases for published preclinical and clinical studies; moreover, abstract of international cancer meetings (AACR, ASCO, and ESMO) were reviewed.Expert opinion: Despite recent advances in medical oncology, the overall survival of BTC patients remains low and there is an urgent need for novel and more effective treatments. Although HER2 blockade has been suggested to induce durable tumor responses in selected subjects with BTC, controversial results have been reported so far and data from ongoing prospective clinical trials are awaited to further clarify the role of anti-HER2 therapies in BTC.
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Affiliation(s)
- Alessandro Rizzo
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy.,Division of Oncology, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Angela Dalia Ricci
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy.,Division of Oncology, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Chiara Bonucci
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy.,Division of Oncology, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Nastassja Tober
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy.,Division of Oncology, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Andrea Palloni
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy.,Division of Oncology, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giorgio Frega
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy.,Division of Oncology, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Brandi
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy.,Division of Oncology, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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24
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Cusick JK, Alhomsy Y, Wong S, Talbott G, Uversky VN, Hart C, Hejazi N, Jacobs AT, Shi Y. RELT stains prominently in B-cell lymphomas and binds the hematopoietic transcription factor MDFIC. Biochem Biophys Rep 2020; 24:100868. [PMID: 33367115 PMCID: PMC7749370 DOI: 10.1016/j.bbrep.2020.100868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/02/2020] [Accepted: 11/23/2020] [Indexed: 11/30/2022] Open
Abstract
Receptor Expressed in Lymphoid Tissues (RELT) is a human tumor necrosis factor receptor superfamily member (TNFRSF) that is expressed most prominently in cells and tissues of the hematopoietic system. RELL1 and RELL2 are two homologs that physically interact with RELT and co-localize with RELT at the plasma membrane. This study sought to further elucidate the function of RELT by identifying novel protein interactions with RELT family members. The transcription factor MyoD family inhibitor domain-containing (MDFIC) was identified in a yeast two-hybrid genetic screen using RELL1 as bait. MDFIC co-localizes with RELT family members at the plasma membrane; this co-localization was most prominently observed with RELL1 and RELL2. In vitro co-immunoprecipitation (Co-IP) was utilized to demonstrate that MDFIC physically interacts with RELT, RELL1, and RELL2. Co-IP using deletion mutants of MDFIC and RELT identified regions important for physical association between MDFIC and RELT family members and a computational analysis revealed that RELT family members are highly disordered proteins. Immunohistochemistry of normal human lymph nodes revealed RELT staining that was most prominent in macrophages. Interestingly, the level of RELT staining significantly increased progressively in low and high-grade B-cell lymphomas versus normal lymph nodes. RELT co-staining with CD20 was observed in B-cell lymphomas, indicating that RELT is expressed in malignant B cells. Collectively, these results further our understanding of RELT-associated signaling pathways, the protein structure of RELT family members, and provide preliminary evidence indicating an association of RELT with B-cell lymphomas.
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Affiliation(s)
- John K. Cusick
- Department of Basic Science, California Northstate University, College of Medicine, Elk Grove, CA, 95757, USA
| | - Yasmeen Alhomsy
- Department of Basic Science, California Northstate University, College of Medicine, Elk Grove, CA, 95757, USA
| | - Stephanie Wong
- Department of Medical Education, California University of Science and Medicine, San Bernardino, CA, 92408, USA
| | - George Talbott
- Department of Pharmaceutical and Biomedical Sciences, California Northstate University College of Pharmacy, Elk Grove, CA, 95757, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Cara Hart
- Department of Biology, The University of Hawaii at Hilo, Hilo, HI, 96720, USA
| | - Nazila Hejazi
- Department of Clinical Science, California Northstate University, College of Medicine, Elk Grove, CA, 95757, USA
| | - Aaron T. Jacobs
- Department of Medical Education, California University of Science and Medicine, San Bernardino, CA, 92408, USA
| | - Yihui Shi
- Department of Basic Science, California Northstate University, College of Medicine, Elk Grove, CA, 95757, USA
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25
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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: 3.0] [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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26
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Bagante F, Tripepi M, Spolverato G, Tsilimigras DI, Pawlik TM. Assessing prognosis in cholangiocarcinoma: a review of promising genetic markers and imaging approaches. Expert Opin Orphan Drugs 2020. [DOI: 10.1080/21678707.2020.1801410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fabio Bagante
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
- Department of Surgery, University of Verona, Verona, Italy
| | - Marzia Tripepi
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
- Department of Surgery, University of Verona, Verona, Italy
| | - Gaya Spolverato
- Clinica Chirurgica I, Department of Surgical, Oncological and Gastroenterological Sciences (Discog), University of Padova, Padova, Italy
| | - Diamantis I. Tsilimigras
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | - Timothy M. Pawlik
- Department of Surgery, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
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27
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Ma J, Feng J, Zhou X. Long non-coding RNA HAGLROS regulates lipid metabolism reprogramming in intrahepatic cholangiocarcinoma via the mTOR signaling pathway. Exp Mol Pathol 2020; 115:104466. [PMID: 32446859 DOI: 10.1016/j.yexmp.2020.104466] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/09/2020] [Accepted: 05/14/2020] [Indexed: 02/08/2023]
Abstract
Alternation of long non-coding RNA (lncRNA) is implicated in intrahepatic cholangiocarcinoma (ICC) development. HAGLROS is a lncRNA with a length of 699 bp, which is involved in the progression of various cancers. But the mechanism of HAGLROS in ICC remains unknown. In this study, the sh-HAGLROS-1 or sh-HAGLROS-2 was transfected into QBC939 cells, and overexpressing HAGLROS vector was transfected into KMCH cells. HAGLROS expression in ICC tissues and cell lines was detected, and its association with ICC prognosis was further analyzed. Lipid accumulation and lipid-related indicators (TG, LDL-C, TC and HDLC) in QBC939 and KMCH cells were measured. ICC cell viability, invasion and migration were measured. Western blot analysis was used to detect levels of the mTOR axis-related proteins and autophagy-related proteins (LC3I, LC3II, Beclin and P62). The levels of serum lipids and SREBP1 positive expression in transplanted tumors of nude mice were detected. HAGLROS was highly expressed in ICC and negatively correlated with prognosis. QBC939 cells with knocking down HAGLROS exhibited reduced lipid-related protein levels, blocked ICC cellular processes, inactivated mTOR axis, and increased autophagy. QBC939 cells with overexpressing HAGLROS showed opposite trends. The lipid-related protein levels in serum of nude mice and SREBP1 positive expression in transplanted tumors were diminished. Taken together, sh-HAGLROS inactivated the mTOR axis and promoted autophagy, thereby improving lipid metabolism reprogramming in ICC. This study may offer novel ICC treatments.
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Affiliation(s)
- Jun Ma
- Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201100, PR China
| | - Jinfeng Feng
- Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201100, PR China
| | - Xiang Zhou
- Department of General Surgery, Minhang Hospital, Fudan University, Shanghai 201100, PR China.
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28
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Bekric D, Neureiter D, Ritter M, Jakab M, Gaisberger M, Pichler M, Kiesslich T, Mayr C. Long Non-Coding RNAs in Biliary Tract Cancer-An Up-to-Date Review. J Clin Med 2020; 9:jcm9041200. [PMID: 32331331 PMCID: PMC7231154 DOI: 10.3390/jcm9041200] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
The term long non-coding RNA (lncRNA) describes non protein-coding transcripts with a length greater than 200 base pairs. The ongoing discovery, characterization and functional categorization of lncRNAs has led to a better understanding of the involvement of lncRNAs in diverse biological and pathological processes including cancer. Aberrant expression of specific lncRNA species was demonstrated in various cancer types and associated with unfavorable clinical characteristics. Recent studies suggest that lncRNAs are also involved in the development and progression of biliary tract cancer, a rare disease with high mortality and limited therapeutic options. In this review, we summarize current findings regarding the manifold roles of lncRNAs in biliary tract cancer and give an overview of the clinical and molecular consequences of aberrant lncRNA expression as well as of underlying regulatory functions of selected lncRNA species in the context of biliary tract cancer.
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Affiliation(s)
- Dino Bekric
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria;
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Markus Ritter
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Paracelsus Medical University, 5020 Salzburg, Austria
- Gastein Research Institute, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Martin Jakab
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
| | - Martin Gaisberger
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Paracelsus Medical University, 5020 Salzburg, Austria
- Gastein Research Institute, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Martin Pichler
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Clinical Oncology, Department of Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria;
| | - Tobias Kiesslich
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria
| | - Christian Mayr
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria
- Correspondence:
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Abstract
PURPOSE OF REVIEW Cholangiocarcinoma (CCA) are heterogeneous tumors that arise from the malignant transformation of cholangiocytes along the biliary tree. CCA heterogeneity occurs at multiple levels and results in resistance to therapy and poor prognosis. Here, we review the molecular classification of CCA by focusing on the latest progresses based on genetic, epigenetic, transcriptomic and proteomic profiles. In addition, we introduce the emerging field of radiogenomics. RECENT FINDINGS Genome-wide integrative omics approaches have been widely reported by using large cohorts of CCA patients. Morphomolecular correlations have been established, including enrichment of FGFR2 gene fusions and IDH1/2 mutations in iCCA. A specific IDH mutant iCCA subtype displays high mitochondrial and low chromatin modifier expression linked to ARID1A promoter hypermethylation. Examples of translation of these classifications for the management of CCA have also been reported, with prediction of drug efficacy based on genetic alterations. SUMMARY Although there is currently no international consensus on CCA morphomolecular classification, the recent initiatives developed under the umbrella of The European Network for the Study of Cholangiocarcinoma (ENSCCA) should favor new collaborative research. Identifying distinct molecular subgroups and developing appropriate targeted therapies will improve the clinical outcome of patients with CCA.
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30
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LNCRNA CDKN2B-AS1 regulates mesangial cell proliferation and extracellular matrix accumulation via miR-424-5p/HMGA2 axis. Biomed Pharmacother 2020; 121:109622. [PMID: 31707340 DOI: 10.1016/j.biopha.2019.109622] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/18/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Previous study has demonstrated that long noncoding RNA cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1) was abnormally expressed in diabetic nephropathy (DN). However, the underlying mechanism that allows CDKN2B-AS1 in the progression of DN remains to be further elucidated. METHODS Peripheral blood cells of 24 diabetes patients with DN and 20 without DN were collected. Human glomerular mesangial cells (HGMC) were cultured in high glucose or low glucose medium. The expression levels of CDKN2B-AS1, microRNA (miR)-424-5p and high mobility group AT hook 2 (HMGA2) were detected by quantitative real-time polymerase chain reaction or western blot. The target association between miR-424-5p and CDKN2B-AS1 or HMGA2 was confirmed by dual-luciferase reporter and RNA immunoprecipitation assays. Cell proliferation, extracellular matrix (ECM) accumulation and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling were investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) and western blot, respectively. RESULTS CDKN2B-AS1 expression was up-regulated and miR-424-5p level was down-regulated in peripheral blood of DN patients and high glucose-treated HGMC cells. CDKN2B-AS1 was validated as a sponge of miR-424-5p. Silence of CDKN2B-AS1 repressed proliferation and ECM accumulation by increasing miR-424-5p. HMGA2 was a target of miR-424-5p and miR-424-5p overexpression inhibited proliferation, ECM accumulation and PI3K/AKT pathway by targeting HMGA2. Moreover, knockdown of CDKN2B-AS1 inhibited HMGA2 expression and PI3K/AKT pathway by increasing miR-424-5p. CONCLUSION Knockdown of CDKN2B-AS1 suppressed proliferation, ECM accumulation and PI3K/AKT signaling by increasing miR-424-5p and decreasing HMGA2 in high glucose-treated HMGC cells.
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31
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Papoutsoglou P, Louis C, Coulouarn C. Transforming Growth Factor-Beta (TGFβ) Signaling Pathway in Cholangiocarcinoma. Cells 2019; 8:cells8090960. [PMID: 31450767 PMCID: PMC6770250 DOI: 10.3390/cells8090960] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/12/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
Cholangiocarcinoma is a deadly cancer worldwide, associated with a poor prognosis and limited therapeutic options. Although cholangiocarcinoma accounts for less than 15% of liver primary cancer, its silent nature restricts early diagnosis and prevents efficient treatment. Therefore, it is of clinical relevance to better understand the molecular basis of cholangiocarcinoma, including the signaling pathways that contribute to tumor onset and progression. In this review, we discuss the genetic, molecular, and environmental factors that promote cholangiocarcinoma, emphasizing the role of the transforming growth factor β (TGFβ) signaling pathway in the progression of this cancer. We provide an overview of the physiological functions of TGFβ signaling in preserving liver homeostasis and describe how advanced cholangiocarcinoma benefits from the tumor-promoting effects of TGFβ. Moreover, we report the importance of noncoding RNAs as effector molecules downstream of TGFβ during cholangiocarcinoma progression, and conclude by highlighting the need for identifying novel and clinically relevant biomarkers for a better management of patients with cholangiocarcinoma.
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Affiliation(s)
- Panagiotis Papoutsoglou
- Inserm, Univ Rennes, Inra, Institut NuMeCan (Nutrition Metabolisms and Cancer), UMR_S 1241, 35033 Rennes, France
| | - Corentin Louis
- Inserm, Univ Rennes, Inra, Institut NuMeCan (Nutrition Metabolisms and Cancer), UMR_S 1241, 35033 Rennes, France
| | - Cédric Coulouarn
- Inserm, Univ Rennes, Inra, Institut NuMeCan (Nutrition Metabolisms and Cancer), UMR_S 1241, 35033 Rennes, France.
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