1
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Wu L, Zhang Y, Ren J. Targeting non-coding RNAs and N 6-methyladenosine modification in hepatocellular carcinoma. Biochem Pharmacol 2024; 223:116153. [PMID: 38513741 DOI: 10.1016/j.bcp.2024.116153] [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: 02/09/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Hepatocellular carcinoma (HCC), the most common form of primary liver cancers, accounts for a significant portion of cancer-related death globally. However, the molecular mechanisms driving the onset and progression of HCC are still not fully understood. Emerging evidence has indicated that non-protein-coding regions of genomes could give rise to transcripts, termed non-coding RNA (ncRNA), forming novel functional driving force for aberrant cellular activity. Over the past decades, overwhelming evidence has denoted involvement of a complex array of molecular function of ncRNAs at different stages of HCC tumorigenesis and progression. In this context, several pre-clinical studies have highlighted the potentials of ncRNAs as novel therapeutic modalities in the management of human HCC. Moreover, N6-methyladenosine (m6A) modification, the most prevalent form of internal mRNA modifications in mammalian cells, is essential for the governance of biological processes within cells. Dysregulation of m6A in ncRNAs has been implicated in human carcinogenesis, including HCC. In this review, we will discuss dysregulation of several hallmark ncRNAs (miRNAs, lncRNAs, and circRNAs) in HCC and address the latest advances for their involvement in the onset and progression of HCC. We also focus on dysregulation of m6A modification and various m6A regulators in the etiology of HCC. In the end, we discussed the contemporary preclinical and clinical application of ncRNA-based and m6A-targeted therapies in HCC.
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Affiliation(s)
- Lin Wu
- Department of Cardiology and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai 200032, China
| | - Yingmei Zhang
- Department of Cardiology and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai 200032, China
| | - Jun Ren
- Department of Cardiology and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai 200032, China.
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2
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Han L, Cheng B, Wei W, Liu L, Cheng S, Liu H, Jia Y, Wen Y, Zhang F. Whole-Transcriptome Sequencing of Knee Joint Cartilage from Kashin-Beck Disease and Osteoarthritis Patients. Int J Mol Sci 2024; 25:4348. [PMID: 38673933 PMCID: PMC11049856 DOI: 10.3390/ijms25084348] [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: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of this study was to provide a comprehensive understanding of similarities and differences in mRNAs, lncRNAs, and circRNAs within cartilage for Kashin-Beck disease (KBD) compared to osteoarthritis (OA). We conducted a comparison of the expression profiles of mRNAs, lncRNAs, and circRNAs via whole-transcriptome sequencing in eight KBD and ten OA individuals. To facilitate functional annotation-enriched analysis for differentially expressed (DE) genes, DE lncRNAs, and DE circRNAs, we employed bioinformatic analysis utilizing Gene Ontology (GO) and KEGG. Additionally, using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), we validated the expression levels of four cartilage-related genes in chondrocytes. We identified a total of 43 DE mRNAs, 1451 DE lncRNAs, and 305 DE circRNAs in KBD cartilage tissue compared to OA (q value < 0.05; |log2FC| > 1). We also performed competing endogenous RNA network analysis, which identified a total of 65 lncRNA-mRNA interactions and 4714 miRNA-circRNA interactions. In particular, we observed that circRNA12218 had binding sites for three miRNAs targeting ACAN, while circRNA12487 had binding sites for seven miRNAs targeting COL2A1. Our results add a novel set of genes and non-coding RNAs that could potentially serve as candidate diagnostic biomarkers or therapeutic targets for KBD patients.
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Affiliation(s)
- Lixin Han
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Bolun Cheng
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Wenming Wei
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Li Liu
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Shiqiang Cheng
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Huan Liu
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Yumeng Jia
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Yan Wen
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Feng Zhang
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
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3
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Augello G, Cusimano A, Cervello M, Cusimano A. Extracellular Vesicle-Related Non-Coding RNAs in Hepatocellular Carcinoma: An Overview. Cancers (Basel) 2024; 16:1415. [PMID: 38611093 PMCID: PMC11011022 DOI: 10.3390/cancers16071415] [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: 12/30/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver cancer. It is a major public health problem worldwide, and it is often diagnosed at advanced stages, when no effective treatment options are available. Extracellular vesicles (EVs) are nanosized double-layer lipid vesicles containing various biomolecule cargoes, such as lipids, proteins, and nucleic acids. EVs are released from nearly all types of cells and have been shown to play an important role in cell-to-cell communication. In recent years, many studies have investigated the role of EVs in cancer, including HCC. Emerging studies have shown that EVs play primary roles in the development and progression of cancer, modulating tumor growth and metastasis formation. Moreover, it has been observed that non-coding RNAs (ncRNAs) carried by tumor cell-derived EVs promote tumorigenesis, regulating the tumor microenvironment (TME) and playing critical roles in the progression, angiogenesis, metastasis, immune escape, and drug resistance of HCC. EV-related ncRNAs can provide information regarding disease status, thus encompassing a role as biomarkers. In this review, we discuss the main roles of ncRNAs present in HCC-derived EVs, including micro(mi) RNAs, long non-coding (lnc) RNAs, and circular (circ) RNAs, and their potential clinical value as biomarkers and therapeutic targets.
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Affiliation(s)
- Giuseppa Augello
- Institute for Biomedical Research and Innovation, National Research Council (CNR), 90146 Palermo, Italy; (A.C.); (M.C.)
| | - Alessandra Cusimano
- Institute for Biomedical Research and Innovation, National Research Council (CNR), 90146 Palermo, Italy; (A.C.); (M.C.)
- Department of Biological, Chemical and Pharmaceutical Science and Technology (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Melchiorre Cervello
- Institute for Biomedical Research and Innovation, National Research Council (CNR), 90146 Palermo, Italy; (A.C.); (M.C.)
| | - Antonella Cusimano
- Institute for Biomedical Research and Innovation, National Research Council (CNR), 90146 Palermo, Italy; (A.C.); (M.C.)
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4
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Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC. Deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial sections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545365. [PMID: 37645893 PMCID: PMC10461981 DOI: 10.1101/2023.06.21.545365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tumors may contain billions of cells including distinct malignant clones and nonmalignant cell types. Clarifying the evolutionary histories, prevalence, and defining molecular features of these cells is essential for improving clinical outcomes, since intratumoral heterogeneity provides fuel for acquired resistance to targeted therapies. Here we present a statistically motivated strategy for deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial tumor sections (MOMA). By combining deep sampling of IDH-mutant astrocytomas with integrative analysis of single-nucleotide variants, copy-number variants, and gene expression, we reconstruct and validate the phylogenies, spatial distributions, and transcriptional profiles of distinct malignant clones. By genotyping nuclei analyzed by single-nucleus RNA-seq for truncal mutations, we further show that commonly used algorithms for identifying cancer cells from single-cell transcriptomes may be inaccurate. We also demonstrate that correlating gene expression with tumor purity in bulk samples can reveal optimal markers of malignant cells and use this approach to identify a core set of genes that is consistently expressed by astrocytoma truncal clones, including AKR1C3, whose expression is associated with poor outcomes in several types of cancer. In summary, MOMA provides a robust and flexible strategy for precisely deconstructing intratumoral heterogeneity and clarifying the core molecular properties of distinct cellular populations in solid tumors.
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Affiliation(s)
- Patrick G. Schupp
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Samuel J. Shelton
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Daniel J. Brody
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Rebecca Eliscu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Brett E. Johnson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, USA
- Medical Scientist Training Program and Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Kevin W. Kelley
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Medical Scientist Training Program and Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
- Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Matthew B. Potts
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Michael W. McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Eric J. Huang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Daniel A. Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Russell O. Pieper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Mitchel S. Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Joanna J. Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Michael C. Oldham
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
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5
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Liao X, Wei R, Zhou J, Wu K, Li J. Emerging roles of long non-coding RNAs in osteosarcoma. Front Mol Biosci 2024; 11:1327459. [PMID: 38516191 PMCID: PMC10955361 DOI: 10.3389/fmolb.2024.1327459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
Osteosarcoma (OS) is a highly aggressive and lethal malignant bone tumor that primarily afflicts children, adolescents, and young adults. However, the molecular mechanisms underlying OS pathogenesis remain obscure. Mounting evidence implicates dysregulated long non-coding RNAs (lncRNAs) in tumorigenesis and progression. These lncRNAs play a pivotal role in modulating gene expression at diverse epigenetic, transcriptional, and post-transcriptional levels. Uncovering the roles of aberrant lncRNAs would provide new insights into OS pathogenesis and novel tools for its early diagnosis and treatment. In this review, we summarize the significance of lncRNAs in controlling signaling pathways implicated in OS development, including the Wnt/β-catenin, PI3K/AKT/mTOR, NF-κB, Notch, Hippo, and HIF-1α. Moreover, we discuss the multifaceted contributions of lncRNAs to drug resistance in OS, as well as their potential to serve as biomarkers and therapeutic targets. This review aims to encourage further research into lncRNA field and the development of more effective therapeutic strategies for patients with OS.
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Affiliation(s)
- Xun Liao
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan, China
| | - Rong Wei
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Junxiu Zhou
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan, China
| | - Ke Wu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiao Li
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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6
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Liang J, Bi G, Huang Y, Zhao G, Sui Q, Zhang H, Bian Y, Yin J, Wang Q, Chen Z, Zhan C. MAFF confers vulnerability to cisplatin-based and ionizing radiation treatments by modulating ferroptosis and cell cycle progression in lung adenocarcinoma. Drug Resist Updat 2024; 73:101057. [PMID: 38266355 DOI: 10.1016/j.drup.2024.101057] [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: 06/04/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
AIMS Lung cancer is the leading cause of cancer mortality and lung adenocarcinoma (LUAD) accounts for more than half of all lung cancer cases. Tumor elimination is mostly hindered by drug resistance and the mechanisms remain to be explored in LUAD. METHODS CRISPR screens in cell and murine models and single-cell RNA sequencing were conducted, which identified MAF bZIP transcription factor F (MAFF) as a critical factor regulating tumor growth and treatment resistance in LUAD. RNA and ChIP sequencing analyses were performed for transcriptional target expression and specific binding sites of MAFF. Functions of MAFF in inhibiting tumor growth and promoting cisplatin or irradiation efficacy were investigated using cellular and xenograft models. RESULTS Patients with lung adenocarcinoma and reduced MAFF expression had worse clinical outcomes. MAFF inhibited tumor cell proliferation by regulating the expression of SLC7A11, CDK6, and CDKN2C, promoting ferroptosis and preventing cell cycle progression from G1 to S. MAFF also conferred tumor cells vulnerable to cisplatin-based or ionizing radiation treatments. MAFF reduction was a final event in the acquisition of cisplatin resistance of LUAD cells. The intracellular cAMP/PKA/CREB1 pathway upregulated MAFF in response to cisplatin-based or ionizing radiation treatments. CONCLUSIONS MAFF suppresses tumor growth, and pharmacological agonists targeting MAFF may improve cisplatin or irradiation therapies for lung adenocarcinoma patients.
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Affiliation(s)
- Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Guangyin Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Qihai Sui
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Huan Zhang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Yunyi Bian
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Jiacheng Yin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China.
| | - Zhencong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China.
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, China.
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Guo Z, Xie Y, Zhang L, Liu S, Jiang W. A novel disulfidptosis-related lncRNAs signature for predicting survival and immune response in hepatocellular carcinoma. Aging (Albany NY) 2024; 16:267-284. [PMID: 38180745 PMCID: PMC10817373 DOI: 10.18632/aging.205367] [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: 06/26/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024]
Abstract
The accumulation of intracellular disulfides induces a novel and unique form of metabolic-related cell death known as disulfidptosis. A previous study revealed the prognostic value of a risk model of disulfidptosis-related genes in hepatocellular carcinoma (HCC). However, to date, no studies have investigated the relationship between disulfidptosis-related long non-coding RNAs (DRLs) and HCC. In this study, we collected and analyzed RNA sequencing data from 370 HCC samples to explore the DRLs in the tumorigenesis and development of HCC. By employing Lasso Cox regression and multivariate Cox regression analyses, we identified five prognostic DRLs, which were used to construct a prognostic signature. The signature was subsequently validated using receiver operating characteristic (ROC) curves, Kaplan-Meier analysis, Cox regression analyses, nomograms, and calibration curves. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were performed, revealing that the DRLs signature was associated with HCC and several cancer-related pathways. Furthermore, the DRLs signature showed correlations with the infiltration of M0 and M1 macrophages, immune-related functions, and multiple immune checkpoints, including PDCD1, LAG3, CTLA4, TIGIT, CD47, and others. Analysis using the tumor immune dysfunction and exclusion (TIDE) approach demonstrated that the DRLs signature could predict the response to immunotherapy. Finally, we screened potential chemotherapy drugs that could sensitize HCC. In conclusion, our novel DRLs signature provides valuable insights into predicting patient survival and immunotherapy responses.
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Affiliation(s)
- Zhoubo Guo
- The First Central Clinical School, Tianjin Medical University, Tianjin, China
- Department of Liver Transplantation, Tianjin First Central Hospital, Tianjin Medical University, Key Laboratory of Transplantation, Chinese Academy of Medical Sciences, Tianjin Key Laboratory for Organ Transplantation, Tianjin Key Laboratory of Molecular and Treatment of Liver Cancer, Tianjin, China
| | - Yan Xie
- Department of Liver Transplantation, Tianjin First Central Hospital, Tianjin Medical University, Key Laboratory of Transplantation, Chinese Academy of Medical Sciences, Tianjin Key Laboratory for Organ Transplantation, Tianjin Key Laboratory of Molecular and Treatment of Liver Cancer, Tianjin, China
| | - Li Zhang
- Department of Liver Transplantation, Tianjin First Central Hospital, Tianjin Medical University, Key Laboratory of Transplantation, Chinese Academy of Medical Sciences, Tianjin Key Laboratory for Organ Transplantation, Tianjin Key Laboratory of Molecular and Treatment of Liver Cancer, Tianjin, China
| | - Shuaichen Liu
- Department of Liver Transplantation, Tianjin First Central Hospital, Tianjin Medical University, Key Laboratory of Transplantation, Chinese Academy of Medical Sciences, Tianjin Key Laboratory for Organ Transplantation, Tianjin Key Laboratory of Molecular and Treatment of Liver Cancer, Tianjin, China
| | - Wentao Jiang
- Department of Liver Transplantation, Tianjin First Central Hospital, Tianjin Medical University, Key Laboratory of Transplantation, Chinese Academy of Medical Sciences, Tianjin Key Laboratory for Organ Transplantation, Tianjin Key Laboratory of Molecular and Treatment of Liver Cancer, Tianjin, China
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8
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Yao X, Liu S, Xia H, Li H, Wang Z, Su L, Guo W, Chen H. Transcriptomic sequencing analysis of key long noncoding RNAs and mRNAs expression profiles in postoperative recurrence of hepatocellular carcinoma. Technol Health Care 2024; 32:735-747. [PMID: 37545269 DOI: 10.3233/thc-230123] [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] [Indexed: 08/08/2023]
Abstract
BACKGROUND Recurrence is the main cause of death in hepatocellular carcinoma (HCC) patients after liver resection. OBJECTIVE The long non-coding RNAs (lncRNAs) have been reported participated in progression and prognosis of HCC, however, the vital role of lncRNA in postoperative recurrence of HCC has rarely been systematically identified. METHODS RNA-sequencing (RNA-seq) was performed between orthotopic model of HCC and hepatoma postoperative recurrent model to comprehensively analyze the integrated transcriptome expression profiles of lncRNA and mRNA. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) was then conducted to quantify the expression levels of DElncRNAs and their target mRNAs. RESULTS In our study, 211 lncRNAs (P-value < 0.05) and 1125 mRNAs (P-adjust < 0.05) were significantly differentially expressed (DE) between two groups. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that DElncRNAs and DEmRNAs were mainly enriched in lipid metabolism, including Arachidonic acid metabolism, PPAR signaling pathway, Steroid hormone biosynthesis, Linoleic acid metabolism, Inflammatory mediator regulation of TRP channels, and Fatty acid degradation. Furthermore, we constructed lncRNA-mRNA interaction networks and protein-protein interaction (PPI) network, and verified by qRT-PCR, suggesting that increased DEIncRNAs (XLOC_063499 and XLOC_042016) may prevent HCC recurrence after surgery by upregulating on targeted cytochrome P450 (CYP) family genes in the lipid metabolism pathway, such as cyp3a16, cyp3a44, cyp2c39, cyp2c40 and cyp2c68. CONCLUSION Overall, Our findings provided new insights for further investigation of biological function in lncRNA related HCC recurrence.
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Affiliation(s)
- Xiaohui Yao
- The Research Center of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Shenzhen TCM Anorectal Hospital (Futian), Shenzhen, Guangdong, China
- The Research Center of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Shan Liu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- The Research Center of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Huan Xia
- College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
- The Research Center of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Hanhan Li
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhijie Wang
- Shanxi Province Hospital of Traditional Chinese Medicine, Taiyuan, Shanxi, China
| | - Le Su
- Department of Gynecology and Pediatrics, Traditional Chinese Medicine Hospital of Haizhu District, Guangzhou, Guangdong, China
| | - Wei Guo
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Hanrui Chen
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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9
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El-Aziz MKA, Dawoud A, Kiriacos CJ, Fahmy SA, Hamdy NM, Youness RA. Decoding hepatocarcinogenesis from a noncoding RNAs perspective. J Cell Physiol 2023; 238:1982-2009. [PMID: 37450612 DOI: 10.1002/jcp.31076] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Being a leading lethal malignancy worldwide, the pathophysiology of hepatocellular carcinoma (HCC) has gained a lot of interest. Yet, underlying mechanistic basis of the liver tumorigenesis is poorly understood. The role of some coding genes and their respective translated proteins, then later on, some noncoding RNAs (ncRNAs) such as microRNAs have been extensively studied in context of HCC pathophysiology; however, the implication of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) in HCC is indeed less investigated. As a subclass of the ncRNAs which has been elusive for long time ago, lncRNAs was found to be involved in plentiful cellular functions such as DNA, RNA, and proteins regulation. Hence, it is undisputed that lncRNAs dysregulation profoundly contributes to HCC via diverse etiologies. Accordingly, lncRNAs represent a hot research topic that requires prime focus in HCC. In this review, the authors discuss breakthrough discoveries involving lncRNAs and circRNAs dysregulation that have contributed to the contemporary concepts of HCC pathophysiology and how these concepts could be leveraged as potential novel diagnostic and prognostic HCC biomarkers. Further, this review article sheds light on future trends, thereby discussing the pathological roles of lncRNAs and circRNAs in HCC proliferation, migration, and epithelial-to-mesenchymal transition. Along this line of reasoning, future recommendations of how these targets could be exploited to achieve effective HCC-related drug development is highlighted.
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Affiliation(s)
- Mostafa K Abd El-Aziz
- Biochemistry Department, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, Egypt
- Molecular Genetics Research Team (MGRT), Biology and Biochemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, Cairo, Egypt
| | - Alyaa Dawoud
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Caroline J Kiriacos
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Sherif Ashraf Fahmy
- Chemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, Cairo, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Rana A Youness
- Molecular Genetics Research Team (MGRT), Biology and Biochemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, Cairo, Egypt
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
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10
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Hjazi A, Ghaffar E, Asghar W, Alauldeen Khalaf H, Ikram Ullah M, Mireya Romero-Parra R, Hussien BM, Abdulally Abdulhussien Alazbjee A, Singh Bisht Y, Fakri Mustafa Y, Reza Hosseini-Fard S. CDKN2B-AS1 as a novel therapeutic target in cancer: Mechanism and clinical perspective. Biochem Pharmacol 2023; 213:115627. [PMID: 37257723 DOI: 10.1016/j.bcp.2023.115627] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
Long non-coding RNAs (lncRNA) have been identified as essential components having considerable modulatory impactson biological activities through altering gene transcription, epigenetic changes, and protein translation. Cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1), a recently discovered lncRNA, was shown to be substantially elevated in various cancers.Furthermore, via modulation ofvarious signalingaxes, it is effectively connected to the control of critical cancer-associatedbiological pathways likecell proliferation, apoptosis, cell cycle, epithelial-mesenchymal transition(EMT), invasion, and migration. Considering the crucial functions ofCDKN2B-AS1in cancer onset and development, this lncRNA offers immense therapeutic implications for usage as a new diagnostic or treatment approach. In this article, we evaluate the most recent discoveries made into the functions of the lncRNA CDKN2B-AS1 in cancer, in addition to its prospect asbeneficial properties,prognostic anddiagnostic biomarkersin the cancer-related treatment, emphasizingits participation in a broad network of signalingaxes whichcould affectvariouscancers and investigating its promising therapeutic possibility.
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Affiliation(s)
- Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | | | | | - Muhammad Ikram Ullah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 75471, Aljouf, Saudi Arabia
| | | | - Beneen M Hussien
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | | | - Yashwant Singh Bisht
- Uttaranchal Institute of Technology, Uttaranchal University, Dehradun 248007, India
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul 41001, Iraq
| | - Seyed Reza Hosseini-Fard
- Biochemistry Department, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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11
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Cheah M, Cheng Y, Petrova V, Cimpean A, Jendelova P, Swarup V, Woolf CJ, Geschwind DH, Fawcett JW. Integrin-Driven Axon Regeneration in the Spinal Cord Activates a Distinctive CNS Regeneration Program. J Neurosci 2023; 43:4775-4794. [PMID: 37277179 PMCID: PMC10312060 DOI: 10.1523/jneurosci.2076-22.2023] [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: 11/06/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 06/07/2023] Open
Abstract
The peripheral branch of sensory dorsal root ganglion (DRG) neurons regenerates readily after injury unlike their central branch in the spinal cord. However, extensive regeneration and reconnection of sensory axons in the spinal cord can be driven by the expression of α9 integrin and its activator kindlin-1 (α9k1), which enable axons to interact with tenascin-C. To elucidate the mechanisms and downstream pathways affected by activated integrin expression and central regeneration, we conducted transcriptomic analyses of adult male rat DRG sensory neurons transduced with α9k1, and controls, with and without axotomy of the central branch. Expression of α9k1 without the central axotomy led to upregulation of a known PNS regeneration program, including many genes associated with peripheral nerve regeneration. Coupling α9k1 treatment with dorsal root axotomy led to extensive central axonal regeneration. In addition to the program upregulated by α9k1 expression, regeneration in the spinal cord led to expression of a distinctive CNS regeneration program, including genes associated with ubiquitination, autophagy, endoplasmic reticulum (ER), trafficking, and signaling. Pharmacological inhibition of these processes blocked the regeneration of axons from DRGs and human iPSC-derived sensory neurons, validating their causal contributions to sensory regeneration. This CNS regeneration-associated program showed little correlation with either embryonic development or PNS regeneration programs. Potential transcriptional drivers of this CNS program coupled to regeneration include Mef2a, Runx3, E2f4, and Yy1. Signaling from integrins primes sensory neurons for regeneration, but their axon growth in the CNS is associated with an additional distinctive program that differs from that involved in PNS regeneration.SIGNIFICANCE STATEMENT Restoration of neurologic function after spinal cord injury has yet to be achieved in human patients. To accomplish this, severed nerve fibers must be made to regenerate. Reconstruction of nerve pathways has not been possible, but recently, a method for stimulating long-distance axon regeneration of sensory fibers in rodents has been developed. This research uses profiling of messenger RNAs in the regenerating sensory neurons to discover which mechanisms are activated. This study shows that the regenerating neurons initiate a novel CNS regeneration program which includes molecular transport, autophagy, ubiquitination, and modulation of the endoplasmic reticulum (ER). The study identifies mechanisms that neurons need to activate to regenerate their nerve fibers.
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Affiliation(s)
- Menghon Cheah
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, United Kingdom
| | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095
| | - Veselina Petrova
- Department of Neurobiology, Harvard Medical School; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Anda Cimpean
- Centre for Reconstructive Neuroscience, Institute of Experimental Medicine Czech Academy of Science, Prague, Czech Republic
| | - Pavla Jendelova
- Centre for Reconstructive Neuroscience, Institute of Experimental Medicine Czech Academy of Science, Prague, Czech Republic
| | - Vivek Swarup
- Program in Neurogenetics, Department of Neurology, and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095
- Department of Neurobiology and Behavior, University of California, Irvine, California 92697
| | - Clifford J Woolf
- Department of Neurobiology, Harvard Medical School; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095
| | - James W Fawcett
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, United Kingdom
- Centre for Reconstructive Neuroscience, Institute of Experimental Medicine Czech Academy of Science, Prague, Czech Republic
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12
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Liu Y, Xing K, Ao H, Zhang F, Zhao X, Liu H, Shi Y, Yu Y, Wang C. Competing endogenous RNA network construction based on long non-coding RNAs, microRNAs, and mRNAs related to fat deposition in Songliao black swine. Anim Genet 2023; 54:132-143. [PMID: 36596449 DOI: 10.1111/age.13283] [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: 07/18/2021] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 01/05/2023]
Abstract
China has a long history of pig breeding and a number of local breeds. The Songliao Black pig, bred in China in 2009, shows high variation in backfat thickness and therefore is well-suited to fat deposition research. Fat deposition is a complex trait, and the underlying regulatory factors are not fully characterized. In this study, the molecular basis of fat deposition traits was evaluated by comparisons between three individuals with extremely high-backfat thickness and three with extremely low-backfat thickness selected from 53 gilts. Subcutaneous adipose tissues of the back were collected for strand-specific library RNA sequencing (RNA-seq) and small RNA-seq. We identified 13 184 mRNAs, 2046 long non-coding (lnc)RNAs, and 494 micro (mi)RNAs by high-throughput sequencing. Furthermore, we detected 150 differentially expressed mRNAs, 66 differentially expressed lncRNAs, and eight differentially expressed miRNAs. A functional enrichment analysis indicated that these genes are involved in multiple fat metabolism-related pathways, including positive regulation of fat cell differentiation, and fat digestion and absorption. We used various algorithms (miRanda, TargetScan, and RNAhybrid) to predict targeting relationships and constructed a competing endogenous RNA network containing seven lncRNAs, three miRNAs, and six mRNAs. All these genes were differentially expressed between the extremely high and low backfat thickness groups or enriched in pathways related to fat metabolism. Our results provide insight into the regulatory mechanisms by which non-coding RNAs and their target genes influence backfat deposition in pigs. Furthermore, our newly constructed competing endogenous RNA (lncRNA-miRNA-mRNA) network provides a basis for further exploration of fat deposition traits and non-coding RNA functions.
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Affiliation(s)
- Yibing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Hong Ao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengxia Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xitong Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huatao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yong Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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13
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Yu N, Qin H, Zhang F, Liu T, Cao K, Yang Y, Chen Y, Cai J. The role and mechanism of long non-coding RNAs in homologous recombination repair of radiation-induced DNA damage. J Gene Med 2023; 25:e3470. [PMID: 36537017 DOI: 10.1002/jgm.3470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022] Open
Abstract
DNA double-strand breaks can seriously damage the genetic information that organisms depend on for survival and reproduction. Therefore, cells require a robust DNA damage response mechanism to repair the damaged DNA. Homologous recombination (HR) allows error-free repair, which is key to maintaining genomic integrity. Long non-coding RNAs (lncRNAs) are RNA molecules that are longer than 200 nucleotides. In recent years, a number of studies have found that lncRNAs can act as regulators of gene expression and DNA damage response mechanisms, including HR repair. Moreover, they have significant effects on the occurrence, development, invasion and metastasis of tumor cells, as well as the sensitivity of tumors to radiotherapy and chemotherapy. These studies have therefore begun to expose the great potential of lncRNAs for clinical applications. In this review, we focus on the regulatory roles of lncRNAs in HR repair.
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Affiliation(s)
- Nanxi Yu
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China
| | - Hongran Qin
- Department of Nuclear Radiation, Shanghai Pulmonary Hospital,School of Medicine, Tongji University, Shanghai, China
| | - Fangxiao Zhang
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China
| | - Tingting Liu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Kun Cao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yanyong Yang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yuanyuan Chen
- South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China.,Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Jianming Cai
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China
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14
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Li T, Zhang T, Gao H, Wang H, Yan H, Wan Z, Liu R, Yin C. Tempol modulates lncRNA-miRNA-mRNA ceRNA networks in ovaries of DHEA induced PCOS rats. J Steroid Biochem Mol Biol 2023; 226:106175. [PMID: 36374793 DOI: 10.1016/j.jsbmb.2022.106175] [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: 06/30/2022] [Revised: 08/11/2022] [Accepted: 08/31/2022] [Indexed: 11/11/2022]
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common endocrine and metabolic disorders in reproductive age women. Our previous results demonstrated that tempol was able to ameliorate PCOS phenotype in rats. However, the exact pathophysiological effect of tempol on PCOS remains largely unknown. To extend this research, deep RNA-sequencing was performed to investigate the long noncoding RNA (lncRNA) associated ceRNA mechanisms in the ovarian tissues of control rats, dehydropiandrosterone (DHEA) induced PCOS rats and tempol treated PCOS rats. Our results identified total 164, 79, and 914 significantly dysregulated lncRNAs, miRNAs, and mRNAs in three groups, respectively. The total of 7 lncRNAs, 8 mRNAs and 5 miRNAs were involved in lncRNA-associated ceRNA networks were constructed. Among them, mRNAs including C1qtnf1, Dipk2a, IL4r and lncRNAs including MSTRG.16751.2, MSTRG.8065.2 had high RNA connectivity in the ceRNA network, which also showed significant alterations in these three groups by using qPCR validation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the involvement of the identified ceRNA networks in regulating the development of PCOS from distinct origins, such as metabolic pathway, immune cell differentiation. The study presents the first systematic dissection of lncRNA-associated ceRNA profiles in tempol treated PCOS rats. The identified ceRNA networks could provide insights that help facilitate PCOS diagnosis and treatment.
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Affiliation(s)
- Tianhe Li
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Tingting Zhang
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Huimin Gao
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Huanhuan Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huihui Yan
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Zhihui Wan
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Ruixia Liu
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100026, China
| | - Chenghong Yin
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing 100026, China.
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15
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Hong Y, Zhang Y, Zhao H, Chen H, Yu QQ, Cui H. The roles of lncRNA functions and regulatory mechanisms in the diagnosis and treatment of hepatocellular carcinoma. Front Cell Dev Biol 2022; 10:1051306. [PMID: 36467404 PMCID: PMC9716033 DOI: 10.3389/fcell.2022.1051306] [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: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 10/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most frequent and deadly type of liver cancer. While the underlying molecular mechanisms are poorly understood, it is documented that lncRNAs may play key roles. Many HCC-associated lncRNAs have been linked to HBV and HCV infection, mediating gene expression, cell growth, development, and death. Studying the regulatory mechanisms and biological functions of HCC-related lncRNAs will assist our understanding of HCC pathogenesis as well as its diagnosis and management. Here, we address the potential of dysregulated lncRNAs in HCC as diagnostic and therapeutic biomarkers, and we evaluate the oncogenic or tumor-suppressive properties of these lncRNAs.
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Affiliation(s)
- Yuling Hong
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Yunxing Zhang
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Haibo Zhao
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Hailing Chen
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Qing-Qing Yu
- Jining First People’s Hospital, Jining Medical College, Jining, China
| | - Hongxia Cui
- Jining First People’s Hospital, Jining Medical College, Jining, China
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16
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Chen Y, Wang N, Cao L, Zhang D, Peng H, Xue P. Long non-coding RNA HOXB-AS1 is a prognostic marker and promotes hepatocellular carcinoma cells' proliferation and invasion. Open Life Sci 2022; 17:944-951. [PMID: 36045719 PMCID: PMC9380905 DOI: 10.1515/biol-2022-0040] [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: 06/16/2021] [Revised: 11/12/2021] [Accepted: 01/03/2022] [Indexed: 11/15/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are broadly transcribed in the genome of human and play critical roles in the progression of multiple diseases. Long non-coding HOXB cluster antisense RNA 1 (HOXB-AS1) is a tumor exciter in various cancers. This study aimed to investigate the involvement of HOXB-AS1 in hepatocellular carcinoma (HCC). In the following study, HOXB-AS1 was unveiled to be highly expressed in HCC tissues as opposed to normal tissues. Silencing of HOXB-AS1 led to the loss of proliferation, migration, and invasiveness of HCC cells, namely Hep3B and Huh7. Moreover, the data showed that expression levels of HOXB-AS1 contribute significantly to the patient's survival rates. Otherwise, HOXB-AS1 levels in the serum of patients proved HOXB-AS1 as a biomarker for analysis and treatment of HCC. In summary, this study highlights HOXB-AS1 as key upregulated lncRNA in HCC which being an oncogene can cause proliferation and metastasis of HCC cells. The results also highlighted HOXB-AS1 as a promising biomarker for early diagnosis and prognosis of patients with HCC.
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Affiliation(s)
- Yubin Chen
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Na Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Liangqi Cao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Dawei Zhang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Heping Peng
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Ping Xue
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
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17
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Holliday KM, Gondalia R, Baldassari A, Justice AE, Stewart JD, Liao D, Yanosky JD, Jordahl KM, Bhatti P, Assimes TL, Pankow JS, Guan W, Fornage M, Bressler J, North KE, Conneely KN, Li Y, Hou L, Vokonas PS, Ward-Caviness CK, Wilson R, Wolf K, Waldenberger M, Cyrys J, Peters A, Boezen HM, Vonk JM, Sayols-Baixeras S, Lee M, Baccarelli AA, Whitsel EA. Gaseous air pollutants and DNA methylation in a methylome-wide association study of an ethnically and environmentally diverse population of U.S. adults. ENVIRONMENTAL RESEARCH 2022; 212:113360. [PMID: 35500859 PMCID: PMC9354583 DOI: 10.1016/j.envres.2022.113360] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 06/03/2023]
Abstract
Epigenetic mechanisms may underlie air pollution-health outcome associations. We estimated gaseous air pollutant-DNA methylation (DNAm) associations using twelve subpopulations within Women's Health Initiative (WHI) and Atherosclerosis Risk in Communities (ARIC) cohorts (n = 8397; mean age 61.3 years; 83% female; 46% African-American, 46% European-American, 8% Hispanic/Latino). We used geocoded participant address-specific mean ambient carbon monoxide (CO), nitrogen oxides (NO2; NOx), ozone (O3), and sulfur dioxide (SO2) concentrations estimated over the 2-, 7-, 28-, and 365-day periods before collection of blood samples used to generate Illumina 450 k array leukocyte DNAm measurements. We estimated methylome-wide, subpopulation- and race/ethnicity-stratified pollutant-DNAm associations in multi-level, linear mixed-effects models adjusted for sociodemographic, behavioral, meteorological, and technical covariates. We combined stratum-specific estimates in inverse variance-weighted meta-analyses and characterized significant associations (false discovery rate; FDR<0.05) at Cytosine-phosphate-Guanine (CpG) sites without among-strata heterogeneity (PCochran's Q > 0.05). We attempted replication in the Cooperative Health Research in Region of Augsburg (KORA) study and Normative Aging Study (NAS). We observed a -0.3 (95% CI: -0.4, -0.2) unit decrease in percent DNAm per interquartile range (IQR, 7.3 ppb) increase in 28-day mean NO2 concentration at cg01885635 (chromosome 3; regulatory region 290 bp upstream from ZNF621; FDR = 0.03). At intragenic sites cg21849932 (chromosome 20; LIME1; intron 3) and cg05353869 (chromosome 11; KLHL35; exon 2), we observed a -0.3 (95% CI: -0.4, -0.2) unit decrease (FDR = 0.04) and a 1.2 (95% CI: 0.7, 1.7) unit increase (FDR = 0.04), respectively, in percent DNAm per IQR (17.6 ppb) increase in 7-day mean ozone concentration. Results were not fully replicated in KORA and NAS. We identified three CpG sites potentially susceptible to gaseous air pollution-induced DNAm changes near genes relevant for cardiovascular and lung disease. Further harmonized investigations with a range of gaseous pollutants and averaging durations are needed to determine the effect of gaseous air pollutants on DNA methylation and ultimately gene expression.
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Affiliation(s)
- Katelyn M Holliday
- Department of Family Medicine and Community Health, School of Medicine, Duke University, Durham, NC, USA; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.
| | - Rahul Gondalia
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Antoine Baldassari
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | | | - James D Stewart
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Duanping Liao
- Division of Epidemiology, Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jeff D Yanosky
- Division of Epidemiology, Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kristina M Jordahl
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | | | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Weihua Guan
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA; Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University Chicago, Evanston, IL, USA; Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University Chicago, Evanston, IL, USA
| | - Pantel S Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, Schools of Medicine and Public Health, Boston University, Boston, MA, USA
| | - Cavin K Ward-Caviness
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, 104 Mason Farm Rd, Chapel Hill, NC, 27514, USA
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Kathrin Wolf
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Josef Cyrys
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany; Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig Maximilians University, Munich, Germany
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, the Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, the Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, the Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, the Netherlands
| | - Sergi Sayols-Baixeras
- Cardiovascular Epidemiology and Genetics Research Group, Hospital Del Mar Medical Research Institute (IMIM), Campus Del Mar, Universitat Pompeu Fabra, Barcelona, Spain; Consorcio CIBER, M.P. Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain; Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Mikyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Andrea A Baccarelli
- Laboratory of Environmental Epigenetics, Departments of Environmental Health Sciences and Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA; Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
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18
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Kunadirek P, Pinjaroen N, Nookaew I, Tangkijvanich P, Chuaypen N. Transcriptomic Analyses Reveal Long Non-Coding RNA in Peripheral Blood Mononuclear Cells as a Novel Biomarker for Diagnosis and Prognosis of Hepatocellular Carcinoma. Int J Mol Sci 2022; 23:ijms23147882. [PMID: 35887228 PMCID: PMC9324406 DOI: 10.3390/ijms23147882] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 02/06/2023] Open
Abstract
Novel biomarkers are highly required for the diagnosis and predicting prognosis of hepatocellular carcinoma (HCC). In this study, we investigated the profiles of long non-coding RNAs (lncRNAs) obtained from the peripheral blood mononuclear cells (PBMCs) of patients with HCC and PBMCs from a co-culture model using transcriptomic analysis. The differentially expressed lncRNAs (DElncRNAs) were then characterized and integrated as cancer-induced lncRNAs. Among them, three up-regulating DElncRNAs including MIR4435-2HG, SNHG9 and lnc-LCP2-1 and one down-regulating, lnc-POLD3-2, were identified. The functional analysis showed that these enriched lncRNAs were mainly associated with carcinogenesis and immune responses. Following further validation in PBMCs samples (100 HBV-related HCC, 100 chronic hepatitis B and 100 healthy controls), MIR4435-2HG, lnc-POLD3-2 and their combination were revealed to be sensitive biomarkers in discriminating HCC from non-HCC (AUROC = 0.78, 0.80, and 0.87, respectively), particularly among individuals with normal serum alpha-fetoprotein levels. Additionally, high circulating SNHG9 expression was shown to be an independent prognostic factor of overall survival in patients with HCC. These results indicate that determining these lncRNAs in PBMCs could serve as novel diagnostic and prognostic biomarkers for HBV-related HCC.
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Affiliation(s)
- Pattapon Kunadirek
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Nutcha Pinjaroen
- Department of Radiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- Correspondence: (P.T.); (N.C.); Tel.: +66-2-256-4482 (N.C.)
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- Correspondence: (P.T.); (N.C.); Tel.: +66-2-256-4482 (N.C.)
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19
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Swaminathan B, Youn SW, Naiche LA, Du J, Villa SR, Metz JB, Feng H, Zhang C, Kopan R, Sims PA, Kitajewski JK. Endothelial Notch signaling directly regulates the small GTPase RND1 to facilitate Notch suppression of endothelial migration. Sci Rep 2022; 12:1655. [PMID: 35102202 PMCID: PMC8804000 DOI: 10.1038/s41598-022-05666-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/07/2022] [Indexed: 11/24/2022] Open
Abstract
To control sprouting angiogenesis, endothelial Notch signaling suppresses tip cell formation, migration, and proliferation while promoting barrier formation. Each of these responses may be regulated by distinct Notch-regulated effectors. Notch activity is highly dynamic in sprouting endothelial cells, while constitutive Notch signaling drives homeostatic endothelial polarization, indicating the need for both rapid and constitutive Notch targets. In contrast to previous screens that focus on genes regulated by constitutively active Notch, we characterized the dynamic response to Notch. We examined transcriptional changes from 1.5 to 6 h after Notch signal activation via ligand-specific or EGTA induction in cultured primary human endothelial cells and neonatal mouse brain. In each combination of endothelial type and Notch manipulation, transcriptomic analysis identified distinct but overlapping sets of rapidly regulated genes and revealed many novel Notch target genes. Among the novel Notch-regulated signaling pathways identified were effectors in GPCR signaling, notably, the constitutively active GTPase RND1. In endothelial cells, RND1 was shown to be a novel direct Notch transcriptional target and required for Notch control of sprouting angiogenesis, endothelial migration, and Ras activity. We conclude that RND1 is directly regulated by endothelial Notch signaling in a rapid fashion in order to suppress endothelial migration.
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Affiliation(s)
- Bhairavi Swaminathan
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Seock-Won Youn
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - L A Naiche
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Jing Du
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Stephanie R Villa
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Jordan B Metz
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Huijuan Feng
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Raphael Kopan
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Peter A Sims
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Jan K Kitajewski
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, 60612, USA.
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20
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Lin Z, Ji X, Tian N, Gan Y, Ke L. Mapping Intellectual Structure for the Long Non-Coding RNA in Hepatocellular Carcinoma Development Research. Front Genet 2022; 12:771810. [PMID: 35047004 PMCID: PMC8762053 DOI: 10.3389/fgene.2021.771810] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/22/2021] [Indexed: 01/09/2023] Open
Abstract
Background: Emerging research suggests that long non-coding RNAs (lncRNAs) play an important role in a variety of developmental or physiological processes of hepatocellular carcinoma (HCC). Various differentially expressed lncRNAs have been identified in HCC. Thus, a deeper analysis of recent research concerning lncRNA and HCC development could provide scientists with a valuable reference for future studies. Methods: Related publications were retrieved from the Web of Science Core Collection database. CiteSpace version 5.6.R4 was employed to conduct bibliometric analysis. Several network maps were constructed to evaluate the collaborations between different countries, institutions, authors, journals, and keywords. Results: A total of 2,667 records were initially found from the year of 2010–2020. The annual related publications output had increased dramatically during these years. Although China was the most prolific country in terms of research publication, the United States played a leading role in collaborative network. The Nanjing Medical University was the most productive institute in the field of lncRNAs in HCC development. Gang Chen was the most prolific researcher, while Yang F was the most frequently co-cited author. Oncotarget, Cell, and Oncogene were the most highly co-cited journals. The most recent burst keywords were interaction, database, and pathway. Conclusion: This study provides a comprehensive overview for the field of lncRNAs in HCC development based on bibliometric and visualized methods. The results would provide a reference for scholars focusing on this field.
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Affiliation(s)
- Zhifeng Lin
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Medical Record, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaohui Ji
- Department of Obstetrics and Gynaecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Nana Tian
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Gan
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Ke
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Medical Record, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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21
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李 壬. Bioinformatics Analysis of ceRNA Regulatory Network in Alzheimer’s Disease. Biophysics (Nagoya-shi) 2022. [DOI: 10.12677/biphy.2022.101001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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22
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Zhou H, Tang W, Yang J, Peng J, Guo J, Fan C. MicroRNA-Related Strategies to Improve Cardiac Function in Heart Failure. Front Cardiovasc Med 2021; 8:773083. [PMID: 34869689 PMCID: PMC8639862 DOI: 10.3389/fcvm.2021.773083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/25/2021] [Indexed: 12/18/2022] Open
Abstract
Heart failure (HF) describes a group of manifestations caused by the failure of heart function as a pump that supports blood flow through the body. MicroRNAs (miRNAs), as one type of non-coding RNA molecule, have crucial roles in the etiology of HF. Accordingly, miRNAs related to HF may represent potential novel therapeutic targets. In this review, we first discuss the different roles of miRNAs in the development and diseases of the heart. We then outline commonly used miRNA chemical modifications and delivery systems. Further, we summarize the opportunities and challenges for HF-related miRNA therapeutics targets, and discuss the first clinical trial of an antisense drug (CDR132L) in patients with HF. Finally, we outline current and future challenges and potential new directions for miRNA-based therapeutics for HF.
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Affiliation(s)
- Huatao Zhou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Weijie Tang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jinfu Yang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Department of Pharmacology, Hunan Provincial Key Laboratory of Cardiovascular Research, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jun Peng
- Department of Pharmacology, Hunan Provincial Key Laboratory of Cardiovascular Research, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jianjun Guo
- Hunan Fangsheng Pharmaceutical Co., Ltd. Changsha, China
| | - Chengming Fan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Department of Pharmacology, Hunan Provincial Key Laboratory of Cardiovascular Research, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China.,Hunan Fangsheng Pharmaceutical Co., Ltd. Changsha, China
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23
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Shang H, Zhang H, Ren Z, Zhao H, Zhang Z, Tong J. Characterization of the Potential Role of NTPCR in Epithelial Ovarian Cancer by Integrating Transcriptomic and Metabolomic Analysis. Front Genet 2021; 12:695245. [PMID: 34539736 PMCID: PMC8442909 DOI: 10.3389/fgene.2021.695245] [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: 04/14/2021] [Accepted: 07/27/2021] [Indexed: 11/13/2022] Open
Abstract
Background Epithelial ovarian carcinoma (EOC) is a malignant tumor with high motility in women. Our previous study found that dysregulated nucleoside-triphosphatase cancer-related (NTPCR) was associated with the prognosis of EOC patients, and thus, this present study attempted to explore the potential roles of NTPCR in disease progression. Methods Expressed level of NTPCR was investigated in EOC tissues by RT-qPCR and Western blot analysis. NTPCR shRNA and overexpression vector were generated and transfected into OVCAR-3 or SKOV3 cells to detect the effect of NTPCR on cell proliferation, cell cycle, cell migration, and invasion. Transcriptomic sequencing and metabolite profiling analysis were performed in shNTPCR groups to identify transcriptome or metabolite alteration that might contribute to EOC. Finally, we searched the overlapped signaling pathways correlated with differential metabolites and differentially expressed genes (DEGs) by integrating analysis. Results Comparing para-cancerous tissues, we found that NTPCR is highly expressed in cancer tissues (p < 0.05). Overexpression of NTPCR inhibited cell proliferation, migration, and invasion and reduced the proportion of S- and G2/M-phase cells, while downregulation of NTPCR showed the opposite results. RNA sequencing analysis demonstrated cohorts of DEGs were identified in shNTPCR samples. Protein–protein interaction networks were constructed for DEGs. STAT1 (degree = 43) and OAS2 (degree = 36) were identified as hub genes in the network. Several miRNAs together with target genes were predicted to be crucial genes related to disease progression, including hsa-miR-124-3p, hsa-miR-30a-5p, hsa-miR-146a-5, EP300, GATA2, and STAT3. We also screened the differential metabolites from shNTPCR samples, including 22 upregulated and 22 downregulated metabolites. By integrating transcriptomics and metabolomics analysis, eight overlapped pathways were correlated with these DEGs and differential metabolites, such as primary bile acid biosynthesis, protein digestion, and absorption, pentose, and glucuronate interconversions. Conclusion NTPCR might serve as a tumor suppressor in EOC progression. Our results demonstrated that DEGs and differential metabolites were mainly related to several signaling pathways, which might be a crucial role in the progression of NTPCR regulation of EOC.
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Affiliation(s)
- Hongkai Shang
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gynecology, Hangzhou First People's Hospital, Hangzhou, China.,Department of Gynecology, Zhejiang University School of Medicine, Hangzhou, China
| | - Huizhi Zhang
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gynecology, Hangzhou First People's Hospital, Hangzhou, China
| | - Ziyao Ren
- Department of Gynecology, Hangzhou First People's Hospital, Hangzhou, China.,Department of Gynecology, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongjiang Zhao
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gynecology, Hangzhou First People's Hospital, Hangzhou, China
| | - Zhifen Zhang
- Department of Gynecology, Hangzhou Women's Hospital (Maternity and Child Health Care Hospital), Hangzhou, China
| | - Jinyi Tong
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Gynecology, Hangzhou Women's Hospital (Maternity and Child Health Care Hospital), Hangzhou, China
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24
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Obikane Y, Toyono T, Kokabu S, Matsuyama K, Kataoka S, Nakatomi M, Hosokawa R, Seta Y. Myogenic differentiation 1 and transcription factor 12 activate the gene expression of mouse taste receptor type 1 member 1. J Oral Biosci 2021; 63:420-428. [PMID: 34492379 DOI: 10.1016/j.job.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Myogenic differentiation 1 (Myod1) is involved in the expression of taste receptor type 1 member 1 (Tas1r1) during myogenic differentiation. Further, the target genes of Myod1 participate in transcriptional control, muscle development, and synaptic function. We examined, for the first time, the function of Myod1 in the transcriptional regulation of Tas1r1. METHODS ENCODE chromatin immunoprecipitation and sequencing (ChIP-seq) data of myogenically differentiated C2C12 cells were analyzed to identify the Myod1 and transcription factor 12 (Tcf12) binding sites in the Tas1r1 promoter region. Luciferase reporter assays, DNA affinity precipitation assays, and co-immunoprecipitation assays were also performed to identify the functions of Myod1, Tcf12, and Krüppel-like factor 5 (Klf5). RESULTS Based on ENCODE ChIP-seq, Myod1 bound to the Tas1r1 promoter region containing E-boxes 1-3. Luciferase reporter assays revealed that site-directed E-box1 mutations significantly reduced promoter activation induced by Myod1 overexpression. According to the DNA affinity precipitation assay and co-immunoprecipitation assay, Myod1 formed a heterodimer with Tcf12 and bound to E-box1. Further, Klf5 bound to the GT box near E-box1, activating Tas1r1 expression. CONCLUSIONS During myogenic differentiation, the Myod1/Tcf12 heterodimer, in collaboration with Klf5, binds to E-box1 and activates Tas1r1 expression.
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Affiliation(s)
- Yui Obikane
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University, 2-6-1 Manazuru, Kokurakita-ku, Kitakyushu 803-8580, Japan
| | - Takashi Toyono
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University, 2-6-1 Manazuru, Kokurakita-ku, Kitakyushu 803-8580, Japan.
| | - Shoichiro Kokabu
- Division of Molecular Signaling and Biochemistry, Department of Health Promotion, Kyushu Dental University, 2-6-1 Manazuru, Kokurakita-ku, Kitakyushu 803-8580, Japan
| | - Kae Matsuyama
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University, 2-6-1 Manazuru, Kokurakita-ku, Kitakyushu 803-8580, Japan
| | - Shinji Kataoka
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University, 2-6-1 Manazuru, Kokurakita-ku, Kitakyushu 803-8580, Japan
| | - Mitsushiro Nakatomi
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University, 2-6-1 Manazuru, Kokurakita-ku, Kitakyushu 803-8580, Japan
| | - Ryuji Hosokawa
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University, 2-6-1 Manazuru, Kokurakita-ku, Kitakyushu 803-8580, Japan
| | - Yuji Seta
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University, 2-6-1 Manazuru, Kokurakita-ku, Kitakyushu 803-8580, Japan
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25
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Pereira DA, Sandrim VC, Palei AC, Amaral LM, Belo VA, Lacchini R, Cavalli RC, Tanus-Santos JE, Luizon MR. NAMPT single-nucleotide polymorphism rs1319501 and visfatin/NAMPT affect nitric oxide formation, sFlt-1 and antihypertensive therapy response in preeclampsia. Pharmacogenomics 2021; 22:451-464. [PMID: 33944612 DOI: 10.2217/pgs-2021-0006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: We examined the relationships between visfatin/NAMPT and nitrite concentrations (a marker of nitric oxide [NO] formation) or sFlt-1 levels in 205 patients with preeclampsia (PE) responsive or nonresponsive to antihypertensive therapy, and whether NAMPT SNPs rs1319501 and rs3801266 affect nitrite concentrations in PE and 206 healthy pregnant women. Patients & methods: Circulating visfatin/NAMPT and sFlt-1 levels were measured by ELISA, and nitrite concentrations by using an ozone-based chemiluminescence assay. Results: In nonresponsive PE patients, visfatin/NAMPT levels were inversely related to nitrite concentrations and positively related to sFlt-1 levels. NAMPT SNP rs1319501 affected nitrite concentrations in nonresponsive PE patients and was tightly linked with NAMPT functional SNPs in Europeans. Conclusion: NAMPT SNP rs1319501 and visfatin/NAMPT affect NO formation, sFlt-1 levels and antihypertensive therapy response in PE.
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Affiliation(s)
- Daniela A Pereira
- Graduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Valeria C Sandrim
- Department of Biophysics & Pharmacology, Institute of Biosciences, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
| | - Ana C Palei
- Department of Surgery, University of Mississippi Medical Center, Jackson, MS 392164, USA
| | - Lorena M Amaral
- Department of Pharmacology & Toxicology, University of Mississippi Medical Center, Jackson, MS 392164, USA
| | - Vanessa A Belo
- Graduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Riccardo Lacchini
- Department of Psychiatric Nursing & Human Sciences, Ribeirao Preto College of Nursing, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Ricardo C Cavalli
- Department of Gynecology & Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Jose E Tanus-Santos
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Marcelo R Luizon
- Graduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Department of Genetics, Ecology & Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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26
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Nuclear functions of microRNAs relevant to the cardiovascular system. Transl Res 2021; 230:151-163. [PMID: 33186782 DOI: 10.1016/j.trsl.2020.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/22/2020] [Accepted: 11/05/2020] [Indexed: 12/30/2022]
Abstract
A fraction of the transcriptome is translated into proteins. The rest is classified as non-protein coding RNA (Ribonucleic Acid) but has gained increased attention as functional and regulatory group of transcripts. The gene regulatory role of non-coding RNAs (ncRNAs) has now been widely accepted in diverse biological processes in both physiology and disease. MicroRNAs fall into this latter group and are widely known for their diverse post-transcriptional regulatory role. MicroRNA sequences are embedded in the long ncRNAs, known as primary microRNAs, are processed into precursor microRNAs and are typically transported out of the nucleus for maturation and loading into a protein complex forming RNA-induced silencing complex (RISC) that either drives the degradation of messenger RNA (mRNA) or blocks its translation. A new phenomenon is emerging where microRNAs have active roles within the nucleus. The presence of RISC components including microRNAs in the nucleus supports this notion. They may integrate with chromatin modifiers, microprocessing machinery and mRNA stabilizing transcripts to play a multifunctional role in the nucleus. Although a limited number of studies appreciate this novel activity of microRNAs relevant to the cardiovascular system, they provide proof-of-concept that requires consideration while targeting miRNAs with therapeutic potential.
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27
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Cruz JDO, Silva AO, Ribeiro JM, Luizon MR, Ceron CS. Epigenetic Regulation of the N-Terminal Truncated Isoform of Matrix Metalloproteinase-2 (NTT-MMP-2) and Its Presence in Renal and Cardiac Diseases. Front Genet 2021; 12:637148. [PMID: 33732288 PMCID: PMC7959838 DOI: 10.3389/fgene.2021.637148] [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] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/26/2021] [Indexed: 12/19/2022] Open
Abstract
Several clinical and experimental studies have documented a compelling and critical role for the full-length matrix metalloproteinase-2 (FL-MMP-2) in ischemic renal injury, progressive renal fibrosis, and diabetic nephropathy. A novel N-terminal truncated isoform of MMP-2 (NTT-MMP-2) was recently discovered, which is induced by hypoxia and oxidative stress by the activation of a latent promoter located in the first intron of the MMP2 gene. This NTT-MMP-2 isoform is enzymatically active but remains intracellular in or near the mitochondria. In this perspective article, we first present the findings about the discovery of the NTT-MMP-2 isoform, and its functional and structural differences as compared with the FL-MMP-2 isoform. Based on publicly available epigenomics data from the Encyclopedia of DNA Elements (ENCODE) project, we provide insights into the epigenetic regulation of the latent promoter located in the first intron of the MMP2 gene, which support the activation of the NTT-MMP-2 isoform. We then focus on its functional assessment by covering the alterations found in the kidney of transgenic mice expressing the NTT-MMP-2 isoform. Next, we highlight recent findings regarding the presence of the NTT-MMP-2 isoform in renal dysfunction, in kidney and cardiac diseases, including damage observed in aging, acute ischemia-reperfusion injury (IRI), chronic kidney disease, diabetic nephropathy, and human renal transplants with delayed graft function. Finally, we briefly discuss how our insights may guide further experimental and clinical studies that are needed to elucidate the underlying mechanisms and the role of the NTT-MMP-2 isoform in renal dysfunction, which may help to establish it as a potential therapeutic target in kidney diseases.
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Affiliation(s)
- Juliana de Oliveira Cruz
- Graduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alessandra O Silva
- Department of Food and Drugs, Faculty of Pharmaceutical Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - Jessyca M Ribeiro
- Department of Food and Drugs, Faculty of Pharmaceutical Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - Marcelo R Luizon
- Graduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Carla S Ceron
- Department of Biological Sciences, Institute of Exact and Biological Sciences, Federal University of Ouro Preto, Ouro Preto, Brazil
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Bakshi D, Katoch A, Chakraborty S, Shah R, Sharma B, Bhat A, Verma S, Bhat GR, Nagpal A, Vaishnavi S, Goswami A, Kumar R. ANKLE1 as New Hotspot Mutation for Breast Cancer in Indian Population and Has a Role in DNA Damage and Repair in Mammalian Cells. Front Genet 2021; 11:609758. [PMID: 33584808 PMCID: PMC7873468 DOI: 10.3389/fgene.2020.609758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer has replaced cervical cancer as being the most common and having the highest mortality among women in India. ANKLE gene is conserved among organisms during evolutionary succession and is a member of LEM family proteins in lower metazoans and is involved in critical functions in the nuclear architecture, gene expression and cell signaling. ANKLE1 is the human orthologous of LEM-3 and is involved in DNA damage response and DNA repair. Whole Exome Sequencing (WES) of paired breast cancer samples was performed and ANKLE1 was found to be a new possible hotspot for predisposition of breast cancer. The mass array genotyping for breast cancer variant rs2363956 further confirmed the ANKLE1 association with the studied population of breast cancer. To elucidate the role of ANKLE1 in DNA damage, it was knocked down in MCF-7 breast cancer cell line and the expression of γH2AX was assessed. ANKLE1 knockdown cells displayed elevated levels of γ-H2AX foci in response to the cisplatin induced replication stress. The localization pattern of ANKLE1 further emphasized the role of ANKLE1 in DNA repair process. We observed that ANKLE1 is required for maintaining genomic stability and plays a role in DNA damage and repair process. These findings provided a molecular basis for the suspected role of ANKLE1 in human breast cancer and suggested an important role of this gene in controlling breast cancer development among women in India.
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Affiliation(s)
| | - Archana Katoch
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR) Jammu, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Souneek Chakraborty
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR) Jammu, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Ruchi Shah
- Shri Mata Vaishno Devi University, Katra, India
| | | | - Amrita Bhat
- Shri Mata Vaishno Devi University, Katra, India
| | | | | | | | | | - Anindya Goswami
- Cancer Pharmacology Division, Indian Institute of Integrative Medicine (CSIR) Jammu, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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29
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Shang H, Zheng J, Tong J. Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer. Aging (Albany NY) 2020; 12:21874-21889. [PMID: 33177242 PMCID: PMC7695408 DOI: 10.18632/aging.104004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022]
Abstract
The aim of this study was to explore prognosis-related biomarkers and underlying mechanisms during ovarian carcinoma progression and development. mRNA expression profiles and GSE49997 dataset were downloaded. Survival analyses were performed for genes with high expression levels. Expression level of candidate genes was explored in four ovarian cancer cells lines. Pyruvate carboxylase (PC) was found to be one of significantly differentially expressed gene (DEG). The role of PC knockdown was analyzed in SKOV cells using cell proliferation, flow cytometric, and Transwell migration and invasion assays. DEGs and metabolites in PC-shRNA (shPC)-treated samples vs. control groups were identified. PC was a prognosis-related gene and related to metabolic pathway. Knockdown of PC regulated cell proliferation, cell cycle progression, and migration and invasion of SKOV-3 cells. Transcriptome sequencing analyses showed STAT1 and TP53 gained higher degrees in PPI network. A total of 44 metabolites were identified. These DEGs and metabolites in PC samples were related with neuroactive ligands receptor interaction, glycine, serine and threonine metabolism, and ABC transporter pathways. PC may affect the tumor biology of ovarian cancer through the dysregulation of glycine, serine, and threonine metabolism, and ABC transporter pathways, as well as STAT1 and TP53 expression.
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Affiliation(s)
- Hongkai Shang
- Department of Gynecology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang Province, China
| | - Jianfeng Zheng
- Department of Gynecology, Affiliated Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou 310006, Zhejiang Province, China
| | - Jinyi Tong
- Department of Gynecology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang Province, China.,Department of Gynecology, Affiliated Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou 310006, Zhejiang Province, China
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30
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Ji X, Li P, Fuscoe JC, Chen G, Xiao W, Shi L, Ning B, Liu Z, Hong H, Wu J, Liu J, Guo L, Kreil DP, Łabaj PP, Zhong L, Bao W, Huang Y, He J, Zhao Y, Tong W, Shi T. A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. Nucleic Acids Res 2020; 48:8320-8331. [PMID: 32749457 PMCID: PMC7470976 DOI: 10.1093/nar/gkaa638] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 01/01/2023] Open
Abstract
The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.
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Affiliation(s)
- Xiangjun Ji
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Peng Li
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,Massachusetts General Hospital, Harvard Medical School, 51 Blossom St, Boston, MA 02114, USA
| | - James C Fuscoe
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Geng Chen
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wenzhong Xiao
- Massachusetts General Hospital, Harvard Medical School, 51 Blossom St, Boston, MA 02114, USA
| | - Leming Shi
- Center for Pharmacogenomics, School of Pharmacy, Fudan University, Shanghai, 200438, China
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Zhichao Liu
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jinghua Liu
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Lei Guo
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - David P Kreil
- Department of Biotechnology, Boku University Vienna, 1190 Muthgasse 18, Austria
| | - Paweł P Łabaj
- Department of Biotechnology, Boku University Vienna, 1190 Muthgasse 18, Austria.,Małopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7A, 30-387 Kraków, Poland
| | - Liping Zhong
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Wenjun Bao
- SAS Institute Inc., Cary, NC, 27513, USA
| | - Yong Huang
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Jian He
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning 530021, China
| | - Weida Tong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China
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31
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Islam ABMMK, Mohammad E, Khan MAAK. Aberration of the modulatory functions of intronic microRNA hsa-miR-933 on its host gene ATF2 results in type II diabetes mellitus and neurodegenerative disease development. Hum Genomics 2020; 14:34. [PMID: 32993798 PMCID: PMC7526404 DOI: 10.1186/s40246-020-00285-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 09/01/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND MicroRNAs are ~ 22-nucleotide-long biological modifiers that act as the post-transcriptional modulator of gene expression. Some of them are identified to be embedded within the introns of protein-coding genes, these miRNAs are called the intronic miRNAs. Previous findings state that these intronic miRNAs are co-expressed with their host genes. This co-expression is necessary to maintain the robustness of the biological system. Till to date, only a few experiments are performed discretely to elucidate the functional relationship between few co-expressed intronic miRNAs and their associated host genes. RESULTS In this study, we have interpreted the underlying modulatory mechanisms of intronic miRNA hsa-miR-933 on its target host gene ATF2 and found that aberration can lead to several disease conditions. A protein-protein interaction network-based approach was adopted, and functional enrichment analysis was performed to elucidate the significantly over-represented biological functions and pathways of the common targets. Our approach delineated that hsa-miR-933 might control the hyperglycemic condition and hyperinsulinism by regulating ATF2 target genes MAP4K4, PRKCE, PEA15, BDNF, PRKACB, and GNAS which can otherwise lead to the development of type II diabetes mellitus. Moreover, we showed that hsa-miR-933 can regulate a target of ATF2, brain-derived neurotrophic factor (BDNF), to modulate the optimal expression of ATF2 in neuron cells to render neuroprotection for the inhibition of neurodegenerative diseases. CONCLUSIONS Our in silico model provides interesting resources for experimentations in a model organism or cell line for further validation. These findings may extend the common perception of gene expression analysis with new regulatory functionality.
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Affiliation(s)
| | - Eusra Mohammad
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
- Current Affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Md. Abdullah-Al-Kamran Khan
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
- Current Affiliation: Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
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32
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Cui NH, Yang JM, Liu X, Wang XB. Poly(ADP-Ribose) Polymerase Activity and Coronary Artery Disease in Type 2 Diabetes Mellitus: An Observational and Bidirectional Mendelian Randomization Study. Arterioscler Thromb Vasc Biol 2020; 40:2516-2526. [PMID: 32757651 DOI: 10.1161/atvbaha.120.314712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Experimental evidence suggests a close link between PARP (poly[ADP-ribose] polymerase) activation and diabetic endothelial dysfunction. Here, we tested whether PARP activity in circulating leukocytes was associated with coronary artery disease (CAD) among patients with type 2 diabetes mellitus (T2DM). Approach and Results: We performed observational and bidirectional Mendelian randomization studies of 3149 Chinese individuals with T2DM who underwent coronary angiography, with leukocyte PARP activity, 16 tag single-nucleotide polymorphisms in PARP1 and PARP2, and 17 CAD risk single-nucleotide polymorphisms analyzed. Of 3149 participants, 1180 who further received percutaneous coronary intervention were prospectively followed for 1 year to track major adverse cardiovascular and cerebrovascular events. Overall, greater PARP activity was cross-sectionally associated with an odds ratio of 1.23 for obstructive CAD, and prospectively with a hazard ratio of 1.34 for 1-year major adverse cardiovascular and cerebrovascular events after percutaneous coronary intervention (both P<0.001). Using a genetic score of 5 screened single-nucleotide polymorphisms in PARP1 and PARP2 as the instrumental variable, genetically predicted elevation in PARP activity showed a causal association with obstructive CAD (odds ratio=1.35, P<0.001). In contrast, the genetic risk of CAD had no significant effect on PARP activity. Ex vivo and in vitro cultures of human monocytes showed that rs747657, as the lead single-nucleotide polymorphism strongly associated with PARP activity, caused the differential binding of transcription factor GATA2 (GATA-binding protein 2) to an intronic regulatory region in PARP1, thus modulating PARP1 expression and PARP activity. CONCLUSIONS Greater PARP activity may have causal roles in the development of obstructive CAD among patients with diabetes mellitus.
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Affiliation(s)
- Ning-Hua Cui
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan, China (N.-h.C., J.-m.Y.)
| | - Jun-Mei Yang
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan, China (N.-h.C., J.-m.Y.)
| | - Xia'nan Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, China (X.L., X.-b.W.)
| | - Xue-Bin Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, China (X.L., X.-b.W.)
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33
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Chen Q, Meng X, Liao Q, Chen M. Versatile interactions and bioinformatics analysis of noncoding RNAs. Brief Bioinform 2020; 20:1781-1794. [PMID: 29939215 DOI: 10.1093/bib/bby050] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Indexed: 02/07/2023] Open
Abstract
Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as inconsequential results of transcriptional promiscuity, ncRNAs were later found to exert great roles in various aspects of biological functions. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). Here, we provide an overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions. To better investigate the ncRNA-mediated regulation, it is necessary to make full use of innovative sequencing techniques and computational tools. We further describe a comprehensive workflow for in silico ncRNA analysis, providing up-to-date platforms, databases and tools dedicated to ncRNA identification and functional annotation.
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Affiliation(s)
- Qi Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Qi Liao
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Ming Chen
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University, Ningbo, Zhejiang, P. R. China
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34
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Linhares ND, Pereira DA, Conceição IM, Franco GR, Eckalbar WL, Ahituv N, Luizon MR. Noncoding SNPs associated with increased GDF15 levels located in a metformin-activated enhancer region upstream of GDF15. Pharmacogenomics 2020; 21:509-520. [PMID: 32427048 DOI: 10.2217/pgs-2020-0010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: GDF15 levels are a biomarker for metformin use. We performed the functional annotation of noncoding genome-wide association study (GWAS) SNPs for GDF15 levels and the Genotype-Tissue Expression (GTEx)-expression quantitative trait loci (eQTLs) for GDF15 expression within metformin-activated enhancers around GDF15. Materials & methods: These enhancers were identified using chromatin immunoprecipitation followed by sequencing data for active (H3K27ac) and silenced (H3K27me3) histone marks on human hepatocytes treated with metformin, Encyclopedia of DNA Elements data and cis-regulatory elements assignment tools. Results: The GWAS lead SNP rs888663, the SNP rs62122429 associated with GDF15 levels in the Outcome Reduction with Initial Glargine Intervention trial, and the GTEx-expression quantitative trait locus rs4808791 for GDF15 expression in whole blood are located in a metformin-activated enhancer upstream of GDF15 and tightly linked in Europeans and East Asians. Conclusion: Noncoding variation within a metformin-activated enhancer may increase GDF15 expression and help to predict GDF15 levels.
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Affiliation(s)
- Natália D Linhares
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Daniela A Pereira
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Izabela McA Conceição
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Glória R Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Walter L Eckalbar
- Institute for Human Genetics, The University of California, San Francisco, CA 94143, USA.,Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Institute for Human Genetics, The University of California, San Francisco, CA 94143, USA.,Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marcelo R Luizon
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.,Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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35
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Berrio A, Haygood R, Wray GA. Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral. BMC Genomics 2020; 21:359. [PMID: 32404186 PMCID: PMC7222330 DOI: 10.1186/s12864-020-6752-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/21/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Adaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype. RESULTS We used ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments. We applied the method to noncoding Human Accelerated Elements as well as open chromatin elements previously identified in 125 human tissues and cell lines to demonstrate its utility. Then, we evaluated the impact of query region length, proxy neutral sequence length, and branch count on test sensitivity and specificity. We found that the length of the query alignment can vary between 150 bp and 1 kb without affecting the estimation of selection, while for the reference alignment, we found that a length of 3 kb is adequate for proper testing. We also simulated sequence alignments under different classes of evolution and validated our ability to distinguish positive selection from relaxation of constraint and neutral evolution. Finally, we re-confirmed that a quarter of all non-coding Human Accelerated Elements are evolving by positive selection. CONCLUSION Here, we introduce a method we called adaptiPhy, which adds significant improvements to our earlier method that tests for branch-specific directional selection in noncoding sequences. The motivation for these improvements is to provide a more sensitive and better targeted characterization of directional selection and neutral evolution across the genome.
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Affiliation(s)
- Alejandro Berrio
- Department of Biology, Duke University, Biological Sciences Building, 124 Science Drive, Durham, NC, 27708, USA.
| | - Ralph Haygood
- Ronin Institute for Independent Scholarship, 127 Haddon Pl., Montclair, NJ, 07043, USA
| | - Gregory A Wray
- Department of Biology, Duke University, Biological Sciences Building, 124 Science Drive, Durham, NC, 27708, USA
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36
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Wang Y, Wan G, Wang H, Zhang G, Li Z, Lu L, Wu Y, Yu X, Du J. Mechanism of aberrant long non-coding RNA expression in an adriamycin-resistant liver cancer cell strain. Dig Liver Dis 2020; 52:582-587. [PMID: 31704308 DOI: 10.1016/j.dld.2019.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Aberrant long non-coding RNA (lncRNA) expression in cancer can be used as a potential diagnostic biomarker and therapeutic target. In the present study we determined the potential pathogenic mechanism underlying significant aberrant expression of lncRNAs in HepG2-ADR. METHODS First, we identified different levels of lncRNA expression in liver cancer and adjacent non-tumor tissues obtained from public data (GSE70880) in NCBI. Then, the results were verified in a sensitive liver cancer cell line (HepG2) and a adriamycin-resistant liver cancer cell line (HepG2-ADR). Then, the effects of lncRNAs on the phenotype and some biological characteristics were also determined in HepG2 and HepG2-ADR through overexpression and using siRNA interference methods. RESULTS We showed that lncRNA ENST00000425005 is highly expressed in a liver cancer-resistant cell line when compared with adjacent non-tumor tissues based on bioinformatics analysis and qPCR verification. Compared with the control group, overexpression of lncRNA ENST00000425005 significantly promoted proliferation and adhesiveness, but inhibited apoptosis in HepG2-ADR cells. In contrast, interference of lncRNA in HepG2-ADR cells suppressed proliferation and adhesiveness, and induced apoptosis. CONCLUSION In conclusion, lncRNA ENST00000425005 promotes cell proliferation and invasion in drug-resistant liver cancer cells by regulating epithelial-mesenchymal transition-related gene expression and participating in the regulation of EGF and FGF7.
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Affiliation(s)
- Yuan Wang
- Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmaceutical Sciences and The Affiliated Fifth Hospital, Guangzhou Medical University, Guangzhou, China; Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Guohui Wan
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hongsheng Wang
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ge Zhang
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziqian Li
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Linlin Lu
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingming Wu
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiyong Yu
- Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmaceutical Sciences and The Affiliated Fifth Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Jun Du
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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Abstract
Hepatocellular carcinoma (HCC) is the most frequent subtype of primary liver cancer and one of the leading causes of cancer-related death worldwide. However, the molecular mechanisms underlying HCC pathogenesis have not been fully understood. Emerging evidences have recently suggested the crucial role of long noncoding RNAs (lncRNAs) in the tumorigenesis and progression of HCC. Various HCC-related lncRNAs have been shown to possess aberrant expression and participate in cancerous phenotypes (e.g. persistent proliferation, evading apoptosis, accelerated vessel formation and gain of invasive capability) through their binding with DNA, RNA or proteins, or encoding small peptides. Thus, a deeper understanding of lncRNA dysregulation would provide new insights into HCC pathogenesis and novel tools for the early diagnosis and treatment of HCC. In this review, we summarize the dysregulation of lncRNAs expression in HCC and their tumor suppressive or oncogenic roles during HCC tumorigenesis. Moreover, we discuss the diagnostic and therapeutic potentials of lncRNAs in HCC.
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38
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Lin Y, Qian F, Shen L, Chen F, Chen J, Shen B. Computer-aided biomarker discovery for precision medicine: data resources, models and applications. Brief Bioinform 2020; 20:952-975. [PMID: 29194464 DOI: 10.1093/bib/bbx158] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Biomarkers are a class of measurable and evaluable indicators with the potential to predict disease initiation and progression. In contrast to disease-associated factors, biomarkers hold the promise to capture the changeable signatures of biological states. With methodological advances, computer-aided biomarker discovery has now become a burgeoning paradigm in the field of biomedical science. In recent years, the 'big data' term has accumulated for the systematical investigation of complex biological phenomena and promoted the flourishing of computational methods for systems-level biomarker screening. Compared with routine wet-lab experiments, bioinformatics approaches are more efficient to decode disease pathogenesis under a holistic framework, which is propitious to identify biomarkers ranging from single molecules to molecular networks for disease diagnosis, prognosis and therapy. In this review, the concept and characteristics of typical biomarker types, e.g. single molecular biomarkers, module/network biomarkers, cross-level biomarkers, etc., are explicated on the guidance of systems biology. Then, publicly available data resources together with some well-constructed biomarker databases and knowledge bases are introduced. Biomarker identification models using mathematical, network and machine learning theories are sequentially discussed. Based on network substructural and functional evidences, a novel bioinformatics model is particularly highlighted for microRNA biomarker discovery. This article aims to give deep insights into the advantages and challenges of current computational approaches for biomarker detection, and to light up the future wisdom toward precision medicine and nation-wide healthcare.
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Affiliation(s)
- Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Fuliang Qian
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Li Shen
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Feifei Chen
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Jiajia Chen
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
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39
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Burley M, Roberts S, Parish JL. Epigenetic regulation of human papillomavirus transcription in the productive virus life cycle. Semin Immunopathol 2020; 42:159-171. [PMID: 31919577 PMCID: PMC7174255 DOI: 10.1007/s00281-019-00773-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022]
Abstract
Human papillomaviruses (HPV) are a large family of viruses which contain a circular, double-stranded DNA genome of approximately 8000 base pairs. The viral DNA is chromatinized by the recruitment of cellular histones which are subject to host cell-mediated post-translational epigenetic modification recognized as an important mechanism of virus transcription regulation. The HPV life cycle is dependent on the terminal differentiation of the target cell within epithelia-the keratinocyte. The virus life cycle begins in the undifferentiated basal compartment of epithelia where the viral chromatin is maintained in an epigenetically repressed state, stabilized by distal chromatin interactions between the viral enhancer and early gene region. Migration of the infected keratinocyte towards the surface of the epithelium induces cellular differentiation which disrupts chromatin looping and stimulates epigenetic remodelling of the viral chromatin. These epigenetic changes result in enhanced virus transcription and activation of the virus late promoter facilitating transcription of the viral capsid proteins. In this review article, we discuss the complexity of virus- and host-cell-mediated epigenetic regulation of virus transcription with a specific focus on differentiation-dependent remodelling of viral chromatin during the HPV life cycle.
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Affiliation(s)
- Megan Burley
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Sally Roberts
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Joanna L Parish
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK.
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40
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Ma N, Tie C, Yu B, Zhang W, Wan J. Identifying lncRNA-miRNA-mRNA networks to investigate Alzheimer's disease pathogenesis and therapy strategy. Aging (Albany NY) 2020; 12:2897-2920. [PMID: 32035423 PMCID: PMC7041741 DOI: 10.18632/aging.102785] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/19/2020] [Indexed: 12/23/2022]
Abstract
Alzheimer’s disease (AD), the most common cause of dementia, leads to neuronal damage and deterioration of cognitive functions in aging brains. There is evidence suggesting the participation of noncoding RNAs in AD-associated pathophysiology. A potential linkage between AD and lncRNA-associated competing endogenous RNA (ceRNA) networks has been revealed. Nevertheless, there are still no genome-wide studies which have identified the lncRNA-associated ceRNA pairs involved in AD. For this reason, deep RNA-sequencing was performed to systematically investigate lncRNA-associated ceRNA mechanisms in AD model mice (APP/PS1) brains. Our results identified 487, 89, and 3,025 significantly dysregulated lncRNAs, miRNAs, and mRNAs, respectively, and the most comprehensive lncRNA-associated ceRNA networks to date are constructed in the APP/PS1 brain. GO analysis revealed the involvement of the identified networks in regulating AD development from distinct origins, such as synapses and dendrites. Following rigorous selection, the lncRNA-associated ceRNA networks in this AD mouse model were found to be mainly involved in synaptic plasticity as well as memory (Akap5) and regulation of amyloid-β (Aβ)-induced neuroinflammation (Klf4). This study presents the first systematic dissection of lncRNA-associated ceRNA profiles in the APP/PS1 mouse brain. The identified lncRNA-associated ceRNA networks could provide insights that facilitate AD diagnosis and future treatment strategies.
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Affiliation(s)
- Nana Ma
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen 518000, Guangdong Province, China
| | - Changrui Tie
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen 518000, Guangdong Province, China
| | - Bo Yu
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen 518000, Guangdong Province, China.,Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, China
| | - Wei Zhang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen 518000, Guangdong Province, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen 518000, Guangdong Province, China.,Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong 999077, China
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41
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das Chagas PF, de Sousa GR, Kodama MH, de Biagi Junior CAO, Yunes JA, Brandalise SR, Calin GA, Tone LG, Scrideli CA, de Oliveira JC. Ultraconserved long non-coding RNA uc.112 is highly expressed in childhood T versus B-cell acute lymphoblastic leukemia. Hematol Transfus Cell Ther 2020; 43:28-34. [PMID: 32014474 PMCID: PMC7910170 DOI: 10.1016/j.htct.2019.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 10/02/2019] [Accepted: 12/05/2019] [Indexed: 12/29/2022] Open
Abstract
Aberrant expression of long non-coding RNAs (lncRNAs) has been detected in several types of cancer, including acute lymphoblastic leukemia (ALL), but lncRNA mapped on transcribed ultraconserved regions (T-UCRs) are little explored. The T-UCRs uc.112, uc.122, uc.160 and uc.262 were evaluated by quantitative real-time PCR in bone marrow samples from children with T-ALL (n = 32) and common-ALL/pre-B ALL (n = 30). In pediatric ALL, higher expression levels of uc.112 were found in patients with T-ALL, compared to patients with B-ALL. T-cells did not differ significantly from B-cells regarding uc.112 expression in non-tumor precursors from public data. Additionally, among B-ALL patients, uc.112 was also found to be increased in patients with hyperdiploidy, compared to other karyotype results. The uc.122, uc.160, and uc.262 were not associated with biological or clinical features. These findings suggest a potential role of uc.112 in pediatric ALL and emphasize the need for further investigation of T-UCR in pediatric ALL.
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Affiliation(s)
- Pablo Ferreira das Chagas
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil; Universidade Federal de Alfenas (UNIFAL), Alfenas, MG, Brazil
| | - Graziella Ribeiro de Sousa
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Márcio Hideki Kodama
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | | | | | | | | | - Luiz Gonzaga Tone
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Carlos Alberto Scrideli
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Jaqueline Carvalho de Oliveira
- Universidade Federal de Alfenas (UNIFAL), Alfenas, MG, Brazil; Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil.
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Dong Z, Zhou J, Jiang S, Li Y, Zhao D, Yang C, Ma Y, He H, Ji H, Jin L, Zou H, Wang J. Epistatic interaction between PKD2 and ABCG2 influences the pathogenesis of hyperuricemia and gout. Hereditas 2020; 157:2. [PMID: 32000861 PMCID: PMC6986014 DOI: 10.1186/s41065-020-0116-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/14/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Genetic background affects serum urate concentration and gout risk, especially regarding these variants in the urate-transporter gene ABCG2. However, the role of epistasis between PKD2 and ABCG2 on the pathogenesis of gout is poorly understood. Here we assess this epistatic interaction in the progression from elevated serum urate to gout. RESULTS We identified two epistatic interaction pairs (rs2728121: rs1481012 and rs2728121: rs2231137) were associated with urate levels in 4914 Chinese individuals (Pint = 0.018 and 0.004, respectively). Using subgroup analysis for gender and BMI, we found the degree of associations was varied by gender and BMI. The SNP pair rs2728121:rs1481012 influenced urate levels in females and overweight subjects (Pint = 0.006 and 0.022, respectively), but rs2728121:rs2231137 did in males, overweight and normal-weight subjects (Pint = 0.017, 0.047 and 0.013, respectively). Consistent results were also observed in associations between these epistatic interactions with hyperuricemia. Next, the SNP pair rs2728121:rs2231137 was identified to influence the development of gout from both hyperuricemia and healthy (Pint = 0.035 and 0.001, respectively), especially in males (Pint = 0.030 and 0.001, respectively). Furthermore, we demonstrated that interacting regions were enriched by regulatory elements. Finally, we observed a strong gene co-expression pattern between PKD2 and ABCG2 (r = 0.743, P = 5.83E-06). CONCLUSION Our findings indicate epistasis between PKD2 and ABCG2 influence serum urate concentrations, hyperuricemia and gout risk, thus providing insight into the pathogenesis of gout.
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Affiliation(s)
- Zheng Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Jingru Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Shuai Jiang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Yuan Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Dongbao Zhao
- Division of Rheumatology and Immunology, Changhai Hospital, Shanghai, China
| | - Chengde Yang
- Division of Rheumatology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yanyun Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Hongjun He
- Division of Rheumatology, Taixing People's Hospital, Jiangsu Province, China
| | - Hengdong Ji
- Division of Rheumatology, Taizhou People's Hospital, Jiangsu Province, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu Province, China
| | - Hejian Zou
- Division of Rheumatology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, People's Republic of China.
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China.
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Jiangwan Campus, 2005 Songhu Road, Shanghai, 200438, People's Republic of China.
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu Province, China.
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China.
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Katzir R, Polat IH, Harel M, Katz S, Foguet C, Selivanov VA, Sabatier P, Cascante M, Geiger T, Ruppin E. The landscape of tiered regulation of breast cancer cell metabolism. Sci Rep 2019; 9:17760. [PMID: 31780802 PMCID: PMC6882817 DOI: 10.1038/s41598-019-54221-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 10/21/2019] [Indexed: 01/10/2023] Open
Abstract
Altered metabolism is a hallmark of cancer, but little is still known about its regulation. In this study, we measure transcriptomic, proteomic, phospho-proteomic and fluxomics data in a breast cancer cell-line (MCF7) across three different growth conditions. Integrating these multiomics data within a genome scale human metabolic model in combination with machine learning, we systematically chart the different layers of metabolic regulation in breast cancer cells, predicting which enzymes and pathways are regulated at which level. We distinguish between two types of reactions, directly and indirectly regulated. Directly-regulated reactions include those whose flux is regulated by transcriptomic alterations (~890) or via proteomic or phospho-proteomics alterations (~140) in the enzymes catalyzing them. We term the reactions that currently lack evidence for direct regulation as (putative) indirectly regulated (~930). Many metabolic pathways are predicted to be regulated at different levels, and those may change at different media conditions. Remarkably, we find that the flux of predicted indirectly regulated reactions is strongly coupled to the flux of the predicted directly regulated ones, uncovering a tiered hierarchical organization of breast cancer cell metabolism. Furthermore, the predicted indirectly regulated reactions are predominantly reversible. Taken together, this architecture may facilitate rapid and efficient metabolic reprogramming in response to the varying environmental conditions incurred by the tumor cells. The approach presented lays a conceptual and computational basis for mapping metabolic regulation in additional cancers.
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Affiliation(s)
- Rotem Katzir
- Center for BioInformatics and Computational Biology, Dept. of Computer Science and the University of Maryland Institute of Advanced Computer Studies (UMIACS), University of Maryland, College Park, MD, 20742, USA
| | - Ibrahim H Polat
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.,Equipe environnement et prédiction de la santé des populations, Laboratoire TIMC (UMR 5525), CHU de Grenoble, Université Grenoble Alpes, La Tronche, France
| | - Michal Harel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shir Katz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of medicine, Tel Aviv University, Tel Aviv, Israel
| | - Carles Foguet
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Vitaly A Selivanov
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Philippe Sabatier
- Equipe environnement et prédiction de la santé des populations, Laboratoire TIMC (UMR 5525), CHU de Grenoble, Université Grenoble Alpes, La Tronche, France
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Eytan Ruppin
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA.
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Rojano E, Seoane P, Ranea JAG, Perkins JR. Regulatory variants: from detection to predicting impact. Brief Bioinform 2019; 20:1639-1654. [PMID: 29893792 PMCID: PMC6917219 DOI: 10.1093/bib/bby039] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/18/2018] [Indexed: 02/01/2023] Open
Abstract
Variants within non-coding genomic regions can greatly affect disease. In recent years, increasing focus has been given to these variants, and how they can alter regulatory elements, such as enhancers, transcription factor binding sites and DNA methylation regions. Such variants can be considered regulatory variants. Concurrently, much effort has been put into establishing international consortia to undertake large projects aimed at discovering regulatory elements in different tissues, cell lines and organisms, and probing the effects of genetic variants on regulation by measuring gene expression. Here, we describe methods and techniques for discovering disease-associated non-coding variants using sequencing technologies. We then explain the computational procedures that can be used for annotating these variants using the information from the aforementioned projects, and prediction of their putative effects, including potential pathogenicity, based on rule-based and machine learning approaches. We provide the details of techniques to validate these predictions, by mapping chromatin-chromatin and chromatin-protein interactions, and introduce Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein 9 (CRISPR-Cas9) technology, which has already been used in this field and is likely to have a big impact on its future evolution. We also give examples of regulatory variants associated with multiple complex diseases. This review is aimed at bioinformaticians interested in the characterization of regulatory variants, molecular biologists and geneticists interested in understanding more about the nature and potential role of such variants from a functional point of views, and clinicians who may wish to learn about variants in non-coding genomic regions associated with a given disease and find out what to do next to uncover how they impact on the underlying mechanisms.
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Affiliation(s)
- Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Juan A G Ranea
- CIBER de Enfermedades Raras, ISCIII, Madrid, Spain and Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - James R Perkins
- Research laboratory, IBIMA-Regional University Hospital of Malaga, UMA, Malaga 29009, Spain
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Mann A, Bhatia S. Zebrafish: A Powerful Model for Understanding the Functional Relevance of Noncoding Region Mutations in Human Genetic Diseases. Biomedicines 2019; 7:E71. [PMID: 31527394 PMCID: PMC6784013 DOI: 10.3390/biomedicines7030071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
Determining aetiology of genetic disorders caused by damaging mutations in protein-coding genes is well established. However, understanding how mutations in the vast stretches of the noncoding genome contribute to genetic abnormalities remains a huge challenge. Cis-regulatory elements (CREs) or enhancers are an important class of noncoding elements. CREs function as the primary determinants of precise spatial and temporal regulation of their target genes during development by serving as docking sites for tissue-specific transcription factors. Although a large number of potential disease-associated CRE mutations are being identified in patients, lack of robust methods for mechanistically linking these mutations to disease phenotype is currently hampering the understanding of their roles in disease aetiology. Here, we have described the various systems available for testing the CRE potential of stretches of noncoding regions harbouring mutations implicated in human disease. We highlight advances in the field leading to the establishment of zebrafish as a powerful system for robust and cost-effective functional assays of CRE activity, enabling rapid identification of causal variants in regulatory regions and the validation of their role in disruption of appropriate gene expression.
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Affiliation(s)
- Anita Mann
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Shipra Bhatia
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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Hirata Y, Toyono T, Kokabu S, Obikane Y, Kataoka S, Nakatomi M, Masaki C, Hosokawa R, Seta Y. Krüppel-like factor 5 (Klf5) regulates expression of mouse T1R1 amino acid receptor gene (Tas1r1) in C2C12 myoblast cells. Biomed Res 2019; 40:67-78. [PMID: 30982802 DOI: 10.2220/biomedres.40.67] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
T1R1 and T1R3 are receptors expressed in taste buds that detect L-amino acids. These receptors are also expressed throughout diverse organ systems, such as the digestive system and muscle tissue, and are thought to function as amino acid sensors. The mechanism of transcriptional regulation of the mouse T1R1 gene (Tas1r1) has not been determined; therefore, in this study, we examined the function of Tas1r1 promoter in the mouse myoblast cell line, C2C12. Luciferase reporter assays showed that a 148-bp region upstream of the ATG start codon of Tas1r1 had a promoter activity. The GT box in the Tas1r1 promoter was conserved in the dog, human, mouse, and pig. Site-directed mutagenesis of this GT box significantly reduced the promoter activation. The GT box in promoters is a recurring motif for Sp/KLF family members. RNAi-mediated depletion of Sp4 and Klf5 decreased Tas1r1 expression, while overexpression of Klf5, but not Sp4, significantly increased Tas1r1 expression. The ENCODE data of chromatin immunoprecipitation and sequencing (ChIP-seq) showed that Klf5 bound to the GT box during the myogenic differentiation. Furthermore, the Klf5 knockout cell lines led to a considerable decrease in the levels of Tas1r1 expression. Collectively, these results showed that Klf5 binds to the GT box in the Tas1r1 promoter and regulates Tas1r1 expression in C2C12 cells.
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Affiliation(s)
- Yuki Hirata
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University
| | - Takashi Toyono
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University
| | - Shoichiro Kokabu
- Division of Molecular Signaling and Biochemistry, Department of Health Promotion, Kyushu Dental University
| | - Yui Obikane
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University
| | - Shinji Kataoka
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University
| | - Mitsushiro Nakatomi
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University
| | - Chihiro Masaki
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University
| | - Ryuji Hosokawa
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University
| | - Yuji Seta
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University
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Pazmandi J, Kalinichenko A, Ardy RC, Boztug K. Early-onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms. Immunol Rev 2019; 287:162-185. [PMID: 30565237 PMCID: PMC7379380 DOI: 10.1111/imr.12726] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 09/23/2018] [Indexed: 12/11/2022]
Abstract
Rare, monogenetic diseases present unique models to dissect gene functions and biological pathways, concomitantly enhancing our understanding of the etiology of complex (and often more common) traits. Although inflammatory bowel disease (IBD) is a generally prototypic complex disease, it can also manifest in an early-onset, monogenic fashion, often following Mendelian modes of inheritance. Recent advances in genomic technologies have spurred the identification of genetic defects underlying rare, very early-onset IBD (VEO-IBD) as a disease subgroup driven by strong genetic influence, pinpointing key players in the delicate homeostasis of the immune system in the gut and illustrating the intimate relationships between bowel inflammation, systemic immune dysregulation, and primary immunodeficiency with increased susceptibility to infections. As for other human diseases, it is likely that adult-onset diseases may represent complex diseases integrating the effects of host genetic susceptibility and environmental triggers. Comparison of adult-onset IBD and VEO-IBD thus provides beautiful models to investigate the relationship between monogenic and multifactorial/polygenic diseases. This review discusses the present and novel findings regarding monogenic IBD as well as key questions and future directions of IBD research.
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Affiliation(s)
- Julia Pazmandi
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Artem Kalinichenko
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Rico Chandra Ardy
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of Pediatrics and Adolescent MedicineMedical University of ViennaViennaAustria
- Department of PediatricsSt. Anna Kinderspital and Children's Cancer Research InstituteMedical University of ViennaViennaAustria
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Liu M, Wang Z, Liu Q, Zhu H, Xu N. Expression of Micro-RNA-492 (MiR-492) in Human Cervical Cancer Cell Lines is Upregulated by Transfection with Wild-Type P53, Irradiation, and 5-Fluorouracil Treatment In Vitro. Med Sci Monit 2018; 24:7750-7758. [PMID: 30374014 PMCID: PMC6354641 DOI: 10.12659/msm.911585] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The status of p53 is critical to the chemoradiosensitivity of cervical cancer cells. Wild-type p53 is essential to orchestrate the cellular response to cytotoxic stimuli. Our previous data illustrated that cervical cancer patients whose specimens overexpressed microR-492 (miR-492) were highly sensitive to concurrent chemoradiation. Although p53 activation has been reported to upregulate miR-492 by a miRNA profiling assay in lung cancer cells, the transcriptional regulation of miR-492 in cervical cancer cells remains poorly understood. Therefore, we aimed to decipher the relationship between p53 and miR-492 in cervical cancer cells. Material/Methods The expression of p53 and miR-492 in cervical cancer cell lines was measured by western blot and real-time PCR. After cells were transfected with wild-type p53 plasmid or were treated by irradiation and 5-fluorouracil (5-FU), the expression changes of p53 as well as miR-492 were examined by western blot and real-time PCR. The putative p53 binding site of miR-492 was first analyzed by bioinformatics tools, then validated by chromatin immunoprecipitation and dual-luciferase reporter assays. Results We found that miR-492 was upregulated in cells with wild-type p53 compared to cells with mutant p53. Transfection of wild-type p53 plasmid or treatments with cytotoxic reagents including irradiation and 5-FU all induced miR-492 overexpression. Bioinformatics analysis and experimental validations further proved p53 interacted with miR-492 promoter directly. Conclusions In cervical cancer cells, p53 activated miR-492 expression transcriptionally.
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Affiliation(s)
- Mei Liu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Zaozao Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, China (mainland)
| | - Qiao Liu
- Key Laboratory of Experimental Teratology (Ministry of Education), Department of Molecular Medicine and Genetics, School of Basic Medicine Sciences, Shandong University, Jinan, Shandong, China (mainland)
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China (mainland)
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
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Gabdank I, Chan ET, Davidson JM, Hilton JA, Davis CA, Baymuradov UK, Narayanan A, Onate KC, Graham K, Miyasato SR, Dreszer TR, Strattan JS, Jolanki O, Tanaka FY, Hitz BC, Sloan CA, Cherry JM. Prevention of data duplication for high throughput sequencing repositories. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4913687. [PMID: 29688363 PMCID: PMC5829560 DOI: 10.1093/database/bay008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/10/2018] [Indexed: 01/01/2023]
Abstract
Database URL https://www.encodeproject.org/.
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Affiliation(s)
- Idan Gabdank
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Esther T Chan
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Jason A Hilton
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Carrie A Davis
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | | | - Aditi Narayanan
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Kathrina C Onate
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Keenan Graham
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Stuart R Miyasato
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Timothy R Dreszer
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Forrest Y Tanaka
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
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50
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Cai Y, Wan J. Competing Endogenous RNA Regulations in Neurodegenerative Disorders: Current Challenges and Emerging Insights. Front Mol Neurosci 2018; 11:370. [PMID: 30344479 PMCID: PMC6182084 DOI: 10.3389/fnmol.2018.00370] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/18/2018] [Indexed: 12/14/2022] Open
Abstract
The past decade has witnessed exciting breakthroughs that have contributed to the richness and complexity of a burgeoning modern RNA world, and one particular breakthrough-the competing endogenous RNA (ceRNA) hypothesis-has been described as the "Rosetta Stone" for decoding the RNA language used in regulating RNA crosstalk and modulating biological functions. The proposed far-reaching mechanism unites diverse RNA species and provides new insights into previously unrecognized RNA-RNA interactions and RNA regulatory networks that perhaps determine gene expression in an organized, hierarchical manner. The recently uncovered ceRNA regulatory loops and networks have emphasized the power of ceRNA regulation in a wide range of developmental stages and pathological contexts, such as in tumorigenesis and neurodegenerative disorders. Although the ceRNA hypothesis drastically enhanced our understanding of RNA biology, shortly after the hypothesis was proposed, disputes arose in relation mainly to minor discrepancies in the reported effects of ceRNA regulation under physiological conditions, and this resulted in ceRNA regulation becoming an extensively studied and fast-growing research field. Here, we focus on the evidence supporting ceRNA regulation in neurodegenerative disorders and address three critical points related to the ceRNA regulatory mechanism: the microRNA (miRNA) and ceRNA hierarchies in cross-regulations; the balance between destabilization and stable binding in ceRNA-miRNA interactions; and the true extent to which ceRNA regulatory mechanisms are involved in both health and disease, and the experimental shortcomings in current ceRNA studies.
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Affiliation(s)
- Yifei Cai
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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