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Mehmandar-Oskuie A, Jahankhani K, Rostamlou A, Mardafkan N, Karamali N, Razavi ZS, Mardi A. Molecular mechanism of lncRNAs in pathogenesis and diagnosis of auto-immune diseases, with a special focus on lncRNA-based therapeutic approaches. Life Sci 2024; 336:122322. [PMID: 38042283 DOI: 10.1016/j.lfs.2023.122322] [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: 10/05/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/04/2023]
Abstract
Autoimmune diseases are a diverse set of conditions defined by organ damage due to abnormal innate and acquired immune system responses. The pathophysiology of autoimmune disorders is exceedingly intricate and has yet to be fully understood. The study of long non-coding RNAs (lncRNAs), non-protein-coding RNAs with at least 200 nucleotides in length, has gained significant attention due to the completion of the human genome project and the advancement of high-throughput genomic approaches. Recent research has demonstrated how lncRNA alters disease development to different degrees. Although lncRNA research has made significant progress in cancer and generative disorders, autoimmune illnesses are a relatively new research area. Moreover, lncRNAs play crucial functions in differentiating various immune cells, and their potential relationships with autoimmune diseases have received growing attention. Because of the importance of Th17/Treg axis in auto-immune disease development, in this review, we discuss various molecular mechanisms by which lncRNAs regulate the differentiation of Th17/Treg cells. Also, we reviewed recent findings regarding the several approaches in the application of lncRNAs in the diagnosis and treatment of human autoimmune diseases, as well as current challenges in lncRNA-based therapeutic approaches to auto-immune diseases.
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Affiliation(s)
- Amirreza Mehmandar-Oskuie
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kasra Jahankhani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arman Rostamlou
- Department of Medical Biology, Faculty of Medicine, University of EGE, Izmir, Turkey
| | - Nasibeh Mardafkan
- Department of Laboratory Science, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Negin Karamali
- Student Research Committee, Tabriz University of Medical Science, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Science, Tabriz, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Zahra Sadat Razavi
- Department of Immunology, Faculty of Medicine, Tarbiat Modares University, Tehran, Iran
| | - Amirhossein Mardi
- Student Research Committee, Tabriz University of Medical Science, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Science, Tabriz, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran.
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Tian Q, Liu X, Li A, Wu H, Xie Y, Zhang H, Wu F, Chen Y, Bai C, Zhang X. LINC01936 inhibits the proliferation and metastasis of lung squamous cell carcinoma probably by EMT signaling and immune infiltration. PeerJ 2023; 11:e16447. [PMID: 38084139 PMCID: PMC10710776 DOI: 10.7717/peerj.16447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/21/2023] [Indexed: 12/18/2023] Open
Abstract
Purpose To discover the biological function and potential mechanism of LINC01936 in the development of lung squamous cell carcinoma (LUSC). Methods Transcriptome data of LUSC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to analyze the differentially expressed lncRNAs in LUSC and normal tissues by R "DEseq2", "edgeR" and "limma" packages. The subcellular localization of LINC01936 was predicted by lncLocator. Cell proliferation and apoptosis were measured by CCK-8, MTT assay and Hoechst fluorescence staining. The migration and invasion were detected by Transwell assay. The function and pathway enrichment analysis were performed by Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene set variation analysis (GSVA). The downstream targets of LINC01936 were predicted using RNA-Protein Interaction Prediction (RPISeq) program. The effect of LINC01936 on tumor immune infiltration was analyzed using Pearson Correlation Analysis using R "ggpubr" package. Results Based on the gene expression data of LUSC from TCGA database, 1,603, 1,702 and 529 upregulated and 536, 436 and 630 downregulated lncRNAs were obtained by DEseq2, edgeR and limma programs, respectively. For GSE88862 dataset, we acquired 341 differentially expressed lncRNAs (206 upregulated and 135 downregulated). Venn plot for the intersection of above differential expressed lncRNAs showed that there were 29 upregulated and 23 downregulated genes. LINC01936 was one of downregulated lncRNAs in LUSC tissues. The biological analysis showed that the overexpression of LINC01936 significantly reduced proliferation, migration and invasion of LUSC cells, and promoted cell apoptosis. The knockdown of LINC01936 promoted cell proliferation and metastasis. Pathway and GSVA analysis indicated that LINC01936 might participated in DNA repair, complement, cell adhesion and EMT, etc. LINC01936 was predicted to interact with TCF21, AOC3, RASL12, MEOX2 or HSPB7, which are involved in EMT and PI3K-AKT-MTOR pathway, etc. The expression of LINC01936 was also positively correlated with the infiltrating immune cells in LUSC. Conclusions LINC01936 is downregulated in LUSC. LINC01936 affected proliferation, migration and invasion of LUSC cells probably by EMT and immune infiltration, which might serve as a new target for the treatment of LUSC.
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Affiliation(s)
- Qinqin Tian
- The Second Affiliated Hospital of Army Medical University, Department of Clinical Laboratory, Chongqing, China
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Xiyao Liu
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Ang Li
- North China University of Science and Technology, School of Public Health, Tangshan, China
| | - Hongjiao Wu
- North China University of Science and Technology, School of Public Health, Tangshan, China
| | - Yuning Xie
- North China University of Science and Technology, School of Public Health, Tangshan, China
| | - Hongmei Zhang
- North China University of Science and Technology, School of Public Health, Tangshan, China
| | - Fengjun Wu
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Yating Chen
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Congcong Bai
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Xuemei Zhang
- North China University of Science and Technology, College of Life Science, Tangshan, China
- North China University of Science and Technology, School of Public Health, Tangshan, China
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Khalafiyan A, Emadi-Baygi M, Wolfien M, Salehzadeh-Yazdi A, Nikpour P. Construction of a three-component regulatory network of transcribed ultraconserved regions for the identification of prognostic biomarkers in gastric cancer. J Cell Biochem 2023; 124:396-408. [PMID: 36748954 DOI: 10.1002/jcb.30373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Altered expression and functional roles of the transcribed ultraconserved regions (T-UCRs), as genomic sequences with 100% conservation between the genomes of human, mouse, and rat, in the pathophysiology of neoplasms has already been investigated. Nevertheless, the relevance of the functions for T-UCRs in gastric cancer (GC) is still the subject of inquiry. In the current study, we first used a genome-wide profiling approach to analyze the expression of T-UCRs in GC patients. Then, we constructed a three-component regulatory network and investigated potential diagnostic and prognostic values of the T-UCRs. The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) dataset was used as a resource for the RNA-sequencing data. FeatureCounts was utilized to quantify the number of reads mapped to each T-UCR. Differential expression analysis was then conducted using DESeq2. In the following, interactions between T-UCRs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were combined into a three-component network. Enrichment analyses were performed and a protein-protein interaction (PPI) network was constructed. The R Survival package was utilized to identify survival-related significantly differentially expressed T-UCRs (DET-UCRs). Using an in-house cohort of GC tissues, expression of two DET-UCRs was furthermore experimentally verified. Our results showed that several T-UCRs were dysregulated in TCGA-STAD tumoral samples compared to nontumoral counterparts. The three-component network was constructed which composed of DET-UCRs, miRNAs, and mRNAs nodes. Functional enrichment and PPI network analyses revealed important enriched signaling pathways and gene ontologies such as "pathway in cancer" and regulation of cell proliferation and apoptosis. Five T-UCRs were significantly correlated with the overall survival of GC patients. While no expression of uc.232 was observed in our in-house cohort of GC tissues, uc.343 showed an increased expression, although not statistically significant, in gastric tumoral tissues. The constructed three-component regulatory network of T-UCRs in GC presents a comprehensive understanding of the underlying gene expression regulation processes involved in tumor development and can serve as a basis to investigate potential prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Anis Khalafiyan
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Modjtaba Emadi-Baygi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Markus Wolfien
- Department of System Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Center for Medical Informatics, Dresden, Germany
| | - Ali Salehzadeh-Yazdi
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Parvaneh Nikpour
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Huang Y, Xia L, Tan X, Zhang J, Zeng W, Tan B, Yu X, Fang W, Yang Z. Molecular mechanism of lncRNA SNHG12 in immune escape of non-small cell lung cancer through the HuR/PD-L1/USP8 axis. Cell Mol Biol Lett 2022; 27:43. [PMID: 35658874 PMCID: PMC9164758 DOI: 10.1186/s11658-022-00343-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/05/2022] [Indexed: 02/08/2023] Open
Abstract
Background The pivotal role of long noncoding RNAs (lncRNAs) in cancer immune responses has been well established. This study was conducted with the aim of exploring the molecular mechanism of lncRNA small nucleolar RNA host gene 12 (SNHG12) in immune escape of non-small cell lung cancer (NSCLC). Methods Expression of lncRNA SNHG12, programmed cell death receptor ligand 1 (PD-L1), ubiquitin-specific protease 8 (USP8), and human antigen R (HuR) in NSCLC tissues and cells was measured, and their binding relationship was determined. NSCLC cell proliferation and apoptosis were assessed. Peripheral blood mononuclear cells (PBMCs) were co-cultured with NSCLC cells. The ratio of CD8+ T cells, PBMC proliferation, and inflammatory factors were determined. lncRNA SNHG12 localization was assessed via subcellular fractionation assay. The half-life period of mRNA was determined using actinomycin D. Xenograft tumor models were established to confirm the role of lncRNA SNHG12 in vivo. Results LncRNA SNHG12 was found to be prominently expressed in NSCLC tissues and cells, which was associated with a poor prognosis. Silencing lncRNA SNHG12 resulted in the reduction in proliferation and the promotion of apoptosis of NSCLC cells, while simultaneously increasing PBMC proliferation and the ratio of CD8+ T cells. Mechanically, the binding of lncRNA SNHG12 to HuR improved mRNA stability and expression of PD-L1 and USP8, and USP8-mediated deubiquitination stabilized the protein level of PD-L1. Overexpression of USP8 or PD-L1 weakened the inhibition of silencing lncRNA SNHG12 on the immune escape of NSCLC. Silencing lncRNA SNHG12 restricted tumor growth and upregulated the ratio of CD8+ T cells by decreasing USP8 and PD-L1. Conclusion LncRNA SNHG12 facilitated the immune escape of NSCLC by binding to HuR and increasing PD-L1 and USP8 levels.
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Affiliation(s)
- Yusheng Huang
- Department of Cancer Center, The Second Affiliated Hospital of Chongqing Medical University, Tianwen Avenue No. 288, Nan'an District, Chongqing, 400010, China
| | - Lei Xia
- Department of Cancer Center, The Second Affiliated Hospital of Chongqing Medical University, Tianwen Avenue No. 288, Nan'an District, Chongqing, 400010, China
| | - Xiangwu Tan
- Department of Cancer Center, The Second Affiliated Hospital of Chongqing Medical University, Tianwen Avenue No. 288, Nan'an District, Chongqing, 400010, China
| | - Jingyi Zhang
- Department of Cancer Center, The Second Affiliated Hospital of Chongqing Medical University, Tianwen Avenue No. 288, Nan'an District, Chongqing, 400010, China
| | - Weiwei Zeng
- Department of Cancer Center, The Second Affiliated Hospital of Chongqing Medical University, Tianwen Avenue No. 288, Nan'an District, Chongqing, 400010, China
| | - Benxu Tan
- Department of Cancer Center, The Second Affiliated Hospital of Chongqing Medical University, Tianwen Avenue No. 288, Nan'an District, Chongqing, 400010, China
| | - Xian Yu
- Department of Cancer Center, The Second Affiliated Hospital of Chongqing Medical University, Tianwen Avenue No. 288, Nan'an District, Chongqing, 400010, China
| | - Wei Fang
- Chongqing University, Three Gorges Hospital, No. 165 Xincheng Road, Wanzhou District, Chongqing, 404100, China.
| | - Zhenzhou Yang
- Department of Cancer Center, The Second Affiliated Hospital of Chongqing Medical University, Tianwen Avenue No. 288, Nan'an District, Chongqing, 400010, China.
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Wang Z, Chen K, Li D, Chen M, Li A, Wang J. miR-140-3p is involved in the occurrence and metastasis of gastric cancer by regulating the stability of FAM83B. Cancer Cell Int 2021; 21:537. [PMID: 34656115 PMCID: PMC8520196 DOI: 10.1186/s12935-021-02245-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/03/2021] [Indexed: 12/15/2022] Open
Abstract
Background Gastric cancer (GC) is a malignant tumor and microRNAs (miRNAs) are closely connected to GC development. The purpose of this study is to investigate the effect of miR-140-3p on the occurrence and metastasis of GC. Methods We detected miR-140-3p expression in GC cells and tissues. The correlation between miR-140-3p and prognosis and clinicopathological features in GC was analyzed. The role of miR-140-3p in GC cell migration, invasion, and proliferation was analyzed. The model of tumor transplantation and metastasis in nude mice was established, and the effect of miR-140-3p on the development and metastasis of GC was assessed. The relation between miR-140-3p and SNHG12 and the relations among HuR, SNHG12, and FAM83B were analyzed. Results miR-140-3p was poorly expressed in GC. GC patients with low miR-140-3p expression had a poor prognosis and unfavorable clinicopathologic features. Overexpression of miR-140-3p inhibited GC cell migration, invasion, and proliferation, and inhibited the development and metastasis of GC. miR-140-3p directly bound to SNHG12 in GC tissues and downregulated SNHG12 expression. SNHG12 overexpression induced HuR nuclear transportation. HuR can bind to FAM83B and up-regulate the mRNA level of FAM83B. Overexpression of SNHG12 or FAM83B reduced the inhibition of overexpression of miR-140-3p on GC. Conclusion miR-140-3p directly bound to SNHG12 in GC and down-regulated the expression of SNHG12, reduced the binding of SNHG12 and HuR, thus inhibiting the nuclear transportation of HuR and the binding of HuR and FAM83B, and reducing the transcription of FAM83B, and finally inhibiting the growth and metastasis of GC.
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Affiliation(s)
- Zhengguang Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Shushan District, Hefei, 230022, Anhui, China.
| | - Ke Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Shushan District, Hefei, 230022, Anhui, China
| | - Dongchang Li
- Anhui Medical University, Shushan District, Hefei, 230001, Anhui, China
| | - Mengding Chen
- Anhui Medical University, Shushan District, Hefei, 230001, Anhui, China
| | - Angqing Li
- Anhui Medical University, Shushan District, Hefei, 230001, Anhui, China
| | - Jian Wang
- Anhui Medical University, Shushan District, Hefei, 230001, Anhui, China
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Inhibition of lncRNA DILC attenuates neuropathic pain via the SOCS3/JAK2/STAT3 pathway. Biosci Rep 2021; 40:225196. [PMID: 32510145 PMCID: PMC7300282 DOI: 10.1042/bsr20194486] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been involved in the development of multiple pathological processes including neuropathic pain. The aim of the present study is to investigate the role of lncRNA down-regulated in liver cancer stem cells (DILC) in the progression of neuropathic pain and its underlying mechanism. Neuropathic pain rat model was established with the bilateral chronic constriction injury (bCCI) method. The results from quantitative PCR analysis in the spinal cord showed that DILC was significantly up-regulated in rats with bCCI compared with the sham group. DILC down-regulation mediated by intrathecal administration of DILC siRNA significantly increased the mechanical shrinkage threshold (MWT) and paw withdrawal threshold latency (PWTL), decreased the positive frequency for nerve sensitivity to cold and suppressed the expression of inflammatory genes in bCCI rats. Down-regulation of DILC induced suppressor of cytokine signaling (SOCS3) expression and inhibited the phosphorylation of signal transducer and activator of transcription 3 (p-STAT3) in spinal cord tissues. Western blotting showed that down-regulation of DILC by DILC siRNA transfection induced SOCS3 expression and inhibited the expression of p-Janus kinase 2 (p-JAK2) and p-STAT3 and their downstream genes in primary microglia. Furthermore, down-regulation of DILC increased the viability of primary microglia, suppressed apoptosis, and inhibited the production of interleukin (IL)-6 and IL-1β in microglia. In contrast, overexpression of DILC showed the opposite functions to those of DILC knockdown. In conclusion, silence of lncRNA DILC attenuates neuropathic pain via SOCS3-induced suppression of the JAK2/STAT3 pathway.
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Jha PK, Vijay A, Prabhakar A, Chatterjee T, Nair V, Bajaj N, Kumar B, Sharma M, Ashraf MZ. Transcriptome Profiling Reveals the Endogenous Sponging Role of LINC00659 and UST-AS1 in High-Altitude Induced Thrombosis. Thromb Haemost 2021; 121:1497-1511. [PMID: 33580494 DOI: 10.1055/a-1390-1713] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The pathophysiology of deep vein thrombosis (DVT) is considered as multifactorial, where thrombus formation is an interplay of genetic and acquired risk factors. Little is known about the expression profile and roles of long noncoding RNAs (lncRNAs) in human subjects developing DVT at high altitude. METHODS Using RNAseQ, we compared peripheral blood mRNA and lncRNA expression profile in human high-altitude DVT (HA-DVT) patients with high-altitude control subjects. We used DESeq to identify differentially expressed (DE) genes. We annotated the lncRNAs using NONCODE 3.0 database. In silico putative lncRNA-miRNA association study unravels the endogenous miRNA sponge associated with our candidate lncRNAs. These findings were validated by small-interfering RNA (siRNA) knockdown assay of the candidate lncRNAs conducted in primary endothelial cells. RESULTS We identified 1,524 DE mRNAs and 973 DE lncRNAs. Co-expressed protein-coding gene analysis resulted in a list of 722 co-expressed protein-coding genes with a Pearson correlation coefficients >0.7. The functional annotation of co-expressed genes and putative proteins revealed their involvement in the hypoxia, immune response, and coagulation cascade. Through its miRNA response elements to compete for miR-143 and miR-15, lncRNA-LINC00659 and UXT-AS1 regulate the expression of prothrombotic genes. Furthermore, in vitro RNA interference (siRNA) simultaneously suppressed lncRNAs and target gene mRNA level. CONCLUSION This transcriptome profile describes novel potential mechanisms of interaction between lncRNAs, the coding genes, miRNAs, and regulatory transcription factors that define the thrombotic signature and may be used in establishing lncRNAs as a biomarker in HA-DVT.
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Affiliation(s)
- Prabhash Kumar Jha
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organisation, Delhi, India
| | - Aatira Vijay
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organisation, Delhi, India
| | - Amit Prabhakar
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organisation, Delhi, India
| | | | - Velu Nair
- Armed Forces Medical College, Pune, Maharashtra, India
| | - Nitin Bajaj
- Command Hospital (Western Command), Chandimandir, Chandigarh, India
| | - Bhuvnesh Kumar
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organisation, Delhi, India
| | - Manish Sharma
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organisation, Delhi, India
| | - Mohammad Zahid Ashraf
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organisation, Delhi, India
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Suravajhala R, Gupta S, Kumar N, Suravajhala P. Deciphering LncRNA-protein interactions using docking complexes. J Biomol Struct Dyn 2020; 40:3769-3776. [PMID: 33280525 DOI: 10.1080/07391102.2020.1850354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Deciphering RNA-protein interactions are important to study principal biological mechanisms including transcription and translation regulation, gene silencing, among others. Predicting RNA molecule interaction with the target protein could allow us to understand important cellular processes and design novel treatment therapies for various diseases. As non-coding RNAs do not have coding potential our knowledge about their functions is still limited. Therefore, RNA-binding proteins of non-coding RNAs regulating functions, viz. including cellular maturation, nuclear export and stability may play a very important role. Keeping in view of the need for refined methods to understand protein-RNA interactions, we have attempted a docking model to infer binding sites between lncRNA NONHSAT02007 and protein KIF13A for a rare disease phenotype that we are studying in our lab.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Renuka Suravajhala
- Department of Chemistry, School of Basic Science, Manipal University, Manipal, India
| | - Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India.,Department of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Narayan Kumar
- Department of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India.,Bioclues.org, India
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Shukla N, Siva N, Malik B, Suravajhala P. Current Challenges and Implications of Proteogenomic Approaches in Prostate Cancer. Curr Top Med Chem 2020; 20:1968-1980. [PMID: 32703135 DOI: 10.2174/1568026620666200722112450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/30/2020] [Accepted: 06/29/2020] [Indexed: 12/16/2022]
Abstract
In the recent past, next-generation sequencing (NGS) approaches have heralded the omics era. With NGS data burgeoning, there arose a need to disseminate the omic data better. Proteogenomics has been vividly used for characterising the functions of candidate genes and is applied in ascertaining various diseased phenotypes, including cancers. However, not much is known about the role and application of proteogenomics, especially Prostate Cancer (PCa). In this review, we outline the need for proteogenomic approaches, their applications and their role in PCa.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, RJ, India.,Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Narmadhaa Siva
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, RJ, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, RJ, India
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Zou Y, Xu H. Involvement of long noncoding RNAs in the pathogenesis of autoimmune diseases. J Transl Autoimmun 2020; 3:100044. [PMID: 32743525 PMCID: PMC7388364 DOI: 10.1016/j.jtauto.2020.100044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 03/08/2020] [Indexed: 02/07/2023] Open
Abstract
Autoimmune diseases are a group of heterogeneous disorders characterized by damage to various organs caused by abnormal innate and adaptive immune responses. The pathogenesis of autoimmune diseases is extremely complicated and has not yet been fully elucidated. Long noncoding RNAs (lncRNAs), which are defined as transcripts containing more than 200 nucleotides with no protein-coding capacity, are emerging as important regulators of gene expression via epigenetic modification, transcriptional regulation and posttranscriptional regulation. Accumulating evidence has demonstrated that lncRNAs play a key role in the regulation of immunological functions and autoimmunity. In this review, we discuss various molecular mechanisms by which lncRNAs regulate gene expression and recent findings regarding the involvement of lncRNAs in many human autoimmune diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), idiopathic inflammatory myopathy (IIM), systemic sclerosis (SSc) and Sjögren’s syndrome (pSS). lncRNAs are observed to be differentially expressed in various autoimmune diseases. lncRNAs are involved in abnormal immune regulation and inflammatory responses in autoimmune diseases, which provides new insight into disease pathogenesis. LncRNAs may have the potential of biomarkers for diagnosis and prognosis of autoimmune diseases.
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Affiliation(s)
- Yaoyao Zou
- Department of Rheumatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hanshi Xu
- Department of Rheumatology and Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Abstract
Rheumatic diseases are a group of chronic heterogeneous autoimmune disorders characterized by abnormal regulation of the innate and adaptive immune systems. Despite extensive efforts, the full spectrum of molecular factors that contribute to the pathogenesis of rheumatic diseases remains unclear. ncRNAs can govern gene expression at the transcriptional and post-transcriptional levels in multiple diseases. Recent studies have demonstrated an important role for ncRNAs, such as miRNAs and lncRNAs, in the development of immune cells and rheumatic diseases. Here, we focus on the epigenetic regulatory roles of ncRNAs in the pathogenesis of rheumatic diseases and as biomarkers of disease state.
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Affiliation(s)
- Weilin Chen
- Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Di Liu
- Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Quan-Zhen Li
- Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Honglin Zhu
- Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
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12
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Pang B, Sui S, Wang Q, Wu J, Yin Y, Xu S. Upregulation of DLEU1 expression by epigenetic modification promotes tumorigenesis in human cancer. J Cell Physiol 2019; 234:17420-17432. [PMID: 30793303 DOI: 10.1002/jcp.28364] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
The function of DLEU1 in human cancer is largely unknown. The Cancer Genome Atlas data were applied to identify the landscape of differential genes between tumor tissues and normal tissues, which was further validated by our cohort data and pan-cancer data including 33 cancer types with 11,060 patients. Next, DLEU1 was selected to validate the novel finding and result showed that it promoted tumorigenesis in vitro and in vivo. Mechanistically, DLEU1 promotes SRP4 expression via increasing H3K27ac enrichment to SRP4 locus epigenetically. Moreover, epigenetic modification leads to upregulation of DLEU1 expression via decreased DNA methylation and increased H3K27ac and H3K4me3 histone modification in its locus. Finally, high expression of DLEU1 correlates with worse prognosis not only in specific cancer type patients but also in patients in the pan-cancer cohort. In summary, the work broadens the function landscape of known long noncoding RNAs in human cancer and provides novel insights into their roles in tumorigenesis.
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Affiliation(s)
- Boran Pang
- Department of Surgery, Rui Jin Hospital, Shanghai Key Laboratory of Gastric Neoplasm, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiyao Sui
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Junqiang Wu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanling Yin
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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13
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Tiwari P, Saxena A, Gupta N, Medicherla KM, Suravajhala P, Mathur SK. Systems Genomics of Thigh Adipose Tissue From Asian Indian Type-2 Diabetics Revealed Distinct Protein Interaction Hubs. Front Genet 2019; 9:679. [PMID: 30671081 PMCID: PMC6331691 DOI: 10.3389/fgene.2018.00679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/07/2018] [Indexed: 12/13/2022] Open
Abstract
We performed a systematic analysis of genes implicated in thigh subcutaneous adipose tissue of Asian Indian Type 2 Diabetes Mellitus (AIT2DM) and created a phenome-interactome network. This analysis was performed on 60 subjects specific to limb thigh fat by integrating phenotypic traits and similarity scores associated with AIT2DM. Using a phenotypic attribute, a contextual neighbor was identified across all the traits, viz. body mass index (BMI) statistics, adipocyte size, lipid parameters, homeostatic model assessment- insulin resistance (HOMA-IR), HOMA-ß. In this work, we have attempted to characterize transcription signatures using the phenome-interactome maps where each of the traits under study including the intermediary phenotypes has a distinct set of genes forming the hubs. Furthermore, we have identified various clinical, biochemical, and radiological parameters which show significant correlation with distinct hubs. We observed a number of novel pathways and genes including those that are non-coding RNAs implicated in AIT2DM.We showed that they appear to be associated with pathways, viz. tyrosine kinase JAK2, NOTCH thereby recruiting signaling molecules such as STAT5 and Src family kinases on the cell surface regulated them and our analyses comprising significant hubs suggest that thigh subcutaneous adipose tissue plays a role in pathophysiology of AIT2DM.
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Affiliation(s)
- Pradeep Tiwari
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India.,Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India.,Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Aditya Saxena
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura, India
| | - Nidhi Gupta
- Department of Biotechnology, The IIS University, Jaipur, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Sandeep Kumar Mathur
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
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14
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Li GJ, Ding H, Miao D. Long-noncoding RNA HOTAIR inhibits immunologic rejection of mouse leukemia cells through activating the Wnt/β-catenin signaling pathway in a mouse model of leukemia. J Cell Physiol 2019; 234:10386-10396. [PMID: 30609034 DOI: 10.1002/jcp.27705] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 10/15/2018] [Indexed: 01/01/2023]
Abstract
Long-noncoding RNAs (lncRNAs) is involved in the development of diverse diseases, including leukemia, while the role lncRNA HOX transcript antisense RNA (HOTAIR) played in leukemia remains unclear and in need of further investigation. Therefore, this study was conducted to explore the effects of lncRNA HOTAIR on the immunologic rejection of leukemia cells through the Wnt/β-catenin in mice. Mice were administrated with HOTAIR mimics as well as small interfering RNA HOTAIR to explore the regulatory role of HOTAIR. The numbers of white blood cell (WBC) and platelet (PLT) and the content of hemoglobin in peripheral blood (PB) were determined. The cytokine level in PB was measured. T-lymphocyte proliferation activity, Ig production by B cells, natural killer (NK) cell activity, and the proportion of cluster of differentiation 4 (CD4)/CD8 T cell subsets were detected. Expression of HOTAIR, β-catenin, cyclinD1, GSK-3β, and c-Myc in bone marrow was determined. It was revealed that the WBC number increased, while the PLT number along with the hemoglobin content in PB decreased with the upregulated HOTAIR. Additionally, elevated HOTAIR led to decreased levels of transforming growth factor-β, interferon-γ, interleukin-10, and tumor necrosis factor-α in PB, proliferation activity in T-lymphocyte, and inhibited Ig production, NK cell activity, and the ratio of CD4/CD8 T cell subsets in B-lymphocyte. Furthermore, Wnt/β-catenin was activated by overexpressing HOTAIR. Enhanced survival and proliferation were shown with increased expression of cyclinD1, GSK-3β, and c-Myc in the bone marrow of mice induced by overexpressing HOTAIR. These results indicate that restored HOTAIR reduces the immunologic rejection of leukemia cells in mice by activating Wnt/β-catenin pathway.
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Affiliation(s)
- Guo-Jie Li
- Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Hui Ding
- Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Dong Miao
- Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
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15
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Gupta S, Gupta N, Tiwari P, Menon S, Mathur P, Kothari SL, Nallapeta S, Medicherla KM, Suravajhala P. Lnc-EPB41-Protein Interactions Associated with Congenital Pouch Colon. Biomolecules 2018; 8:biom8030095. [PMID: 30227690 PMCID: PMC6163732 DOI: 10.3390/biom8030095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/12/2022] Open
Abstract
Congenital Pouch Colon (CPC) is a rare anorectal anomaly common to northwestern India, specifically Rajasthan. Despite efforts to understand the clinical genetic makeup of CPC, no attempt on identifying non-coding RNAs was done. We have earlier reported CPC’s rare variants from whole exome sequencing (WES) across 18 affected samples in a total of 64 subjects. A Smith–Waterman algorithm was used to infer a couple of lncRNAs from WES samples of CPC with predictions from the Noncode database. Further screening and quantification using polymerase chain reaction (PCR), we ascertained interactions using Micro Scale Thermophoresis (MST). We report the role of lnc-EPB41-1-1 shown to be promiscuously interacting with KIF13A substantiating their role in regulation.
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Affiliation(s)
- Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India.
- Department of Biotechnology, Amity University Rajasthan, Kant Kalwar, Jaipur 303002, India.
| | - Nidhi Gupta
- Department of Biotechnology, IIS University, Mansarovar, Jaipur 302020, India.
| | - Pradeep Tiwari
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India.
- Department of Chemistry, School of Basic Science, Manipal University, Jaipur 303007, India.
| | - Saji Menon
- NanoTemper Technologies, World Trade Centre, Bengaluru 302017, India.
| | - Praveen Mathur
- Department of Paediatric Surgery, SMS Medical College, JLN Marg, Jaipur 302004, India.
| | - Shanker Lal Kothari
- Department of Biotechnology, Amity University Rajasthan, Kant Kalwar, Jaipur 303002, India.
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India.
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India.
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16
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Skinkyte-Juskiene R, Kogelman LJ, Kadarmideen HN. Transcription Factor Co-expression Networks of Adipose RNA-Seq Data Reveal Regulatory Mechanisms of Obesity. Curr Genomics 2018; 19:289-299. [PMID: 29755291 PMCID: PMC5930450 DOI: 10.2174/1389202918666171005095059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/28/2017] [Accepted: 09/07/2017] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Transcription Factors (TFs) control actuation of genes in the genome and are key mediators of complex processes such as obesity. Master Regulators (MRs) are the genes at the top of a regulation hierarchy which regulate other genes. OBJECTIVE To elucidate clusters of highly co-expressed TFs (modules), involved pathways, highly inter-connected TFs (hub-TFs) and MRs leading to obesity and leanness, using porcine model for human obesity. METHODS We identified 817 expressed TFs in RNA-Sequencing dataset representing extreme degrees of obesity (DO; lean, obese). We built a single Weighted Transcription Factor Co-expression Network (WTFCN) and TF sub-networks (based on the DO). Hub-TFs and MRs (using iRegulon) were identi-fied in biologically relevant WTFCNs modules. RESULTS Single WTFCN detected the Red module significantly associated with DO (P < 0.03). This module was enriched for regulation processes in the immune system, e.g.: Immune system process (Padj = 2.50E-06) and metabolic lifestyle disorders, e.g. Circadian rhythm - mammal pathway (Padj = 2.33E-11). Detected MR, hub-TF SPI1 was involved in obesity, immunity and osteoporosis. Within the obese sub-network, the Red module suggested possible associations with immunity, e.g. TGF-beta signaling pathway (Padj = 1.73E-02) and osteoporosis, e.g. Osteoclast differentiation (Padj = 1.94E-02). Within the lean sub-network, the Magenta module displayed associations with type 2 diabetes, obesity and os-teoporosis e.g. Notch signaling pathway (Padj = 2.40E-03), osteoporosis e.g. hub-TF VDR (a prime candidate gene for osteoporosis). CONCLUSION Our results provide insights into the regulatory network of TFs and biologically relevant hub TFs in obesity.
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Affiliation(s)
- Ruta Skinkyte-Juskiene
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870 Frederiksberg C, Denmark
| | - Lisette J.A. Kogelman
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870 Frederiksberg C, Denmark
- Danish Headache Center, Department of Neurology, Glostrup Research Institute, Rigshospitalet Glostrup, Nordre Ringvej 69, 2600 Glostrup, Denmark
| | - Haja N. Kadarmideen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870 Frederiksberg C, Denmark
- Section of Systems Genomics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kgs. Lyngby, Denmark
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17
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Yang G, Shen T, Yi X, Zhang Z, Tang C, Wang L, Zhou Y, Zhou W. Crosstalk between long non-coding RNAs and Wnt/β-catenin signalling in cancer. J Cell Mol Med 2018; 22:2062-2070. [PMID: 29392884 PMCID: PMC5867104 DOI: 10.1111/jcmm.13522] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 12/06/2017] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts in the human genome which perform crucial functions in diverse biological processes. The abnormal expression of some lncRNAs has been found in tumorigenesis, development and therapy resistance of cancers. They may act as oncogenes or tumour suppressors and can be used as diagnostic or prognostic markers, prompting their therapeutic potentials in cancer treatments. Studies have indicated that many lncRNAs are involved in the regulation of several signal pathways, including Wnt/β-catenin signalling pathway, which has been reported to play a significant role in regulating embryogenesis, cell proliferation and controlling tumour biology. Emerging evidences have suggested that lncRNAs can interact with several components of the Wnt/β-catenin signalling pathway to regulate the expression of Wnt target genes in cancer. Moreover, the expression of lncRNAs can also be influenced by the pathway. Nevertheless, Wnt/β-catenin signalling pathway-related lncRNAs and their interactions in cancer are not systematically analysed before. Considering these, this review emphasized the associations between lncRNAs and Wnt/β-catenin signalling pathway in cancer initiation, progression and their therapeutic influence. We also provided an overview on characteristics of lncRNAs and Wnt/β-catenin signalling pathway and discussed their functions in tumour biology. Finally, targeting lncRNAs or/and molecules associated with the Wnt/β-catenin signalling pathway may be a feasible therapeutic method in the future.
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Affiliation(s)
- Gang Yang
- Department of Urology, Jinling Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Tianyi Shen
- Department of Urology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu Province, China
| | - Xiaoming Yi
- Department of Urology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu Province, China
| | - Zhengyu Zhang
- Department of Urology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu Province, China
| | - Chaopeng Tang
- Department of Urology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu Province, China
| | - Longxin Wang
- Department of Urology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu Province, China
| | - Yulin Zhou
- Department of Urology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu Province, China
| | - Wenquan Zhou
- Department of Urology, Jinling Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China.,Department of Urology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu Province, China
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18
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Xu S, Kong D, Chen Q, Ping Y, Pang D. Oncogenic long noncoding RNA landscape in breast cancer. Mol Cancer 2017; 16:129. [PMID: 28738804 PMCID: PMC5525255 DOI: 10.1186/s12943-017-0696-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/10/2017] [Indexed: 12/20/2022] Open
Abstract
Background Few long noncoding RNAs (lncRNAs) that act as oncogenic genes in breast cancer have been identified. Methods Oncogenic lncRNAs associated with tumourigenesis and worse survival outcomes were examined and validated in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), respectively. Then, the potential biological functions and expression regulation of these lncRNAs were studied via bioinformatics and genome data analysis. Moreover, progressive breast cancer subtype-specific lncRNAs were investigated via high-throughput sequencing in our cohort and TCGA validation. To elucidate the mechanisms of the regulation of these lncRNAs, genomic alterations from the TCGA, Broad, Sanger and BCCRC data, as well as epigenetic modifications from GEO data, were then applied and examined to meet this objective. Finally, cell proliferation assays, flow cytometry analyses and TUNEL assays were applied to validate the oncogenic roles of these lncRNAs in vitro. Results A cluster of oncogenic lncRNAs that was upregulated in breast cancer tissue and was associated with worse survival outcomes was identified. These oncogenic lncRNAs are involved in regulating immune system activation and the TGF-beta and Jak-STAT signalling pathways. Moreover, TINCR, LINC00511, and PPP1R26-AS1 were identified as subtype-specific lncRNAs associated with HER-2, triple-negative and luminal B subtypes of breast cancer, respectively. The up-regulation of these oncogenic lncRNAs is mainly caused by gene amplification in the genome in breast cancer and other solid tumours. Finally, the knockdown of TINCR, DSCAM-AS1 or HOTAIR inhibited breast cancer cell proliferation, increased apoptosis and inhibited cell cycle progression in vitro. Conclusions These findings enhance the landscape of known oncogenic lncRNAs in breast cancer and provide insights into their roles. This understanding may potentially aid in the comprehensive management of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0696-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China
| | - Dejia Kong
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China
| | - Qianlin Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China. .,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin, 150086, China.
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19
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Suravajhala P, Kogelman LJA, Kadarmideen HN. Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare. Genet Sel Evol 2016; 48:38. [PMID: 27130220 PMCID: PMC4850674 DOI: 10.1186/s12711-016-0217-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/16/2016] [Indexed: 02/06/2023] Open
Abstract
In the past years, there has been a remarkable development of high-throughput omics (HTO) technologies such as genomics, epigenomics, transcriptomics, proteomics and metabolomics across all facets of biology. This has spearheaded the progress of the systems biology era, including applications on animal production and health traits. However, notwithstanding these new HTO technologies, there remains an emerging challenge in data analysis. On the one hand, different HTO technologies judged on their own merit are appropriate for the identification of disease-causing genes, biomarkers for prevention and drug targets for the treatment of diseases and for individualized genomic predictions of performance or disease risks. On the other hand, integration of multi-omic data and joint modelling and analyses are very powerful and accurate to understand the systems biology of healthy and sustainable production of animals. We present an overview of current and emerging HTO technologies each with a focus on their applications in animal and veterinary sciences before introducing an integrative systems genomics framework for analysing and integrating multi-omic data towards improved animal production, health and welfare. We conclude that there are big challenges in multi-omic data integration, modelling and systems-level analyses, particularly with the fast emerging HTO technologies. We highlight existing and emerging systems genomics approaches and discuss how they contribute to our understanding of the biology of complex traits or diseases and holistic improvement of production performance, disease resistance and welfare.
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Affiliation(s)
- Prashanth Suravajhala
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg C, Denmark
| | - Lisette J A Kogelman
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg C, Denmark
| | - Haja N Kadarmideen
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg C, Denmark.
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