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Zhang Y, Lyu Y, Chen L, Cao K, Chen J, He C, Lyu X, Jiang Y, Xiang J, Liu B, Wu C. Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS. Int J Mol Sci 2023; 24:15259. [PMID: 37894938 PMCID: PMC10607287 DOI: 10.3390/ijms242015259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The use of metabolome genome-wide association studies (mGWAS) has been shown to be effective in identifying functional genes in complex diseases. While mGWAS has been applied to biomedical and pharmaceutical studies, its potential in predicting gastric cancer prognosis has yet to be explored. This study aims to address this gap and provide insights into the genetic basis of GC survival, as well as identify vital regulatory pathways in GC cell progression. Genome-wide association analysis of plasma metabolites related to gastric cancer prognosis was performed based on the Generalized Linear Model (GLM). We used a log-rank test, LASSO regression, multivariate Cox regression, GO enrichment analysis, and the Cytoscape software to visualize the complex regulatory network of genes and metabolites and explored in-depth genetic variation in gastric cancer prognosis based on mGWAS. We found 32 genetic variation loci significantly associated with GC survival-related metabolites, corresponding to seven genes, VENTX, PCDH 7, JAKMIP1, MIR202HG, MIR378D1, LINC02472, and LINC02310. Furthermore, this study identified 722 Single nucleotide polymorphism (SNP) sites, suggesting an association with GC prognosis-related metabolites, corresponding to 206 genes. These 206 possible functional genes for gastric cancer prognosis were mainly involved in cellular signaling molecules related to cellular components, which are mainly involved in the growth and development of the body and neurological regulatory functions related to the body. The expression of 23 of these genes was shown to be associated with survival outcome in gastric cancer patients in The Cancer Genome Atlas (TCGA) database. Based on the genome-wide association analysis of prognosis-related metabolites in gastric cancer, we suggest that gastric cancer survival-related genes may influence the proliferation and infiltration of gastric cancer cells, which provides a new idea to resolve the complex regulatory network of gastric cancer prognosis.
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Affiliation(s)
- Yuling Zhang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Yanping Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Liangping Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Kang Cao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Jingwen Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Chenzhou He
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Xuejie Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Yu Jiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Jianjun Xiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Baoying Liu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Chuancheng Wu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
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2
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McInerney CE, Lynn JA, Gilmore AR, Flannery T, Prise KM. Using AI-Based Evolutionary Algorithms to Elucidate Adult Brain Tumor (Glioma) Etiology Associated with IDH1 for Therapeutic Target Identification. Curr Issues Mol Biol 2022; 44:2982-3000. [PMID: 35877430 PMCID: PMC9323620 DOI: 10.3390/cimb44070206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
Adult brain tumors (glioma) represent a cancer of unmet need where standard-of-care is non-curative; thus, new therapies are urgently needed. It is unclear whether isocitrate dehydrogenases (IDH1/2) when not mutated have any role in gliomagenesis or tumor growth. Nevertheless, IDH1 is overexpressed in glioblastoma (GBM), which could impact upon cellular metabolism and epigenetic reprogramming. This study characterizes IDH1 expression and associated genes and pathways. A novel biomarker discovery pipeline using artificial intelligence (evolutionary algorithms) was employed to analyze IDH-wildtype adult gliomas from the TCGA LGG-GBM cohort. Ninety genes whose expression correlated with IDH1 expression were identified from: (1) All gliomas, (2) primary GBM, and (3) recurrent GBM tumors. Genes were overrepresented in ubiquitin-mediated proteolysis, focal adhesion, mTOR signaling, and pyruvate metabolism pathways. Other non-enriched pathways included O-glycan biosynthesis, notch signaling, and signaling regulating stem cell pluripotency (PCGF3). Potential prognostic (TSPYL2, JAKMIP1, CIT, TMTC1) and two diagnostic (MINK1, PLEKHM3) biomarkers were downregulated in GBM. Their gene expression and methylation were negatively and positively correlated with IDH1 expression, respectively. Two diagnostic biomarkers (BZW1, RCF2) showed the opposite trend. Prognostic genes were not impacted by high frequencies of molecular alterations and only one (TMTC1) could be validated in another cohort. Genes with mechanistic links to IDH1 were involved in brain neuronal development, cell proliferation, cytokinesis, and O-mannosylation as well as tumor suppression and anaplerosis. Results highlight metabolic vulnerabilities and therapeutic targets for use in future clinical trials.
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Affiliation(s)
- Caitríona E. McInerney
- Patrick G. Johnson Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7AE, Northern Ireland, UK; (J.A.L.); (A.R.G.); (K.M.P.)
| | - Joanna A. Lynn
- Patrick G. Johnson Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7AE, Northern Ireland, UK; (J.A.L.); (A.R.G.); (K.M.P.)
| | - Alan R. Gilmore
- Patrick G. Johnson Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7AE, Northern Ireland, UK; (J.A.L.); (A.R.G.); (K.M.P.)
| | - Tom Flannery
- Department of Neurosurgery, Royal Victoria Hospital, Belfast Health & Social Care Trust, Belfast BT9 7AB, Northern Ireland, UK;
| | - Kevin M. Prise
- Patrick G. Johnson Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7AE, Northern Ireland, UK; (J.A.L.); (A.R.G.); (K.M.P.)
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3
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Genome-wide association analyses of osteochondrosis in Belgian Warmbloods reveal candidate genes associated with chondrocyte development. J Equine Vet Sci 2022; 111:103870. [DOI: 10.1016/j.jevs.2022.103870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/09/2021] [Accepted: 01/17/2022] [Indexed: 01/22/2023]
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Mediator subunit MED1 is required for E2A-PBX1-mediated oncogenic transcription and leukemic cell growth. Proc Natl Acad Sci U S A 2021; 118:1922864118. [PMID: 33542097 DOI: 10.1073/pnas.1922864118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The chimeric transcription factor E2A-PBX1, containing the N-terminal activation domains of E2A fused to the C-terminal DNA-binding domain of PBX1, results in 5% of pediatric acute lymphoblastic leukemias (ALL). We recently have reported a mechanism for RUNX1-dependent recruitment of E2A-PBX1 to chromatin in pre-B leukemic cells; but the subsequent E2A-PBX1 functions through various coactivators and the general transcriptional machinery remain unclear. The Mediator complex plays a critical role in cell-specific gene activation by serving as a key coactivator for gene-specific transcription factors that facilitates their function through the RNA polymerase II transcriptional machinery, but whether Mediator contributes to aberrant expression of E2A-PBX1 target genes remains largely unexplored. Here we show that Mediator interacts directly with E2A-PBX1 through an interaction of the MED1 subunit with an E2A activation domain. Results of MED1 depletion by CRISPR/Cas9 further indicate that MED1 is specifically required for E2A-PBX1-dependent gene activation and leukemic cell growth. Integrated transcriptome and cistrome analyses identify pre-B cell receptor and cell cycle regulatory genes as direct cotargets of MED1 and E2A-PBX1. Notably, complementary biochemical analyses also demonstrate that recruitment of E2A-PBX1 to a target DNA template involves a direct interaction with DNA-bound RUNX1 that can be further stabilized by EBF1. These findings suggest that E2A-PBX1 interactions with RUNX1 and MED1/Mediator are of functional importance for both gene-specific transcriptional activation and maintenance of E2A-PBX1-driven leukemia. The MED1 dependency for E2A-PBX1-mediated gene activation and leukemogenesis may provide a potential therapeutic opportunity by targeting MED1 in E2A-PBX1+ pre-B leukemia.
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Ennour-Idrissi K, Dragic D, Issa E, Michaud A, Chang SL, Provencher L, Durocher F, Diorio C. DNA Methylation and Breast Cancer Risk: An Epigenome-Wide Study of Normal Breast Tissue and Blood. Cancers (Basel) 2020; 12:cancers12113088. [PMID: 33113958 PMCID: PMC7690691 DOI: 10.3390/cancers12113088] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/07/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023] Open
Abstract
Differential DNA methylation is a potential marker of breast cancer risk. Few studies have investigated DNA methylation changes in normal breast tissue and were largely confounded by cancer field effects. To detect methylation changes in normal breast epithelium that are causally associated with breast cancer occurrence, we used a nested case-control study design based on a prospective cohort of patients diagnosed with a primary invasive hormone receptor-positive breast cancer. Twenty patients diagnosed with a contralateral breast cancer (CBC) were matched (1:1) with 20 patients who did not develop a CBC on relevant risk factors. Differentially methylated Cytosine-phosphate-Guanines (CpGs) and regions in normal breast epithelium were identified using an epigenome-wide DNA methylation assay and robust linear regressions. Analyses were replicated in two independent sets of normal breast tissue and blood. We identified 7315 CpGs (FDR < 0.05), 52 passing strict Bonferroni correction (p < 1.22 × 10-7) and 43 mapping to known genes involved in metabolic diseases with significant enrichment (p < 0.01) of pathways involving fatty acids metabolic processes. Four differentially methylated genes were detected in both site-specific and regions analyses (LHX2, TFAP2B, JAKMIP1, SEPT9), and three genes overlapped all three datasets (POM121L2, KCNQ1, CLEC4C). Once validated, the seven differentially methylated genes distinguishing women who developed and who did not develop a sporadic breast cancer could be used to enhance breast cancer risk-stratification, and allow implementation of targeted screening and preventive strategies that would ultimately improve breast cancer prognosis.
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Affiliation(s)
- Kaoutar Ennour-Idrissi
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (K.E.-I.); (D.D.)
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1R 3S3, Canada; (E.I.); (A.M.); (S.-L.C.); (F.D.)
- Département de Biologie Moléculaire, de Biochimie Médicale et de Pathologie de l’Université Laval, Québec, QC G1V 0A6, Canada
| | - Dzevka Dragic
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (K.E.-I.); (D.D.)
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1R 3S3, Canada; (E.I.); (A.M.); (S.-L.C.); (F.D.)
| | - Elissar Issa
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1R 3S3, Canada; (E.I.); (A.M.); (S.-L.C.); (F.D.)
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Annick Michaud
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1R 3S3, Canada; (E.I.); (A.M.); (S.-L.C.); (F.D.)
| | - Sue-Ling Chang
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1R 3S3, Canada; (E.I.); (A.M.); (S.-L.C.); (F.D.)
| | - Louise Provencher
- Centre des Maladies du sein du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada;
| | - Francine Durocher
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1R 3S3, Canada; (E.I.); (A.M.); (S.-L.C.); (F.D.)
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Caroline Diorio
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (K.E.-I.); (D.D.)
- Centre de Recherche sur le Cancer, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1R 3S3, Canada; (E.I.); (A.M.); (S.-L.C.); (F.D.)
- Centre des Maladies du sein du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada;
- Correspondence: ; Tel.: +1-418-682-7511-84726
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6
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Hu Y, Shu XS, Yu J, Sun MA, Chen Z, Liu X, Fang Q, Zhang W, Hui X, Ying Y, Fu L, Lu D, Kumar R, Wang Y. Improving the diversity of captured full-length isoforms using a normalized single-molecule RNA-sequencing method. Commun Biol 2020; 3:403. [PMID: 32732980 PMCID: PMC7393167 DOI: 10.1038/s42003-020-01125-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/02/2020] [Indexed: 12/26/2022] Open
Abstract
Human genes form a large variety of isoforms after transcription, encoding distinct transcripts to exert different functions. Single-molecule RNA sequencing facilitates accurate identification of the isoforms by extending nucleotide read length significantly. However, the gene or isoform diversity is lowly represented by the mRNA molecules captured by single-molecule RNA sequencing. Here, we show that a cDNA normalization procedure before the library preparation for PacBio RS II sequencing captures 3.2–6.0 fold more full-length high-quality isoform species for different human samples, as compared to the non-normalized capture procedure. Many lowly expressed, functionally important isoforms can be detected. In addition, normalized PacBio RNA sequencing also resolves more allele-specific haplotype transcripts. Finally, we apply the cDNA normalization based long-read RNA sequencing method to profile the transcriptome of human gastric signet-ring cell carcinomas, identify new cancer-specific transcriptome signatures, and thus, bring out the utility of the improved protocols in gene expression studies. Hu et al. combine cDNA normalization before library preparation with a software tool to increase the capture of RNA isoform species in single-molecule RNA sequencing. They demonstrate that this approach can detect previously unknown transcripts in gastric signet-ring cell carcinomas that are not present in non-malignant tissue.
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Affiliation(s)
- Yueming Hu
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Xing-Sheng Shu
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Jiaxian Yu
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Ming-An Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zewei Chen
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Xianming Liu
- Department of Gastrointestinal Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, 518020, China
| | - Qiongfang Fang
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Wei Zhang
- Shenzhen GenRead Tech. Co. LTD., Shenzhen, 518132, China
| | - Xinjie Hui
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Ying Ying
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Li Fu
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Desheng Lu
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Rakesh Kumar
- Rajiv Gandhi Centre for Biotechnology, Trivendrum, 695014, Kerala, India.,Virginia Commonwealth University School of Medicine, Richmond, 23298, USA.,Rutgers New Jersey Medical School, Newark, 07103, USA
| | - Yejun Wang
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China.
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7
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Zhou DN, Ye CS, Yang QQ, Deng YF. Integrated analysis of transcriptome profiling predicts potential lncRNA and circRNA targets in human nasopharyngeal carcinoma. Oncol Lett 2020; 19:3123-3136. [PMID: 32218863 PMCID: PMC7068695 DOI: 10.3892/ol.2020.11412] [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: 04/10/2019] [Accepted: 11/08/2019] [Indexed: 01/08/2023] Open
Abstract
Non-coding RNAs (ncRNAs) regulate numerous genes and influence the progression of various human diseases, including cancer. The role of regulatory ncRNAs implicated in nasopharyngeal carcinoma (NPC), as well as their target genes, remains unclear. The present study aimed to investigate specific long non-coding (lnc)RNAs, circular RNAs (circRNAs) and mRNAs associated with the molecular pathogenesis of NPC, and to predict the underlying target genes of specific lncRNAs and circRNAs. The expression levels of lncRNAs, circRNAs and mRNAs in NPC and chronic nasopharyngitis tissues were detected and analyzed using microarray and bioinformatics techniques. A total of 2.80% lncRNAs (425 upregulated and 431 downregulated) were significantly differentially expressed (DE) between the two tissue types. Additionally, 0.96% circRNAs (18 upregulated and 13 downregulated) were significantly DE, while 2.94% mRNAs (426 upregulated and 341 downregulated) were significantly DE between the two tissue types. In total, 420 NPC-associated nearby encoding genes (196 up- and 224 downregulated) of the DE lncRNAs were identified. Overlap analysis identified 23 DE circRNAs and their corresponding target genes, with 37 microRNAs and 50 mRNAs, from which 14 interaction networks were constructed. Subsequent pathway analysis revealed 221 DE target genes corresponding to 31 key signaling pathways associated with NPC, 14 of which may represent hub genes associated with NPC pathophysiology. Thus, certain lncRNAs, circRNAs and mRNAs are aberrantly expressed in NPC tissues, and partially specific lncRNAs, circRNAs and their target genes may influence the tumorigenesis and progression of NPC. Target prediction and regulatory network identification may help to determine the pathogenic mechanisms of NPC.
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Affiliation(s)
- Dong-Ni Zhou
- Department of Pathology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Chun-Sheng Ye
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Qing-Qing Yang
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Yan-Fei Deng
- Department of Otolaryngology-Head and Neck Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China.,Department of Otolaryngology-Head and Neck Surgery, Union School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
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8
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Langie SA, Timms JA, De Boever P, McKay JA. DNA methylation and the hygiene hypothesis: connecting respiratory allergy and childhood acute lymphoblastic leukemia. Epigenomics 2019; 11:1519-1537. [PMID: 31536380 DOI: 10.2217/epi-2019-0052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: The hygiene hypothesis states that a lack of infection in early-life suppresses immune system development, and is linked to respiratory allergy (RA) and childhood acute lymphoblastic leukemia (ALL) risk. Little is known about underlying mechanisms, but DNA methylation is altered in RA and ALL, and in response to infection. We investigated if aberrant methylation may be in common between these diseases and associated with infection. Materials & methods: RA and ALL disease-associated methylation signatures were compared and related to exposure-to-infection signatures. Results: A significant number of genes overlapped between RA and ALL signatures (p = 0.0019). Significant overlaps were observed between exposure-to-infection signatures and disease-associated signatures. Conclusion: DNA methylation may be a mediating mechanism through which the hygiene hypothesis is associated with RA and ALL risk.
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Affiliation(s)
- Sabine As Langie
- VITO-Health, 2400 Mol, Belgium.,Centre for Environmental Sciences, Hasselt University, Diepenbeek, 3590, Belgium
| | - Jessica A Timms
- Institute for Health & Society, Human Nutrition Research Centre, Newcastle University, NE2 4HH, UK.,Systems Cancer Immunology Lab, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Research Oncology, King's College London, Guy's Hospital, SE1 9RT, UK
| | - Patrick De Boever
- VITO-Health, 2400 Mol, Belgium.,Centre for Environmental Sciences, Hasselt University, Diepenbeek, 3590, Belgium
| | - Jill A McKay
- Institute for Health & Society, Human Nutrition Research Centre, Newcastle University, NE2 4HH, UK.,Faculty of Health & Life Sciences, Department of Applied Sciences, Northumbria University, NE1 8ST, UK
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9
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Benjamin AB, Zhou X, Isaac O, Zhao H, Song Y, Chi X, Sun B, Hao L, Zhang L, Liu L, Guan H, Shao S. PRP19 upregulation inhibits cell proliferation in lung adenocarcinomas by p21-mediated induction of cell cycle arrest. Biomed Pharmacother 2014; 68:463-70. [DOI: 10.1016/j.biopha.2014.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/04/2014] [Indexed: 11/25/2022] Open
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