1
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Provasek VE, Kodavati M, Guo W, Wang H, Boldogh I, Van Den Bosch L, Britz G, Hegde ML. lncRNA Sequencing Reveals Neurodegeneration-Associated FUS Mutations Alter Transcriptional Landscape of iPS Cells That Persists in Motor Neurons. Cells 2023; 12:2461. [PMID: 37887305 PMCID: PMC10604943 DOI: 10.3390/cells12202461] [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: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Fused-in sarcoma (FUS) gene mutations have been implicated in amyotrophic lateral sclerosis (ALS). This study aimed to investigate the impact of FUS mutations (R521H and P525L) on the transcriptome of induced pluripotent stem cells (iPSCs) and iPSC-derived motor neurons (iMNs). Using RNA sequencing (RNA Seq), we characterized differentially expressed genes (DEGs) and differentially expressed lncRNAs (DELs) and subsequently predicted lncRNA-mRNA target pairs (TAR pairs). Our results show that FUS mutations significantly altered the expression profiles of mRNAs and lncRNAs in iPSCs. Using this large dataset, we identified and verified six key differentially regulated TAR pairs in iPSCs that were also altered in iMNs. These target transcripts included: GPR149, NR4A, LMO3, SLC15A4, ZNF404, and CRACD. These findings indicated that selected mutant FUS-induced transcriptional alterations persist from iPSCs into differentiated iMNs. Functional enrichment analyses of DEGs indicated pathways associated with neuronal development and carcinogenesis as likely altered by these FUS mutations. Furthermore, ingenuity pathway analysis (IPA) and GO network analysis of lncRNA-targeted mRNAs indicated associations between RNA metabolism, lncRNA regulation, and DNA damage repair. Our findings provide insights into potential molecular mechanisms underlying the pathophysiology of ALS-associated FUS mutations and suggest potential therapeutic targets for the treatment of ALS.
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Affiliation(s)
- Vincent E. Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (M.K.); (H.W.)
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (M.K.); (H.W.)
| | - Wenting Guo
- INSERM, UMR-S1118, Mécanismes Centraux et Périphériques de la Neurodégénérescence, Université de Strasbourg, CRBS, 67000 Strasbourg, France;
- VIB, Center for Brain & Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute (LBI), 3000 Leuven, Belgium
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium;
| | - Haibo Wang
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (M.K.); (H.W.)
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Ludo Van Den Bosch
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium;
| | - Gavin Britz
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA;
| | - Muralidhar L. Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (M.K.); (H.W.)
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
- Department of Neurosurgery, Weill Cornell Medical College, New York, NY 10065, USA
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2
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Cha J, Choi S. Gene-Smoking Interaction Analysis for the Identification of Novel Asthma-Associated Genetic Factors. Int J Mol Sci 2023; 24:12266. [PMID: 37569643 PMCID: PMC10419280 DOI: 10.3390/ijms241512266] [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: 07/01/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
Asthma is a complex heterogeneous disease caused by gene-environment interactions. Although numerous genome-wide association studies have been conducted, these interactions have not been systemically investigated. We sought to identify genetic factors associated with the asthma phenotype in 66,857 subjects from the Health Examination Study, Cardiovascular Disease Association Study, and Korea Association Resource Study cohorts. We investigated asthma-associated gene-environment (smoking status) interactions at the level of single nucleotide polymorphisms, genes, and gene sets. We identified two potentially novel (SETDB1 and ZNF8) and five previously reported (DM4C, DOCK8, MMP20, MYL7, and ADCY9) genes associated with increased asthma risk. Numerous gene ontology processes, including regulation of T cell differentiation in the thymus (GO:0033081), were significantly enriched for asthma risk. Functional annotation analysis confirmed the causal relationship between five genes (two potentially novel and three previously reported genes) and asthma through genome-wide functional prediction scores (combined annotation-dependent depletion, deleterious annotation of genetic variants using neural networks, and RegulomeDB). Our findings elucidate the genetic architecture of asthma and improve the understanding of its biological mechanisms. However, further studies are necessary for developing preventive treatments based on environmental factors and understanding the immune system mechanisms that contribute to the etiology of asthma.
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Affiliation(s)
- Junho Cha
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
| | - Sungkyoung Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
- Department of Mathematical Data Science, College of Science and Convergence Technology, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea
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3
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Hou Y, Zhou M, Li Y, Tian T, Sun X, Chen M, Xu W, Lu M. Risk SNP-mediated LINC01614 upregulation drives head and neck squamous cell carcinoma progression via PI3K/AKT signaling pathway. Mol Carcinog 2022; 61:797-811. [PMID: 35687049 DOI: 10.1002/mc.23422] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/11/2022]
Abstract
As potential biomarkers and therapeutic targets, long noncoding RNAs (lncRNAs) are involved in the tumorigenesis of various tumors. Genetic variation in long noncoding regions can lead to lncRNA dysfunction and even cancer. Nevertheless, studies on the association between lncRNA-associated single-nucleotide polymorphisms (SNPs) and the risk of head and neck squamous cell carcinoma (HNSCC) remain inadequate. Here, we aimed to explore the association between SNPs in LINC01614 and HNSCC risk, and the potential role of LINC01614 in tumorigenesis. In this study, we found that rs16854802 A > G (odds ratio [OR] = 1.42, 95% confidence interval [CI]: 1.22-1.77, p < 0.001) and rs3113503 G > C (OR = 1.38, 95% CI: 1.15-1.64, p < 0.001) in LINC01614 increased the risk of HNSCC in the Chinese population. Functional bioinformatic analysis and luciferase reporter assay revealed that rs3113503 G > C variant disrupted the binding of miRNA-616-3p to LINC01614, which resulted in the increased expression of LINC01614. Further analysis of the TCGA database demonstrated that the upregulated LINC01614 in HNSCC cancer tissues was associated with poor prognostic in HNSCC patients. In vitro experiments showed that knockdown of LINC01614 inhibited the proliferation, invasion, and migration ability of HNSCC cells. Mechanistically, allele C of rs3113503 in LINC01614 was more effective than allele G in activating the PI3K/AKT signaling pathway. Moreover, the reduced expression of LINC01614 also inhibited the activation of the PI3K/AKT signaling pathway. In summary, our findings revealed that the risk SNP rs3113503 G > C in LINC01614 altered the binding to miR-616-3p, which led to increased LINC01614 expression and promoted HNSCC progression by activating the PI3K/AKT signaling pathway.
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Affiliation(s)
- Yaxuan Hou
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Zhou
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuncheng Li
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Tian
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xun Sun
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Mo Chen
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Guidance Center for Social Psychological Service, Wuhan Mental Health Center, Huazhong University of Science and Technology, Wuhan, China
| | - Wenmao Xu
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Public Health, Wuhan No. 1 Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Meixia Lu
- Department of Epidemiology and Biostatistics, and The Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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4
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Parrish RL, Gibson GC, Epstein MP, Yang J. TIGAR-V2: Efficient TWAS tool with nonparametric Bayesian eQTL weights of 49 tissue types from GTEx V8. HGG ADVANCES 2022; 3:100068. [PMID: 35047855 PMCID: PMC8756507 DOI: 10.1016/j.xhgg.2021.100068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/01/2021] [Indexed: 01/12/2023] Open
Abstract
Standard transcriptome-wide association study (TWAS) methods first train gene expression prediction models using reference transcriptomic data and then test the association between the predicted genetically regulated gene expression and phenotype of interest. Most existing TWAS tools require cumbersome preparation of genotype input files and extra coding to enable parallel computation. To improve the efficiency of TWAS tools, we developed Transcriptome-Integrated Genetic Association Resource V2 (TIGAR-V2), which directly reads Variant Call Format (VCF) files, enables parallel computation, and reduces up to 90% of computation cost (mainly due to loading genotype data) compared to the original version. TIGAR-V2 can train gene expression imputation models using either nonparametric Bayesian Dirichlet process regression (DPR) or Elastic-Net (as used by PrediXcan), perform TWASs using either individual-level or summary-level genome-wide association study (GWAS) data, and implement both burden and variance-component statistics for gene-based association tests. We trained gene expression prediction models by DPR for 49 tissues using Genotype-Tissue Expression (GTEx) V8 by TIGAR-V2 and illustrated the usefulness of these Bayesian cis-expression quantitative trait locus (eQTL) weights through TWASs of breast and ovarian cancer utilizing public GWAS summary statistics. We identified 88 and 37 risk genes, respectively, for breast and ovarian cancer, most of which are either known or near previously identified GWAS (∼95%) or TWAS (∼40%) risk genes and three novel independent TWAS risk genes with known functions in carcinogenesis. These findings suggest that TWASs can provide biological insight into the transcriptional regulation of complex diseases. The TIGAR-V2 tool, trained Bayesian cis-eQTL weights, and linkage disequilibrium (LD) information from GTEx V8 are publicly available, providing a useful resource for mapping risk genes of complex diseases.
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Affiliation(s)
- Randy L. Parrish
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Greg C. Gibson
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Michael P. Epstein
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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5
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Li C, Liu M, An Y, Tian Y, Guan D, Wu H, Pei Z. Risk assessment of type 2 diabetes in northern China based on the logistic regression model. Technol Health Care 2021; 29:351-358. [PMID: 33682772 PMCID: PMC8158054 DOI: 10.3233/thc-218033] [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] [Indexed: 12/16/2022]
Abstract
BACKGROUND: Type 2 diabetes mellitus (T2DM) is a complex disease with high incidence and serious harm associated with polygenic determination. This study aimed to develop a predictive model so as to assess the risk of T2DM and apply it to health care and disease prevention in northern China. OBJECTIVE: Based on genotyping results, a risk warning model for type 2 diabetes was established. METHODS: Blood samples of 1042 patients with T2DM in northern China were collected. Multiplex polymerase chain reaction and high-throughput sequencing (NGS) techniques were used to design the amplification-based targeted sequencing panel to sequence the 21 T2DM susceptibility genes. RESULT: The related key gene KQT-like subfamily member 1 played an important role in the T2DM risk model, and single-nucleotide polymorphism rs2237892 was highly significant, with a P value of 1.2 × 10-5. CONCLUSIONS: Susceptibility genes in different populations were examined, and a model was developed to assess the risk-based genetic analysis. The performance of the model reached 92.8%.
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Affiliation(s)
- Chunrui Li
- Beijing Computing Center, Beijing Academy of Science and Technology, Beijing 100094, China.,The Key Laboratory of Beijing Cloud Computing Technology and Applicatio.,School of Computer Science and Engineering, Central South University, Computer Building, Central South University, Yuelu District, Changsha, Hunan 410083, China.,Beijing Computing Center, Beijing Academy of Science and Technology, Beijing 100094, China
| | - Manjiao Liu
- Beijing Computing Center, Beijing Academy of Science and Technology, Beijing 100094, China.,The Key Laboratory of Beijing Cloud Computing Technology and Applicatio.,Beijing Computing Center, Beijing Academy of Science and Technology, Beijing 100094, China
| | - Yunhe An
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.,Beijing Computing Center, Beijing Academy of Science and Technology, Beijing 100094, China
| | - Yanjie Tian
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Di Guan
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Zhiyong Pei
- Beijing Computing Center, Beijing Academy of Science and Technology, Beijing 100094, China.,The Key Laboratory of Beijing Cloud Computing Technology and Applicatio
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6
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Vargas RE, Duong VT, Han H, Ta AP, Chen Y, Zhao S, Yang B, Seo G, Chuc K, Oh S, El Ali A, Razorenova OV, Chen J, Luo R, Li X, Wang W. Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor. EMBO J 2020; 39:e102406. [PMID: 31782549 PMCID: PMC6939200 DOI: 10.15252/embj.2019102406] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022] Open
Abstract
The Hippo pathway, which plays a critical role in organ size control and cancer, features numerous WW domain-based protein-protein interactions. However, ~100 WW domains and 2,000 PY motif-containing peptide ligands are found in the human proteome, raising a "WW-PY" binding specificity issue in the Hippo pathway. In this study, we have established the WW domain binding specificity for Hippo pathway components and uncovered a unique amino acid sequence required for it. By using this criterion, we have identified a WW domain-containing protein, STXBP4, as a negative regulator of YAP. Mechanistically, STXBP4 assembles a protein complex comprising α-catenin and a group of Hippo PY motif-containing components/regulators to inhibit YAP, a process that is regulated by actin cytoskeleton tension. Interestingly, STXBP4 is a potential tumor suppressor for human kidney cancer, whose downregulation is correlated with YAP activation in clear cell renal cell carcinoma. Taken together, our study not only elucidates the WW domain binding specificity for the Hippo pathway, but also reveals STXBP4 as a player in actin cytoskeleton tension-mediated Hippo pathway regulation.
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MESH Headings
- Adaptor Proteins, Signal Transducing/antagonists & inhibitors
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cell Proliferation
- Female
- Gene Expression Regulation, Neoplastic
- Hippo Signaling Pathway
- Humans
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Prognosis
- Protein Binding
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Signal Transduction
- Survival Rate
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Tumor Cells, Cultured
- Vesicular Transport Proteins/genetics
- Vesicular Transport Proteins/metabolism
- WW Domains
- Xenograft Model Antitumor Assays
- YAP-Signaling Proteins
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Affiliation(s)
- Rebecca E Vargas
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Vy Thuy Duong
- Department of ChemistryUniversity of California, IrvineIrvineCAUSA
| | - Han Han
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Albert Paul Ta
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Yuxuan Chen
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Shiji Zhao
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Bing Yang
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Gayoung Seo
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Kimberly Chuc
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Sunwoo Oh
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
| | - Amal El Ali
- Department of Molecular Biology and BiochemistryUniversity of California, IrvineIrvineCAUSA
| | - Olga V Razorenova
- Department of Molecular Biology and BiochemistryUniversity of California, IrvineIrvineCAUSA
| | - Junjie Chen
- Department of Experimental Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Ray Luo
- Department of Molecular Biology and BiochemistryUniversity of California, IrvineIrvineCAUSA
- Department of Chemical and Biomolecular EngineeringUniversity of California, IrvineIrvineCAUSA
- Department of Materials Science and EngineeringUniversity of California, IrvineIrvineCAUSA
- Department of Biomedical EngineeringUniversity of California, IrvineIrvineCAUSA
| | - Xu Li
- School of Life SciencesWestlake UniversityHangzhouZhejiangChina
| | - Wenqi Wang
- Department of Developmental and Cell BiologyUniversity of California, IrvineIrvineCAUSA
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7
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Sušac I, Ozretić P, Gregorić M, Levačić Cvok M, Sabol M, Levanat S, Trnski D, Eljuga D, Seiwerth S, Aralica G, Stanec M, Musani V. Polymorphisms in Survivin ( BIRC5 Gene) Are Associated with Age of Onset in Breast Cancer Patients. JOURNAL OF ONCOLOGY 2019; 2019:3483192. [PMID: 31467536 PMCID: PMC6699404 DOI: 10.1155/2019/3483192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 06/07/2019] [Accepted: 06/25/2019] [Indexed: 02/08/2023]
Abstract
Survivin, encoded by BIRC5 gene (baculoviral IAP repeat containing 5), belongs to the family of inhibitors of apoptosis proteins (IAPs). In mammalian cells it participates in the control of mitosis, apoptosis regulation, and cellular stress response. Its expression is increased in almost all types of cancers. The aim of this study was to investigate the role of BIRC5 polymorphisms in breast cancer (BC) and to connect survivin expression with various clinicopathological characteristics of BC patients. Blood and archival tumour tissue samples were collected from 26 BC patients from Croatia. Survivin expression was determined immunohistochemically. BIRC5 promoter, coding region, and 3'UTR were genotyped. DNA from 74 healthy women was used as control. BIRC5 polymorphisms and survivin expression were tested against age of onset, histological grade, tumour type and size, lymph node status, oestrogen, progesterone, Her2, and Ki67 status. Numbers of samples with weak, moderate, and strong survivin expression were 9 (33.3%), 11 (40.7%), and 7 (25.9%), respectively. Most patients had nuclear survivin staining (92.6%). High survivin expression was significantly associated with negative oestrogen receptor status (p=0.007) and positive Ki67 expression (p=0.032). Ki67 expression was also positively correlated with histological grade (p=0.0009). Fourteen polymorphisms were found in BC samples, located mostly in promoter and 3'UTR of BIRC5. There was no significant difference in the distribution of polymorphisms between BC and control samples. Among clinicopathological characteristics of BC patients, alleles of five BIRC5 polymorphisms were associated with younger age of onset: c.-644T>C (55.8 years [y] vs. 48.1 y; p=0.006), c.-241C>T (54.2 y vs. 45.0; p=0.029), c.9809T>C (55.8 y vs. 48.1 y; p=0.006), c.-1547C>T (58.3 y vs. 50.9 y; p=0.011), and c.9386T>C (50.8 y vs. 59.5 y; p=0.004). To assess the significance of BIRC5 polymorphisms and survivin expression as predictive and prognostic biomarkers for BC further research with a larger sample size is needed.
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Affiliation(s)
| | - Petar Ozretić
- 2Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | | | - Mirela Levačić Cvok
- 2Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
- 4Kardinal Alojzije Stepinac Krašić Primary School, 10454 Krašić, Croatia
| | - Maja Sabol
- 2Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Sonja Levanat
- 2Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Diana Trnski
- 2Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Domagoj Eljuga
- 1Eljuga Polyclinic, 10000 Zagreb, Croatia
- 5Department for Oncoplastic and Reconstructive Surgery, University Hospital for Tumors, 10000 Zagreb, Croatia
| | - Sven Seiwerth
- 6Institute of Pathology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
- 7Clinical Department of Pathology and Cytology, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Gorana Aralica
- 6Institute of Pathology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
- 8Department of Pathology, Clinical Hospital Dubrava, 10000 Zagreb, Croatia
| | - Mladen Stanec
- 5Department for Oncoplastic and Reconstructive Surgery, University Hospital for Tumors, 10000 Zagreb, Croatia
| | - Vesna Musani
- 2Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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8
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Zhao C, Zou H, Wang J, Shen J, Liu H. A Three Long Noncoding RNA-Based Signature for Oral Squamous Cell Carcinoma Prognosis Prediction. DNA Cell Biol 2018; 37:888-895. [PMID: 30234381 DOI: 10.1089/dna.2018.4317] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most common malignancies worldwide. Despite relative high 5-year survival rate, delayed diagnosis still hampers its prognosis improvement. Long noncoding RNA (lncRNA) has recently been demonstrated to involve in development of various cancers. This study aimed to identify a lncRNA-based signature by which we could accurately predict OSCC prognosis. We first downloaded the RNA sequencing datasets for OSCC from The Cancer Genome Atlas (TCGA) and divided samples into training set and validation set. Associations between lncRNAs' expression and OSCC overall survival (OS) were evaluated in training set. Further screening through Random Survival Forest (RSF) method identified a prognostic signature composed of three lncRNAs, including AC013268.5, RP11.65 L3.4, and RP11.15A1.7, and by which OSCC samples in training set could be divided into high-risk and low-risk group with significantly different OS (p < 0.001, hazard ratio [HR] = 1.873). Besides, reliability of the prognostic signature was confirmed in the validation set (p < 0.01, HR = 2.14). Receiver operating characteristic curve analysis showed the superiority of the signature in OSCC prognosis prediction than other clinical characteristics. Gene set enrichment analysis indicated that high-risk score was closely associated with metabolism and spliceosome related pathways. Our findings suggest that lncRNA should be an important biomarker for prognosis of OSCC patients.
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Affiliation(s)
- Chenguang Zhao
- 1 Department of Emergency, Tianjin Stomatological Hospital , Tianjin, China
| | - Huiru Zou
- 2 Central Laboratory of Tianjin Stomatological Hospital, The Affiliated Stomatological Hospital of Nankai University , Tianjin, China
| | - Jinhui Wang
- 1 Department of Emergency, Tianjin Stomatological Hospital , Tianjin, China
| | - Jun Shen
- 3 Department of Oral and Maxillofacial, Tianjin Stomatological Hospital , Tianjin, China
| | - Hao Liu
- 3 Department of Oral and Maxillofacial, Tianjin Stomatological Hospital , Tianjin, China
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9
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Ciccocioppo R, Panelli S, Conti Bellocchi MC, Cangemi GC, Frulloni L, Capelli E, Corazza GR. The Transcriptomic Analysis of Circulating Immune Cells in a Celiac Family Unveils Further Insights Into Disease Pathogenesis. Front Med (Lausanne) 2018; 5:182. [PMID: 29971234 PMCID: PMC6018082 DOI: 10.3389/fmed.2018.00182] [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: 03/16/2018] [Accepted: 05/29/2018] [Indexed: 12/12/2022] Open
Abstract
Celiac disease (CD), the most common chronic enteropathy worldwide, is triggered and sustained by a dysregulated immune response to dietary gluten in genetically susceptible individuals. Up to date either the role of environmental factors and the pathways leading to mucosal damage have been only partially unraveled. Therefore, we seized the unique opportunity to study a naturally-occurring experimental model of a family composed of both parents suffering from CD (one on a gluten-free diet) and two non-celiac daughters. The control group consisted in four unrelated cases, two celiac and two non-celiac subjects, all matching with family members for both disease status and genetic susceptibility. In this privileged setting, we sought to investigate gene expression in peripheral blood mononuclear cells (PBMCs), a population known to mirror the immune response state within the gut. To this purpose, PBMCs were obtained from the four biopsied-proven CD patients and the four non-celiac cases. Each group included two family members and two unrelated control subjects. After RNA purification and cDNA synthesis, each sample underwent a microarray screen on a whole-transcriptome scale, and the hybridization results were visualized by hierarchical clustering. Differentially expressed genes (DEG) were partitioned into clusters displaying comparable regulations among samples. These clusters were subjected to both functional and pathway analysis by using the Kyoto Encyclopedia of Genes and Genomes. Interestingly, on a global gene expression level, the family members clustered together, regardless of their disease status. A relevant fraction of DEG belonged to a limited number of pathways, and could be differentiated based on disease status: active CD vs. treated CD and CD vs. controls. These pathways were mainly involved in immune function regulation, cell-cell junctions, protein targeting and degradation, exosome trafficking, and signal transduction. Worth of noting, a small group of genes mapping on the male-specific region of the Y chromosome, and previously linked to cardiovascular risk, was found to be strongly upregulated in the active CD case belonging to the family, who suddenly died of a heart attack. Our results provide novel information on CD pathogenesis and may be useful in identifying new therapeutic tools and risk factors associated with this condition.
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Affiliation(s)
- Rachele Ciccocioppo
- Gastroenterology Unit, Department of Medicine, Azienda Ospedaliera Universitaria Integrata Verona, University of Verona Verona, Italy
| | - Simona Panelli
- Pediatric Clinical Research Center "Invernizzi", University of Milano Milan, Italy
| | - Maria C Conti Bellocchi
- Gastroenterology Unit, Department of Medicine, Azienda Ospedaliera Universitaria Integrata Verona, University of Verona Verona, Italy
| | - Giuseppina C Cangemi
- Clinica Medica I, Department of Internal Medicine, Fondazione IRCCS Policlinico San Matteo, University of Pavia Pavia, Italy
| | - Luca Frulloni
- Gastroenterology Unit, Department of Medicine, Azienda Ospedaliera Universitaria Integrata Verona, University of Verona Verona, Italy
| | - Enrica Capelli
- Department of Earth and Environmental Sciences, University of Pavia Pavia, Italy
| | - Gino R Corazza
- Clinica Medica I, Department of Internal Medicine, Fondazione IRCCS Policlinico San Matteo, University of Pavia Pavia, Italy
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