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Renfro Z, White BE, Stephens KE. CCAAT enhancer binding protein gamma (C/EBP-γ): An understudied transcription factor. Adv Biol Regul 2022; 84:100861. [PMID: 35121409 PMCID: PMC9376885 DOI: 10.1016/j.jbior.2022.100861] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 05/03/2023]
Abstract
The CCAAT enhancer binding protein (C/EBP) family of transcription factors are important transcriptional mediators of a wide range of physiologic processes. C/EBP-γ is the shortest C/EBP protein and lacks a canonical activation domain for the recruitment of transcriptional machinery. Despite its ubiquitous expression and ability to dimerize with other C/EBP proteins, C/EBP-γ has been studied far less than other C/EBP proteins, and, to our knowledge, no review of its functions has been written. This review seeks to integrate the current knowledge about C/EBP-γ and its physiologic roles, especially in cell proliferation, the integrated stress response, oncogenesis, hematopoietic and nervous system development, and metabolism, as well as to identify areas for future research.
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Affiliation(s)
- Zachary Renfro
- Department of Pediatrics, Division of Infectious Diseases, College of Medicine, University of Arkansas for Medical Sciences, USA; Arkansas Children's Research Institute, 13 Children's Way, Mail slot 512-47, Little Rock, AR, 72202, USA.
| | - Bryan E White
- Department of Pediatrics, Division of Infectious Diseases, College of Medicine, University of Arkansas for Medical Sciences, USA; Arkansas Children's Research Institute, 13 Children's Way, Mail slot 512-47, Little Rock, AR, 72202, USA.
| | - Kimberly E Stephens
- Department of Pediatrics, Division of Infectious Diseases, College of Medicine, University of Arkansas for Medical Sciences, USA; Arkansas Children's Research Institute, 13 Children's Way, Mail slot 512-47, Little Rock, AR, 72202, USA.
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Huang Y, Lin L, Shen Z, Li Y, Cao H, Peng L, Qiu Y, Cheng X, Meng M, Lu D, Yin D. CEBPG promotes esophageal squamous cell carcinoma progression by enhancing PI3K-AKT signaling. Am J Cancer Res 2020; 10:3328-3344. [PMID: 33163273 PMCID: PMC7642652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023] Open
Abstract
CCAAT/enhancer binding proteins (CEBPs, including CEBPA, CEBPB, CEBPD, CEBPE, CEBPG, and CEBPZ) play critical roles in a variety of physiological and pathological processes. However, the molecular characteristics and biological significance of CEBPs in esophageal squamous cell carcinoma (ESCC) have rarely been reported. Here, we show that most of the CEBPs are upregulated and accompanied with copy number amplifications in ESCC. Of note, high CEBPG expression is regulated by the ESCC specific transcription factor TP63 and serves as a prognostic factor for poor survival in ESCC patients. Functionally, CEBPG significantly promotes the proliferation and migration of ESCC cells both in vitro and in vivo. Mechanistically, CEBPG activates the PI3K-AKT signaling pathway through directly binding to distal enhancers and/or promoters of genes involved in this pathway, including genes of CCND1, MYC, CDK2, etc. These findings provide new insights into CEBPs dysregulation in ESCC and elucidate a crucial role for CEBPG in the progression of ESCC, highlighting its potential therapeutic value for ESCC treatment.
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Affiliation(s)
- Yongsheng Huang
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Lehang Lin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Zhuojian Shen
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Yu Li
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Haotian Cao
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Li Peng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Yuntan Qiu
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Xu Cheng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Meng Meng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Daning Lu
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Dong Yin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
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Yeo J, Morales DA, Chen T, Crawford EL, Zhang X, Blomquist TM, Levin AM, Massion PP, Arenberg DA, Midthun DE, Mazzone PJ, Nathan SD, Wainz RJ, Nana-Sinkam P, Willey PFS, Arend TJ, Padda K, Qiu S, Federov A, Hernandez DAR, Hammersley JR, Yoon Y, Safi F, Khuder SA, Willey JC. RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs. BMC Pulm Med 2018; 18:42. [PMID: 29506519 PMCID: PMC5838965 DOI: 10.1186/s12890-018-0603-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/23/2018] [Indexed: 01/09/2023] Open
Abstract
Background There is a need for more powerful methods to identify low-effect SNPs that contribute to hereditary COPD pathogenesis. We hypothesized that SNPs contributing to COPD risk through cis-regulatory effects are enriched in genes comprised by bronchial epithelial cell (BEC) expression patterns associated with COPD. Methods To test this hypothesis, normal BEC specimens were obtained by bronchoscopy from 60 subjects: 30 subjects with COPD defined by spirometry (FEV1/FVC < 0.7, FEV1% < 80%), and 30 non-COPD controls. Targeted next generation sequencing was used to measure total and allele-specific expression of 35 genes in genome maintenance (GM) genes pathways linked to COPD pathogenesis, including seven TP53 and CEBP transcription factor family members. Shrinkage linear discriminant analysis (SLDA) was used to identify COPD-classification models. COPD GWAS were queried for putative cis-regulatory SNPs in the targeted genes. Results On a network basis, TP53 and CEBP transcription factor pathway gene pair network connections, including key DNA repair gene ERCC5, were significantly different in COPD subjects (e.g., Wilcoxon rank sum test for closeness, p-value = 5.0E-11). ERCC5 SNP rs4150275 association with chronic bronchitis was identified in a set of Lung Health Study (LHS) COPD GWAS SNPs restricted to those in putative regulatory regions within the targeted genes, and this association was validated in the COPDgene non-hispanic white (NHW) GWAS. ERCC5 SNP rs4150275 is linked (D’ = 1) to ERCC5 SNP rs17655 which displayed differential allelic expression (DAE) in BEC and is an expression quantitative trait locus (eQTL) in lung tissue (p = 3.2E-7). SNPs in linkage (D’ = 1) with rs17655 were predicted to alter miRNA binding (rs873601). A classifier model that comprised gene features CAT, CEBPG, GPX1, KEAP1, TP73, and XPA had pooled 10-fold cross-validation receiver operator characteristic area under the curve of 75.4% (95% CI: 66.3%–89.3%). The prevalence of DAE was higher than expected (p = 0.0023) in the classifier genes. Conclusions GM genes comprised by COPD-associated BEC expression patterns were enriched for SNPs with cis-regulatory function, including a putative cis-rSNP in ERCC5 that was associated with COPD risk. These findings support additional total and allele-specific expression analysis of gene pathways with high prior likelihood for involvement in COPD pathogenesis. Electronic supplementary material The online version of this article (10.1186/s12890-018-0603-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiyoun Yeo
- Department of Pathology, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Diego A Morales
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Tian Chen
- Department of Mathematics and Statistics, The University of Toledo, 2801 W. Bancroft Street, Toledo, OH, 43606, USA
| | - Erin L Crawford
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Xiaolu Zhang
- Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Thomas M Blomquist
- Department of Pathology, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Albert M Levin
- Department of Biostatistics, Henry Ford Health System, 1 Ford Place Detroit, MI, Detroit, MI, 48202, USA
| | - Pierre P Massion
- Thoracic Program, Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA
| | | | - David E Midthun
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Peter J Mazzone
- Department of Pulmonary Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Steven D Nathan
- Department of Pulmonary Medicine, Inova Fairfax Hospital, 3300 Gallows Road, Falls Church, VA, 22042-3300, USA
| | - Ronald J Wainz
- The Toledo Hospital, 2142 N Cove Blvd, Toledo, OH, 43606, USA
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, USA, Richmond, VA, 23284-2512, USA.,Ohio State University James Comprehensive Cancer Center and Solove Research Institute, Columbus, OH, USA
| | - Paige F S Willey
- American Enterprise Institute, 1789 Massachusetts Ave NW, Washington, DC, 20036, USA
| | - Taylor J Arend
- The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Karanbir Padda
- Emory University School of Medicine, 1648 Pierce Dr NE, Atlanta, GA, 30307, USA
| | - Shuhao Qiu
- Department of Medicine, The University of Toledo Medical Center, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Alexei Federov
- Department of Mathematics and Statistics, The University of Toledo, 2801 W. Bancroft Street, Toledo, OH, 43606, USA.,Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Dawn-Alita R Hernandez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Jeffrey R Hammersley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Youngsook Yoon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Fadi Safi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Sadik A Khuder
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - James C Willey
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA.
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Yeo J, Crawford EL, Zhang X, Khuder S, Chen T, Levin A, Blomquist TM, Willey JC. A lung cancer risk classifier comprising genome maintenance genes measured in normal bronchial epithelial cells. BMC Cancer 2017; 17:301. [PMID: 28464886 PMCID: PMC5412061 DOI: 10.1186/s12885-017-3287-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 04/20/2017] [Indexed: 12/14/2022] Open
Abstract
Background Annual low dose CT (LDCT) screening of individuals at high demographic risk reduces lung cancer mortality by more than 20%. However, subjects selected for screening based on demographic criteria typically have less than a 10% lifetime risk for lung cancer. Thus, there is need for a biomarker that better stratifies subjects for LDCT screening. Toward this goal, we previously reported a lung cancer risk test (LCRT) biomarker comprising 14 genome-maintenance (GM) pathway genes measured in normal bronchial epithelial cells (NBEC) that accurately classified cancer (CA) from non-cancer (NC) subjects. The primary goal of the studies reported here was to optimize the LCRT biomarker for high specificity and ease of clinical implementation. Methods Targeted competitive multiplex PCR amplicon libraries were prepared for next generation sequencing (NGS) analysis of transcript abundance at 68 sites among 33 GM target genes in NBEC specimens collected from a retrospective cohort of 120 subjects, including 61 CA cases and 59 NC controls. Genes were selected for analysis based on contribution to the previously reported LCRT biomarker and/or prior evidence for association with lung cancer risk. Linear discriminant analysis was used to identify the most accurate classifier suitable to stratify subjects for screening. Results After cross-validation, a model comprising expression values from 12 genes (CDKN1A, E2F1, ERCC1, ERCC4, ERCC5, GPX1, GSTP1, KEAP1, RB1, TP53, TP63, and XRCC1) and demographic factors age, gender, and pack-years smoking, had Receiver Operator Characteristic area under the curve (ROC AUC) of 0.975 (95% CI: 0.96–0.99). The overall classification accuracy was 93% (95% CI 88%–98%) with sensitivity 93.1%, specificity 92.9%, positive predictive value 93.1% and negative predictive value 93%. The ROC AUC for this classifier was significantly better (p < 0.0001) than the best model comprising demographic features alone. Conclusions The LCRT biomarker reported here displayed high accuracy and ease of implementation on a high throughput, quality-controlled targeted NGS platform. As such, it is optimized for clinical validation in specimens from the ongoing LCRT blinded prospective cohort study. Following validation, the biomarker is expected to have clinical utility by better stratifying subjects for annual lung cancer screening compared to current demographic criteria alone. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3287-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiyoun Yeo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Erin L Crawford
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Xiaolu Zhang
- Cancer Genetics and Comparative Genomics Branch (CGCGB), National Human Genomes Research Institute (NHGRI), National Institutes of Health (NIH), Bldg 50, Rm 5341, 50 South Dr., Bethesda, MD, 20892, USA
| | - Sadik Khuder
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Tian Chen
- Department of Mathematics and Statistics, The University of Toledo, 2801 W. Bancroft Street, Toledo, OH, 43606, USA
| | - Albert Levin
- Department of Biostatistics, Henry Ford Health System, 1 Ford Place, Detroit, MI, 48202, USA
| | - Thomas M Blomquist
- Department of Pathology, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - James C Willey
- Ruppert 0012, Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA.
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Zhang X, Crawford EL, Blomquist TM, Khuder SA, Yeo J, Levin AM, Willey JC. Haplotype and diplotype analyses of variation in ERCC5 transcription cis-regulation in normal bronchial epithelial cells. Physiol Genomics 2016; 48:537-43. [PMID: 27235448 PMCID: PMC4967224 DOI: 10.1152/physiolgenomics.00021.2016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022] Open
Abstract
Excision repair cross-complementation group 5 (ERCC5) gene plays an important role in nucleotide excision repair, and dysregulation of ERCC5 is associated with increased lung cancer risk. Haplotype and diplotype analyses were conducted in normal bronchial epithelial cells (NBEC) to better understand mechanisms responsible for interindividual variation in transcript abundance regulation of ERCC5 We determined genotypes at putative ERCC5 cis-regulatory SNPs (cis-rSNP) rs751402 and rs2296147, and marker SNPs rs1047768 and rs17655. ERCC5 allele-specific transcript abundance was assessed by a recently developed targeted sequencing method. Syntenic relationships among alleles at rs751402, rs2296147, and rs1047768 were assessed by allele-specific PCR followed by Sanger sequencing. We then assessed association of ERCC5 allele-specific expression at rs1047768 with haplotype and diplotype structure at cis-rSNPs rs751402 and rs2296147. Genotype analysis revealed significantly (P < 0.005) higher interindividual variation in allelic ratios in cDNA samples relative to matched gDNA samples at both rs1047768 and rs17655. By diplotype analysis, mean expression was higher at the rs1047768 alleles syntenic with rs2296147 T allele compared with rs2296147 C allele. Furthermore, mean expression was lower at rs17655 C allele, which is syntenic with G allele at a linked SNP rs873601 (D' = 0.95). These data support the conclusions that in NBEC, T allele at SNP rs2296147 upregulates ERCC5, variation at rs751402 does not alter ERCC5 regulation, and that C allele at SNP rs17655 downregulates ERCC5 Variation in ERCC5 transcript abundance associated with allelic variation at these SNPs could result in variation in NER function in NBEC and lung cancer risk.
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Affiliation(s)
- Xiaolu Zhang
- Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio
| | - Erin L Crawford
- Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio
| | - Thomas M Blomquist
- Department of Pathology, University of Toledo Health Sciences Campus, Toledo, Ohio
| | - Sadik A Khuder
- Departments of Medicine and Public Health and Homeland Security, University of Toledo Health Science Campus, Toledo, Ohio; and
| | - Jiyoun Yeo
- Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - James C Willey
- Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio; Department of Pathology, University of Toledo Health Sciences Campus, Toledo, Ohio;
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Wu X, Ruan L, Yang Y, Mei Q. Identification of crucial regulatory relationships between long non-coding RNAs and protein-coding genes in lung squamous cell carcinoma. Mol Cell Probes 2016; 30:146-52. [PMID: 26928440 DOI: 10.1016/j.mcp.2016.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/22/2016] [Accepted: 02/19/2016] [Indexed: 01/25/2023]
Abstract
PURPOSE This study aimed to analyze the relationships of long non-coding RNAs (lncRNAs) and protein-coding genes in lung squamous cell carcinoma (LUSC). METHODS RNA-seq data of LUSC deposited in the TCGA database were used to identify differentially expressed protein-coding genes (DECGs) and differentially expressed lncRNA genes (DE-lncRNAs) between LUSC samples and normal samples. Functional enrichment analysis of DECGs was then performed. Subsequently, the target genes and regulators of DE-lncRNAs were predicted from the DECGs. Additionally, expression levels of target genes of DE-lncRNAs were validated by RT-qPCR after the silence of DE-lncRNAs. RESULTS In total, 5162 differentially expressed genes (DEGs) were screened from the LUSC samples, and there were seven upregulated lncRNA genes in the DEGs. The upregulated DECGs were enriched in GO terms like RNA binding and metabolic process. Meanwhile, the downregulated DECGs were enriched in GO terms like cell cycle. Furthermore, the lncRNAs PVT1 and TERC targeted multiple DECGs. PVT1 targeted genes related to cell cycle (e.g. POLA2, POLD1, MCM4, MCM5 and MCM6), and reduced expression of PVT1 decreased expression of the genes. TERC regulated several genes (e.g. NDUFAB1, NDUFA11 and NDUFB5), and reduced expression of TERC increased expression of the genes. Additionally, PVT1 was regulated by multiple transcription factors (TFs) identified from DECGs, such as HSF1; and TERC was modulated by TFs, such as PIR. CONCLUSION A set of regulatory relationships between PVT1 and its targets and regulators, as well as TERC and its targets and regulators, may play crucial roles in the progress of LUSC.
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Affiliation(s)
- Xiaofen Wu
- Department of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lei Ruan
- Department of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yi Yang
- Department of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qi Mei
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Bakshi A, Herke SW, Batzer MA, Kim J. DNA methylation variation of human-specific Alu repeats. Epigenetics 2016; 11:163-73. [PMID: 26890526 DOI: 10.1080/15592294.2015.1130518] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
DNA methylation is the major repression mechanism for human retrotransposons, such as the Alu family. Here, we have determined the methylation levels associated with 5238 loci belonging to 2 Alu subfamilies, AluYa5 and AluYb8, using high-throughput targeted repeat element bisulfite sequencing (HT-TREBS). The results indicate that ∼90% of loci are repressed by high methylation levels. Of the remaining loci, many of the hypomethylated elements are found near gene promoters and show high levels of DNA methylation variation. We have characterized this variation in the context of tumorigenesis and interindividual differences. Comparison of a primary breast tumor and its matched normal tissue revealed early DNA methylation changes in ∼1% of AluYb8 elements in response to tumorigenesis. Simultaneously, AluYa5/Yb8 elements proximal to promoters also showed differences in methylation of up to one order of magnitude, even between normal individuals. Overall, the current study demonstrates that early loss of methylation occurs during tumorigenesis in a subset of young Alu elements, suggesting their potential clinical relevance. However, approaches such as deep-bisulfite-sequencing of individual loci using HT-TREBS are required to distinguish clinically relevant loci from the background observed for AluYa5/Yb8 elements in general with regard to high levels of interindividual variation in DNA methylation.
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Affiliation(s)
- Arundhati Bakshi
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Scott W Herke
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Mark A Batzer
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Joomyeong Kim
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
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Crawford EL, Levin A, Safi F, Lu M, Baugh A, Zhang X, Yeo J, Khuder SA, Boulos AM, Nana-Sinkam P, Massion PP, Arenberg DA, Midthun D, Mazzone PJ, Nathan SD, Wainz R, Silvestri G, Tita J, Willey JC. Lung cancer risk test trial: study design, participant baseline characteristics, bronchoscopy safety, and establishment of a biospecimen repository. BMC Pulm Med 2016; 16:16. [PMID: 26801409 PMCID: PMC4722707 DOI: 10.1186/s12890-016-0178-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Lung Cancer Risk Test (LCRT) trial is a prospective cohort study comparing lung cancer incidence among persons with a positive or negative value for the LCRT, a 15 gene test measured in normal bronchial epithelial cells (NBEC). The purpose of this article is to describe the study design, primary endpoint, and safety; baseline characteristics of enrolled individuals; and establishment of a bio-specimen repository. METHODS/DESIGN Eligible participants were aged 50-90 years, current or former smokers with 20 pack-years or more cigarette smoking history, free of lung cancer, and willing to undergo bronchoscopic brush biopsy for NBEC sample collection. NBEC, peripheral blood samples, baseline CT, and medical and demographic data were collected from each subject. DISCUSSION Over a two-year span (2010-2012), 403 subjects were enrolled at 12 sites. At baseline 384 subjects remained in study and mean age and smoking history were 62.9 years and 50.4 pack-years respectively, with 34% current smokers. Obstructive lung disease (FEV1/FVC <0.7) was present in 157 (54%). No severe adverse events were associated with bronchoscopic brushing. An NBEC and matched peripheral blood bio-specimen repository was established. The demographic composition of the enrolled group is representative of the population for which the LCRT is intended. Specifically, based on baseline population characteristics we expect lung cancer incidence in this cohort to be representative of the population eligible for low-dose Computed Tomography (LDCT) lung cancer screening. Collection of NBEC by bronchial brush biopsy/bronchoscopy was safe and well-tolerated in this population. These findings support the feasibility of testing LCRT clinical utility in this prospective study. If validated, the LCRT has the potential to significantly narrow the population of individuals requiring annual low-dose helical CT screening for early detection of lung cancer and delay the onset of screening for individuals with results indicating low lung cancer risk. For these individuals, the small risk incurred by undergoing once in a lifetime bronchoscopic sample collection for LCRT may be offset by a reduction in their CT-related risks. The LCRT biospecimen repository will enable additional studies of genetic basis for COPD and/or lung cancer risk. TRIAL REGISTRATION The LCRT Study, NCT 01130285, was registered with Clinicaltrials.gov on May 24, 2010.
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Affiliation(s)
- E L Crawford
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - A Levin
- Department of Biostatistics, Henry Ford Hospital System, Detroit, MI, USA
| | - F Safi
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - M Lu
- Department of Biostatistics, Henry Ford Hospital System, Detroit, MI, USA
| | - A Baugh
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - X Zhang
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - J Yeo
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - S A Khuder
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - A M Boulos
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - P Nana-Sinkam
- Ohio State University James Comprehensive Cancer Center and Solove Research Institute, Columbus, OH, USA
| | - P P Massion
- Thoracic Program, Vanderbilt Ingram Cancer Center, Nashville, TN, USA
| | | | | | | | - S D Nathan
- Inova Fairfax Hospital, Falls Church, VA, USA
| | - R Wainz
- The Toledo Hospital, Toledo, OH, USA
| | - G Silvestri
- Medical University of South Carolina, Charleston, SC, USA
| | - J Tita
- Mercy/St. Vincent's Hospital, Toledo, OH, USA
| | - J C Willey
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA.
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Genome-wide identification of allele-specific expression in response to Streptococcus suis 2 infection in two differentially susceptible pig breeds. J Appl Genet 2015; 56:481-491. [PMID: 25737137 DOI: 10.1007/s13353-015-0275-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 01/15/2015] [Accepted: 02/10/2015] [Indexed: 12/18/2022]
Abstract
Although allele expression imbalance has been recognized in many species, and strongly linked to diseases, no whole transcriptome allele imbalance has been detected in pigs during pathogen infections. The pathogen Streptococcus suis 2 (SS2) causes serious zoonotic disease. Different pig breeds show differential susceptibility/resistance to pathogen infection, but the biological insight is little known. Here we analyzed allele-specific expression (ASE) using the spleen transcriptome of four pigs belonging to two phenotypically different breeds after SS2 infection. The comparative analysis of allele specific SNPs between control and infected animals revealed 882 and 1096 statistically significant differentially expressed allele SNPs (criteria: ratio ≧ 2 or ≦ 0.5) in Landrace and Enshi black pig, respectively. Twenty nine allelically imbalanced SNPs were further verified by Sanger sequencing, and later six SNPs were quantified by pyrosequencing assay. The pyrosequencing results are in agreement with the RNA-seq results, except two SNPs. Looking at the role of ASE in predisposition to diseases, the discovery of causative variants by ASE analysis might help the pig industry in long term to design breeding programs for improving SS2 resistance.
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