1
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Wang Y, Wu ZW, Mou Q, Chen L, Fang T, Zhang YQ, Yin Z, Du ZQ, Yang CX. Global 3'-UTRome of porcine immature Sertoli cells altered by acute heat stress. Theriogenology 2023; 196:79-87. [PMID: 36401935 DOI: 10.1016/j.theriogenology.2022.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Alternative polyadenylation (APA) affects the composition of cis-elements in 3'-untranslated region (3'-UTR), to regulate gene expression and localization, and subsequently the downstream biological processes. Acute heat stress could change rapidly the cellular transcriptome, however the underlying molecular changes are less explored. Here, we systematically catalogued the global 3'-UTRome dynamics, by analyzing our previously reported transcriptome sequencing data of porcine immature Sertoli (iST) cells before (Control group), acute heat stress treatment at 43 °C for 0.5h (HS0.5 group), and 36h recovery culture (HS0.5-R36h group) after acute heat stress treatment. After three group comparisons (HS0.5 vs. Control, HS0.5-R36 vs. HS0.5, and HS0.5-R36 vs. Control), DaPars (dynamic analysis of alternative polyadenylation) identified 639, 464 and 290 mRNAs, and APAtrap (a tool to identify APA sites and detect changes of APA site usage) identified 713, 518 and 321 mRNAs, with significantly different 3'-UTRs (Padj.≤0.05), respectively. These genes with different 3'-UTR patterns were mainly enriched in P53, glycolysis/gluconeogenesis, HIF-1, apoptosis, PI3K-Akt and AMPK signaling pathways. Further analysis identified that average 3'-UTR lengths of Acss2, Inpp1 and Nr1h4 were more than 140 nt longer (HS0.5-R36 vs. HS0.5), and contained different cis-elements (PAS, CPE and microRNA binding sites). Moreover, Hsp70.2, Inhbb and Dhrs were identified to have extremely different 3'-UTR abundances. Further 3'RACE assays validated several 3'-UTRs of Nr1h4, and RT-qPCR confirmed the abundance changes of different 3'-UTR isoforms for Nr1h4 and Hsp70.2. Our findings provide useful information and resources to further uncover the molecular role of 3'-UTR, in regulating the response of porcine iST cells to acute heat stress.
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Affiliation(s)
- Yi Wang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zi-Wei Wu
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Qiao Mou
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Lu Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Ting Fang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yu-Qing Zhang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Cai-Xia Yang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
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2
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Kozlov A, Alves JM, Stamatakis A, Posada D. CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data. Genome Biol 2022; 23:37. [PMID: 35081992 PMCID: PMC8790911 DOI: 10.1186/s13059-021-02583-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 12/20/2021] [Indexed: 01/15/2023] Open
Abstract
We introduce CellPhy, a maximum likelihood framework for inferring phylogenetic trees from somatic single-cell single-nucleotide variants. CellPhy leverages a finite-site Markov genotype model with 16 diploid states and considers amplification error and allelic dropout. We implement CellPhy into RAxML-NG, a widely used phylogenetic inference package that provides statistical confidence measurements and scales well on large datasets with hundreds or thousands of cells. Comprehensive simulations suggest that CellPhy is more robust to single-cell genomics errors and outperforms state-of-the-art methods under realistic scenarios, both in accuracy and speed. CellPhy is freely available at https://github.com/amkozlov/cellphy .
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Affiliation(s)
- Alexey Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Joao M. Alves
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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3
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Sauerer T, Lischer C, Weich A, Berking C, Vera J, Dörrie J. Single-Molecule RNA Sequencing Reveals IFNγ-Induced Differential Expression of Immune Escape Genes in Merkel Cell Polyomavirus-Positive MCC Cell Lines. Front Microbiol 2021; 12:785662. [PMID: 35003017 PMCID: PMC8727593 DOI: 10.3389/fmicb.2021.785662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
Merkel cell carcinoma (MCC) is a rare and highly aggressive cancer, which is mainly caused by genomic integration of the Merkel cell polyomavirus and subsequent expression of a truncated form of its large T antigen. The resulting primary tumor is known to be immunogenic and under constant pressure to escape immune surveillance. Because interferon gamma (IFNγ), a key player of immune response, is secreted by many immune effector cells and has been shown to exert both anti-tumoral and pro-tumoral effects, we studied the transcriptomic response of MCC cells to IFNγ. In particular, immune modulatory effects that may help the tumor evade immune surveillance were of high interest to our investigation. The effect of IFNγ treatment on the transcriptomic program of three MCC cell lines (WaGa, MKL-1, and MKL-2) was analyzed using single-molecule sequencing via the Oxford Nanopore platform. A significant differential expression of several genes was detected across all three cell lines. Subsequent pathway analysis and manual annotation showed a clear upregulation of genes involved in the immune escape of tumor due to IFNγ treatment. The analysis of selected genes on protein level underlined our sequencing results. These findings contribute to a better understanding of immune escape of MCC and may help in clinical treatment of MCC patients. Furthermore, we demonstrate that single-molecule sequencing can be used to assess characteristics of large eukaryotic transcriptomes and thus contribute to a broader access to sequencing data in the community due to its low cost of entry.
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Affiliation(s)
- Tatjana Sauerer
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christopher Lischer
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Adrian Weich
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Carola Berking
- Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Julio Vera
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Jan Dörrie
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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4
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Li P, Zhang Q, Tang H. INPP1 up-regulation by miR-27a contributes to the growth, migration and invasion of human cervical cancer. J Cell Mol Med 2019; 23:7709-7716. [PMID: 31557403 PMCID: PMC6815772 DOI: 10.1111/jcmm.14644] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 08/07/2019] [Accepted: 08/10/2019] [Indexed: 01/05/2023] Open
Abstract
Inositol polyphosphate‐1‐phosphatase (INPP1) is an enzyme that is responsible for glycolysis and lipid metabolism. Here, we discovered that INPP1 expression was up‐regulated in CC tissues compared to that in adjacent normal tissues by RT‐qPCR. Inositol polyphosphate‐1‐phosphatase overexpression promoted and INPP1 knockdown suppressed cell viability, cellular migration/invasion and EMT in CC cells. To explore the mechanism of dysregulation, INPP1 was predicted to be a target of miR‐27a, and a pmiRGLO dual‐luciferase reporter assay showed that miR‐27a bound to the 3′ UTR of INPP1. RT‐qPCR revealed that miR‐27a was also up‐regulated and had a positive correlation with INPP1 expression in CC tissues. Furthermore, shR‐INPP1 could favour the malignant phenotype reversion induced by miR‐27a, suggesting that miR‐27a up‐regulates INPP1 to promote tumorigenic activities. Altogether, our findings show that the up‐regulation of INPP1 by miR‐27a contributes to tumorigenic activities and may provide a potential biomarker for CC.
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Affiliation(s)
- Pu Li
- Tianjin Central Obstetrics and Gynecology Hospital, Reproductive Medical Center, Tianjin, China
| | - Qiaoge Zhang
- Tianjin Life Science Research Center and Department of Pathogen, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hua Tang
- Tianjin Life Science Research Center and Department of Pathogen, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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Bossé Y, Amos CI. A Decade of GWAS Results in Lung Cancer. Cancer Epidemiol Biomarkers Prev 2018; 27:363-379. [PMID: 28615365 PMCID: PMC6464125 DOI: 10.1158/1055-9965.epi-16-0794] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Genome-wide association studies (GWAS) were successful to identify genetic factors robustly associated with lung cancer. This review aims to synthesize the literature in this field and accelerate the translation of GWAS discoveries into results that are closer to clinical applications. A chronologic presentation of published GWAS on lung cancer susceptibility, survival, and response to treatment is presented. The most important results are tabulated to provide a concise overview in one read. GWAS have reported 45 lung cancer susceptibility loci with varying strength of evidence and highlighted suspected causal genes at each locus. Some genetic risk loci have been refined to more homogeneous subgroups of lung cancer patients in terms of histologic subtypes, smoking status, gender, and ethnicity. Overall, these discoveries are an important step for future development of new therapeutic targets and biomarkers to personalize and improve the quality of care for patients. GWAS results are on the edge of offering new tools for targeted screening in high-risk individuals, but more research is needed if GWAS are to pay off the investment. Complementary genomic datasets and functional studies are needed to refine the underlying molecular mechanisms of lung cancer preliminarily revealed by GWAS and reach results that are medically actionable. Cancer Epidemiol Biomarkers Prev; 27(4); 363-79. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec, Canada.
- Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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6
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An integrative approach for the identification of prognostic and predictive biomarkers in rectal cancer. Oncotarget 2016; 6:32561-74. [PMID: 26359356 PMCID: PMC4741712 DOI: 10.18632/oncotarget.4935] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/20/2015] [Indexed: 12/22/2022] Open
Abstract
Introduction Colorectal cancer is the third most common cancer in the world, a small fraction of which is represented by locally advanced rectal cancer (LARC). If not medically contraindicated, preoperative chemoradiotherapy, represent the standard of care for LARC patients. Unfortunately, patients shows a wide range of response rates in which approximately 20% has a complete pathological response, whereas in 20 to 40% the response is poor or absent. Results The following specific gene signature, able to discriminate responders' patients from non-responders, were founded: AKR1C3, CXCL11, CXCL10, IDO1, CXCL9, MMP12 and HLA-DRA. These genes are mainly involved in immune system pathways and interact with drugs traditionally used in the adjuvant treatment of rectal cancer. Discussion The present study suggests that new ideas for therapy could be found not only limited to studying genes differentially expressed between the two groups of patients but deepening the mechanisms, associated to response, in which they are involved. Methods Gene expression studies performed by: Agostini et al., Rimkus et al. and Kim et al. have been merged through a meta-analysis of the raw data. Gene expression data-sets have been processed using A-MADMAN. Common differentially expressed gene (DEG) were identified through SAM analysis. To further characterize the identified DEG we deeply investigated its biological role using an integrative computational biology approach.
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7
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Benjamin DI, Louie SM, Mulvihill MM, Kohnz RA, Li DS, Chan LG, Sorrentino A, Bandyopadhyay S, Cozzo A, Ohiri A, Goga A, Ng SW, Nomura DK. Inositol phosphate recycling regulates glycolytic and lipid metabolism that drives cancer aggressiveness. ACS Chem Biol 2014; 9:1340-50. [PMID: 24738946 PMCID: PMC4076040 DOI: 10.1021/cb5001907] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Cancer
cells possess fundamentally altered metabolism that supports
their pathogenic features, which includes a heightened reliance on
aerobic glycolysis to provide precursors for synthesis of biomass.
We show here that inositol polyphosphate phosphatase 1 (INPP1) is
highly expressed in aggressive human cancer cells and primary high-grade
human tumors. Inactivation of INPP1 leads to a reduction in glycolytic
intermediates that feed into the synthesis of the oncogenic signaling
lipid lysophosphatidic acid (LPA), which in turn impairs LPA signaling
and further attenuates glycolytic metabolism in a feed-forward mechanism
to impair cancer cell motility, invasiveness, and tumorigenicity.
Taken together these findings reveal a novel mode of glycolytic control
in cancer cells that can serve to promote key oncogenic lipid signaling
pathways that drive cancer pathogenicity.
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Affiliation(s)
- Daniel I. Benjamin
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Sharon M. Louie
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Melinda M. Mulvihill
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Rebecca A. Kohnz
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel S. Li
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Lauryn G. Chan
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | | | | | - Alyssa Cozzo
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Anayo Ohiri
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
| | | | - Shu-Wing Ng
- Laboratory
of Gynecologic Oncology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel K. Nomura
- Program
in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
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8
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Chu M, Zhang R, Zhao Y, Wu C, Guo H, Zhou B, Lu J, Shi Y, Dai J, Jin G, Ma H, Dong J, Wei Y, Wang C, Gong J, Sun C, Zhu M, Qiu Y, Wu T, Hu Z, Lin D, Shen H, Chen F. A genome-wide gene-gene interaction analysis identifies an epistatic gene pair for lung cancer susceptibility in Han Chinese. Carcinogenesis 2013; 35:572-7. [PMID: 24325914 DOI: 10.1093/carcin/bgt400] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. By now, genome-wide association studies (GWAS) have identified numerous loci associated with the risk of developing lung cancer. However, these loci account for only a small fraction of the familial lung cancer risk. We hypothesized that epistasis may contribute to the missing heritability. To test this hypothesis, we systematically evaluated the association of epistasis of genetic variants with risk of lung cancer in Han Chinese cohorts. We conducted a pairwise genetic interaction analysis of 591370 variants, using BOolean Operation-based Screening and Testing (BOOST), in an ongoing GWAS of lung cancer that includes 2331 cases and 3077 controls. Pairs of epistatic loci with P BOOST ≤ 1.00×10(-6) were further evaluated by a logistic regression model (LRM) with covariate adjustment. Four promising epistatic pairs identified at the screening stage (P LRM ≤ 2.86×10(-) (13)) were validated in two replication cohorts: the first from Beijing (1534 cases and 1489 controls) and the second from Shenyang and Guangzhou (2512 cases and 2449 controls). Using this combined analysis, we identified an interaction between rs2562796 and rs16832404 at 2p32.2 that was significantly associated with the risk of developing lung cancer (P LRM = 1.03×10(-13) in total 13 392 subjects). This study is the first investigation of epistasis for lung cancer on a genome-wide scale in Han Chinese. It addresses part of the missing heritability in lung cancer risk and provides novel insight into the multifactorial etiology of lung cancer.
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Affiliation(s)
- Minjie Chu
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE), Key Laboratory for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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9
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Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, Pazzagli M, Bustin SA, Orlando C. Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal Biochem 2002; 309:293-300. [PMID: 12413463 DOI: 10.1016/s0003-2697(02)00311-1] [Citation(s) in RCA: 425] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Careful normalization is essential when using quantitative reverse transcription polymerase chain reaction assays to compare mRNA levels between biopsies from different individuals or cells undergoing different treatment. Generally this involves the use of internal controls, such as mRNA specified by a housekeeping gene, ribosomal RNA (rRNA), or accurately quantitated total RNA. The aim of this study was to compare these methods and determine which one can provide the most accurate and biologically relevant quantitative results. Our results show significant variation in the expression levels of 10 commonly used housekeeping genes and 18S rRNA, both between individuals and between biopsies taken from the same patient. Furthermore, in 23 breast cancers samples mRNA and protein levels of a regulated gene, vascular endothelial growth factor (VEGF), correlated only when normalized to total RNA, as did microvessel density. Finally, mRNA levels of VEGF and the most popular housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were significantly correlated in the colon. Our results suggest that the use of internal standards comprising single housekeeping genes or rRNA is inappropriate for studies involving tissue biopsies.
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MESH Headings
- Biopsy
- Breast Neoplasms/blood supply
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/surgery
- Colonic Neoplasms/blood supply
- Colonic Neoplasms/genetics
- Colonic Neoplasms/metabolism
- Colonic Neoplasms/surgery
- Endothelial Growth Factors/chemistry
- Endothelial Growth Factors/genetics
- Endothelial Growth Factors/metabolism
- Female
- Gene Expression Regulation
- Glyceraldehyde-3-Phosphate Dehydrogenases/genetics
- Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism
- Humans
- Immunohistochemistry
- Intercellular Signaling Peptides and Proteins/chemistry
- Intercellular Signaling Peptides and Proteins/genetics
- Intercellular Signaling Peptides and Proteins/metabolism
- Lymphokines/chemistry
- Lymphokines/genetics
- Lymphokines/metabolism
- Male
- Neovascularization, Pathologic/genetics
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/analysis
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- Reference Standards
- Reproducibility of Results
- Reverse Transcriptase Polymerase Chain Reaction
- Vascular Endothelial Growth Factor A
- Vascular Endothelial Growth Factors
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Affiliation(s)
- Carmela Tricarico
- Clinical Biochemistry Unit, Department of Clinical Physiopathology, University of Florence, Florence, Italy
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10
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Bustin SA, Li SR, Dorudi S. Expression of the Ca2+-activated chloride channel genes CLCA1 and CLCA2 is downregulated in human colorectal cancer. DNA Cell Biol 2001; 20:331-8. [PMID: 11445004 DOI: 10.1089/10445490152122442] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The role of ion channels in carcinogenesis and tumor progression remains unclear. We have used suppression subtractive hybridization of mRNA from paired normal colon epithelium and tumor, followed by quantitative kinetic RT-PCR, to demonstrate that the transcription of two members of a novel Ca(2+)-dependent chloride channel family, CLCA1 and CLCA2, was significantly downregulated in approximately 80% of colorectal carcinomas. This figure rose to >90% when expression was adjusted for tumor cell proliferation. In normal colon epithelium, CLCA1 mRNA levels were significantly associated with c-myc transcription but became decoupled in the tumor samples. There was no association between CLCA2 and either CLCA1 or c-myc mRNA levels. Transcription of both genes in three colorectal cancer cell lines, T84, HT29, and Caco2, was barely detectable. Illegitimate transcription of CLCA1 was detected in 12 of 15 blood samples taken from healthy volunteers, making its use as a marker for the detection of tumor spread unreliable. Our results suggest that CLCA1 could specify a new tumor suppressor and that, as in breast cancer, CLCA2 may function as a tumor suppressor in colorectal cancer.
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Affiliation(s)
- S A Bustin
- Academic Department of Surgery, St. Bartholomew's and the Royal London School of Medicine and Dentistry, London, UK.
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11
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Crosby LM, Hyder KS, DeAngelo AB, Kepler TB, Gaskill B, Benavides GR, Yoon L, Morgan KT. Morphologic analysis correlates with gene expression changes in cultured F344 rat mesothelial cells. Toxicol Appl Pharmacol 2000; 169:205-21. [PMID: 11133343 DOI: 10.1006/taap.2000.9049] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gene expression pattern of mesothelial cells in vitro was determined after 4 or 12 h exposure to the rat mesothelial, kidney, and thyroid carcinogen and oxidative stressor potassium bromate (KBrO(3)). Gene expression changes observed using cDNA arrays indicated oxidative stress, mitotic arrest, and apoptosis in treated immortalized rat peritoneal mesothelial cells. Increases occurred in oxidative stress responsive genes HO-1, QR, HSP70, GADD45, GADD153, p21(WAF1/CIP16), GST's, GAPDH, TPX, and GPX-1(0); transcriptional regulators c-jun, c-fos, jun B, c-myc, and IkappaB; protein repair components Rdelta, RC10-II, C3, RC-7, HR6B ubiquitin-conjugating enzyme and ubiquitin; DNA repair components PCNA, msh2, and O-6 methylguanine DNA methyltransferase; lipid peroxide excision enzyme PLA2; and apoptogenic components TNFalpha, iNOS1 and FasL. Decreases occurred in bcl-2 (antiapoptotic), bax alpha, bad, and bok (proapoptotic) and cell cycle control elements (cyclins). Cyclin G and p14ink4b (which inhibit entry into cell cycle) were increased. Numerous signal transduction, cell membrane transport, membrane-associated receptor, and fatty acid biosynthesis and repair components were altered. Morphologic endpoints examined were number of mitotic figures, number of apoptotic cells, and antibody-specific localization of HO-1 (which demonstrated increased HO-1 protein expression). PCR analysis confirmed HO-1, p21(waf1/cip1), HSP70, GPX1, GADD45, QR, mdr1, PGHS, and cyclin D1 changes. A model for KBrO(3)-induced carcinogenicity in the F344 rat mesothelium is proposed, whereby KBrO(3) generates a redox signal that activates p53 and results in transcriptional activation of oxidative stress and repair genes, dysregulation of growth control, and imperfect DNA repair leading to carcinogenesis.
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Affiliation(s)
- L M Crosby
- Curriculum in Toxicology, University of North Carolina at Chapel Hill, USA
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