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Xavier JM, Magno R, Russell R, de Almeida BP, Jacinta-Fernandes A, Besouro-Duarte A, Dunning M, Samarajiwa S, O'Reilly M, Maia AM, Rocha CL, Rosli N, Ponder BAJ, Maia AT. Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis. Sci Rep 2024; 14:22526. [PMID: 39341862 PMCID: PMC11438911 DOI: 10.1038/s41598-024-72163-y] [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: 02/01/2024] [Accepted: 09/04/2024] [Indexed: 10/01/2024] Open
Abstract
Understanding breast cancer genetic risk relies on identifying causal variants and candidate target genes in risk loci identified by genome-wide association studies (GWAS), which remains challenging. Since most loci fall in active gene regulatory regions, we developed a novel approach facilitated by pinpointing the variants with greater regulatory potential in the disease's tissue of origin. Through genome-wide differential allelic expression (DAE) analysis, using microarray data from 64 normal breast tissue samples, we mapped the variants associated with DAE (daeQTLs). Then, we intersected these with GWAS data to reveal candidate risk regulatory variants and analysed their cis-acting regulatory potential. Finally, we validated our approach by extensive functional analysis of the 5q14.1 breast cancer risk locus. We observed widespread gene expression regulation by cis-acting variants in breast tissue, with 65% of coding and noncoding expressed genes displaying DAE (daeGenes). We identified over 54 K daeQTLs for 6761 (26%) daeGenes, including 385 daeGenes harbouring variants previously associated with BC risk. We found 1431 daeQTLs mapped to 93 different loci in strong linkage disequilibrium with risk-associated variants (risk-daeQTLs), suggesting a link between risk-causing variants and cis-regulation. There were 122 risk-daeQTL with stronger cis-acting potential in active regulatory regions with protein binding evidence. These variants mapped to 41 risk loci, of which 29 had no previous report of target genes and were candidates for regulating the expression levels of 65 genes. As validation, we identified and functionally characterised five candidate causal variants at the 5q14.1 risk locus targeting the ATG10 and ATP6AP1L genes, likely acting via modulation of alternative transcription and transcription factor binding. Our study demonstrates the power of DAE analysis and daeQTL mapping to identify causal regulatory variants and target genes at breast cancer risk loci, including those with complex regulatory landscapes. It additionally provides a genome-wide resource of variants associated with DAE for future functional studies.
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Affiliation(s)
- Joana M Xavier
- Cintesis@Rise, Universidade do Algarve, Faro, Portugal.
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal.
| | - Ramiro Magno
- Cintesis@Rise, Universidade do Algarve, Faro, Portugal
- Pattern Institute PT, Faro, Portugal
| | - Roslin Russell
- Cambridge Institute - CRUK, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Bernardo P de Almeida
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Faro, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal
- InstaDeep, Paris, France
| | - Ana Jacinta-Fernandes
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Faro, Portugal
| | | | - Mark Dunning
- Cambridge Institute - CRUK, University of Cambridge, Cambridge, UK
- Sheffield Bioinformatics Core, The School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Shamith Samarajiwa
- Medical Research Council (MRC) Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
- Genetics and Genomics Section, Imperial College London, London, UK
| | - Martin O'Reilly
- Cambridge Institute - CRUK, University of Cambridge, Cambridge, UK
| | | | - Cátia L Rocha
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Faro, Portugal
- Faculty of Medicine, Instituto de Saúde Ambiental (ISAMB), University of Lisbon, Lisbon, Portugal
| | - Nordiana Rosli
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Faro, Portugal
- Training Division, Ministry of Health Malaysia, Putrajaya, Malaysia
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon, South Korea
| | - Bruce A J Ponder
- Cambridge Institute - CRUK, University of Cambridge, Cambridge, UK
| | - Ana-Teresa Maia
- Cintesis@Rise, Universidade do Algarve, Faro, Portugal.
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal.
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Faro, Portugal.
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Chai T, Yue W, Xu P, Gildea J, Felder R. Caveolin-1, a Determinant of the Fate of MCF-7 Breast Cancer Cells. Breast Cancer (Auckl) 2024; 18:11782234241226802. [PMID: 38298330 PMCID: PMC10829489 DOI: 10.1177/11782234241226802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
Background The scaffolding protein, caveolin-1 (Cav-1), participates in multiple cellular functions including promotion of sodium excretion from the kidney. Loss of expression of Cav-1 is associated with tumorigenesis of various types of cancer. We have shown the potential link between hypertension and breast cancer via abnormal function of the G protein-coupled receptor kinase type 4 (GRK4). Objective The current studies tested the hypothesis that Cav-1 acts as a tumor-suppressive factor in breast cancer cells and enhances the sensitivity to the inhibitory effect of the type 1 dopaminergic receptor (D1R). Methods Michigan Cancer Foundation (MCF) MCF-7 cells stably expressing a Cav-1/mCherry fusion protein or mCherry alone were used as models to examine the effect of Cav-1 on cell growth, apoptosis, and senescence. Cell proliferation was determined by cell counting, cell cycle analysis (flow cytometry), and BrdU incorporation. Apoptosis was determined using the Cell Death Detection ELISA kit from Roche Diagnosis. Senescence was determined using the senescence associated beta galactosidase (SA-β-gal) assay. Reactive oxygen species (ROS) was measured using 2',7'-dichlorodihydrofluorescein diacetate. Western blot analysis was used to measure activation of signaling pathway molecules. All statistical analyses were conducted with Microsoft Excel. Results Overexpression of Cav-1 in MCF-7 cells reduced cellular growth rate. Both inhibition of proliferation and induction of cell death are contributing factors. Multiple signaling pathways were activated in Cav-1-expressing MCF-7 cells. Activation of Akt was prominent. In MCF-7-expressing Cav-1 (MCF-7 Cav-1) cells, the levels of phosphorylated Akt at S473 and T308 were increased 28- and 8.7-fold, respectively. Instead of protecting cells from apoptosis, extremely high levels of activated Akt resulted in increased levels of ROS which led to apoptosis and senescence. The tumor-suppressive effect plus downregulation of GRK4 makes Cav-1-expressing MCF-7 cells significantly more sensitive to the inhibitory effect of the D1R agonist, SKF38393. Conclusion Caveolin-1 acts as a tumor-suppressing factor via extreme activation of Akt and down regulation of survival factors such as GRK4, survivin, and cyclin D1.
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Affiliation(s)
- Tina Chai
- Department of Pathology, University of Virginia Health System, University of Virginia, Charlottesville, VA, USA
| | - Wei Yue
- Department of Pathology, University of Virginia Health System, University of Virginia, Charlottesville, VA, USA
| | - Peng Xu
- Department of Pathology, University of Virginia Health System, University of Virginia, Charlottesville, VA, USA
| | - John Gildea
- Department of Pathology, University of Virginia Health System, University of Virginia, Charlottesville, VA, USA
| | - Robin Felder
- Department of Pathology, University of Virginia Health System, University of Virginia, Charlottesville, VA, USA
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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, de Souza MM, Afonso J, Vieira D, Malheiros J, Andrade BGN, Petrini J, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle. Genes (Basel) 2022; 13:genes13122336. [PMID: 36553605 PMCID: PMC9777870 DOI: 10.3390/genes13122336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos 13560-000, SP, Brazil
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | | | | | | | - Juliana Afonso
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | - Dielson Vieira
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jessica Malheiros
- Federal University of Latin American Integration-UNILA, Foz do Iguaçu 85851-000, PR, Brazil
| | | | - Juliana Petrini
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, University of São Paulo (FMVZ—USP), Pirassununga 13630-000, SP, Brazil
| | | | - Gerson Barreto Mourão
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - Luiz Lehmann Coutinho
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
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Ubiquitin-specific protease TRE17/USP6 promotes tumor cell invasion through the regulation of glycoprotein CD147 intracellular trafficking. J Biol Chem 2022; 298:102335. [PMID: 35926707 PMCID: PMC9440431 DOI: 10.1016/j.jbc.2022.102335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Disordered expression and distribution of plasma membrane proteins at the cell surface leads to diverse malignant phenotypes in tumors, including cell invasion. The ubiquitin-specific protease TRE17/USP6, an oncogene identified in Ewing sarcoma, is highly expressed in several cancers and locally aggressive tumor-like lesions. We have previously demonstrated that TRE17 regulates the trafficking of plasma membrane proteins that enter cells via clathrin-independent endocytosis (CIE); TRE17 prevents CIE cargo proteins from being targeted to lysosomes for degradation by deubiquitylating them. However, functional insights into the effects of TRE17-mediated CIE cargo trafficking on cell invasion remain unknown. Here, we show that increased expression of TRE17 enhances invasiveness of the human sarcoma cell line HT-1080 by elevating the cell surface levels of the membrane glycoprotein CD147, which plays a central role in tumor progression. We demonstrate overexpression of TRE17 decreases ubiquitylated CD147, which is accompanied by suppression of CD147 transport to lysosomes, resulting in the stabilization and increase of cell surface-localized CD147. On the other hand, we show knockdown of TRE17 decreases cell surface CD147, which is coupled with reduced production of matrix metalloproteinases (MMPs), the enzymes responsible for extracellular matrix degradation. Furthermore, we demonstrate that inhibition of CD147 by a specific inhibitor alleviated the TRE17-promoted tumor cell invasion. We therefore propose a model for the pathogenesis of TRE17-driven tumors in which TRE17 increases CD147 at the cell surface by preventing its lysosomal degradation, which in turn enhances MMP synthesis and matrix degradation, thereby promoting tumor cell invasion.
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Yue W, Gildea JJ, Xu P, Felder RA. GRK4, A Potential Link between Hypertension and Breast Cancer. JOURNAL OF CELL SCIENCE & THERAPY 2022; 13:1000343. [PMID: 37994311 PMCID: PMC10664845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Hypertension and breast cancer are two common diseases occurring in women. Clinical studies have shown increased breast cancer incidence in hypertensive women. Several lines of evidence demonstrate that G protein-coupled Receptor Kinase 4 (GRK4) could be a common risk factor for hypertension and breast cancer. This article reviews our current understanding of molecular mechanisms of GRK4 in hypertension and breast cancer.
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Affiliation(s)
- Wei Yue
- Department of Pathology, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - John J Gildea
- Department of Pathology, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Peng Xu
- Department of Pathology, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Robin A Felder
- Department of Pathology, University of Virginia Health System, Charlottesville, VA 22908, USA
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Accelerated aging in normal breast tissue of women with breast cancer. Breast Cancer Res 2021; 23:58. [PMID: 34022936 PMCID: PMC8140515 DOI: 10.1186/s13058-021-01434-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/26/2021] [Indexed: 12/13/2022] Open
Abstract
Background DNA methylation alterations have similar patterns in normal aging tissue and in cancer. In this study, we investigated breast tissue-specific age-related DNA methylation alterations and used those methylation sites to identify individuals with outlier phenotypes. Outlier phenotype is identified by unsupervised anomaly detection algorithms and is defined by individuals who have normal tissue age-dependent DNA methylation levels that vary dramatically from the population mean. Methods We generated whole-genome DNA methylation profiles (GSE160233) on purified epithelial cells and used publicly available Infinium HumanMethylation 450K array datasets (TCGA, GSE88883, GSE69914, GSE101961, and GSE74214) for discovery and validation. Results We found that hypermethylation in normal breast tissue is the best predictor of hypermethylation in cancer. Using unsupervised anomaly detection approaches, we found that about 10% of the individuals (39/427) were outliers for DNA methylation from 6 DNA methylation datasets. We also found that there were significantly more outlier samples in normal-adjacent to cancer (24/139, 17.3%) than in normal samples (15/228, 5.2%). Additionally, we found significant differences between the predicted ages based on DNA methylation and the chronological ages among outliers and not-outliers. Additionally, we found that accelerated outliers (older predicted age) were more frequent in normal-adjacent to cancer (14/17, 82%) compared to normal samples from individuals without cancer (3/17, 18%). Furthermore, in matched samples, we found that the epigenome of the outliers in the pre-malignant tissue was as severely altered as in cancer. Conclusions A subset of patients with breast cancer has severely altered epigenomes which are characterized by accelerated aging in their normal-appearing tissue. In the future, these DNA methylation sites should be studied further such as in cell-free DNA to determine their potential use as biomarkers for early detection of malignant transformation and preventive intervention in breast cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01434-7.
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Yue W, Tran HT, Wang JP, Schiermeyer K, Gildea JJ, Xu P, Felder RA. The Hypertension Related Gene G-Protein Coupled Receptor Kinase 4 Contributes to Breast Cancer Proliferation. Breast Cancer (Auckl) 2021; 15:11782234211015753. [PMID: 34103922 PMCID: PMC8145586 DOI: 10.1177/11782234211015753] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/12/2021] [Indexed: 01/11/2023] Open
Abstract
PURPOSE Clinical studies have shown that breast cancer risk is increased in hypertensive women. The underlying molecular mechanism remains undetermined. The current study tests our hypothesis that G protein coupled receptor kinase 4 (GRK4) is a molecule that links hypertension and breast cancer. GRK4 plays an important role in regulation of renal sodium excretion. Sustained activation of GRK4 as in the circumstances of single nucleotide polymorphism (SNPs) causes hypertension. Expression of GRK4 in the kidney is regulated by cMyc, an oncogene that is amplified in breast cancer. METHODS Western analysis was used to evaluate GRK4 protein expression in seven breast cancer cell lines. GRK4 gene single nucleotide polymorphism in breast cancer cell lines and in breast cancer cDNA arrays were determined using TaqMan Genotyping qPRC. The function of GRK4 was evaluated in MCF-7 cells with cMyc knock-down and GRK4 re-expression and in MDA-MB-468 cells expressing inducible GRK4 shRNA lentivirus constructs. Nuclei counting and 5-Bromo-2'-deoxy-uridine (BrdU) labeling were used to evaluate cell growth and proliferation. RESULTS Genotyping of GRK4 SNPs in breast cancer cDNA arrays (n = 94) revealed that the frequency of carrying two hypertension related SNPs A142 V or R65 L is threefold higher in breast cancer patients than in healthy people (P = 7.53E-11). GRK4 protein is expressed in seven breast cancer cell lines but not the benign mammary epithelial cell line, MCF-10A. Three hypertension related SNPs in the GRK4 gene were identified in the breast cancer cell lines. Except for BT20, all other breast cancer lines have 1-3 GRK4 SNPs of which A142 V occurs in all 6 lines. MDA-MB-468 cells contain homozygous A142 V and R65 L SNPs. Knocking down cMyc in MCF-7 cells significantly reduced the growth rate, which was rescued by re-expression of GRK4. We then generated three stable GRK4 knock-down MDA-MB-468 lines using inducible lentiviral shRNA vectors. Doxycycline (Dox) induced GRK4 silencing significantly reduced GRK4 mRNA and protein levels, growth rates, and proliferation. As a marker of cell proliferation, the percentage of BrdU-labeled cells decreased from 45 ± 3% in the cells without Dox to 32 ± 5% in the cells treated with 0.1 µg/mL Dox. CONCLUSIONS GRK4 acts as an independent proliferation promotor in breast cancer. Our results suggest that targeted inhibition of GRK4 could be a new therapy for both hypertension and breast cancer.
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Affiliation(s)
- Wei Yue
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Hanh T. Tran
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Ji-ping Wang
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Katherine Schiermeyer
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - John J. Gildea
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Peng Xu
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Robin A. Felder
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
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Moecking J, Laohamonthonkul P, Chalker K, White MJ, Harapas CR, Yu CH, Davidson S, Hrovat-Schaale K, Hu D, Eng C, Huntsman S, Calleja DJ, Horvat JC, Hansbro PM, O'Donoghue RJJ, Ting JP, Burchard EG, Geyer M, Gerlic M, Masters SL. NLRP1 variant M1184V decreases inflammasome activation in the context of DPP9 inhibition and asthma severity. J Allergy Clin Immunol 2020; 147:2134-2145.e20. [PMID: 33378691 PMCID: PMC8168955 DOI: 10.1016/j.jaci.2020.12.636] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 02/01/2023]
Abstract
Background NLRP1 is an innate immune sensor that can form cytoplasmic inflammasome complexes. Polymorphisms in NLRP1 are linked to asthma; however, there is currently no functional or mechanistic explanation for this. Objective We sought to clarify the role of NLRP1 in asthma pathogenesis. Methods Results from the GALA II cohort study were used to identify a link between NLRP1 and asthma in Mexican Americans. In vitro and in vivo models for NLRP1 activation were applied to investigate the role of this inflammasome in asthma at the molecular level. Results We document the association of an NLRP1 haplotype with asthma for which the single nucleotide polymorphism rs11651270 (M1184V) individually is the most significant. Surprisingly, M1184V increases NLRP1 activation in the context of N-terminal destabilization, but decreases NLRP1 activation on dipeptidyl peptidase 9 inhibition. In vitro studies demonstrate that M1184V increases binding to dipeptidyl peptidase 9, which can account for its inhibitory role in this context. In addition, in vivo data from a mouse model of airway inflammation reveal a protective role for NLRP1 inflammasome activation reducing eosinophilia in this setting. Conclusions Linking our in vitro and in vivo results, we found that the NLRP1 variant M1184V reduces inflammasome activation in the context of dipeptidyl peptidase 9 inhibition and could thereby increase asthma severity. Our studies may have implications for the treatment of asthma in patients carrying this variant of NLRP1.
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Affiliation(s)
- Jonas Moecking
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia; the Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Pawat Laohamonthonkul
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Katelyn Chalker
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Marquitta J White
- Department of Medicine, University of California, San Francisco, Calif
| | - Cassandra R Harapas
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Chien-Hsiung Yu
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Sophia Davidson
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Katja Hrovat-Schaale
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, Calif
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, Calif
| | - Dale J Calleja
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Jay C Horvat
- the Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, New Lambton, Australia; University of Newcastle, Callaghan, Australia
| | - Phil M Hansbro
- the Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, New Lambton, Australia; University of Newcastle, Callaghan, Australia; Centre for Inflammation, Centenary Institute, Sydney, Australia; Faculty of Science, University of Technology Sydney, Ultimo, Australia
| | - Robert J J O'Donoghue
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Australia
| | - Jenny P Ting
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif
| | - Matthias Geyer
- the Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, Bonn, Germany
| | - Motti Gerlic
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Seth L Masters
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia.
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Clayton EA, Khalid S, Ban D, Wang L, Jordan IK, McDonald JF. Tumor suppressor genes and allele-specific expression: mechanisms and significance. Oncotarget 2020; 11:462-479. [PMID: 32064050 PMCID: PMC6996918 DOI: 10.18632/oncotarget.27468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022] Open
Abstract
Recent findings indicate that allele-specific expression (ASE) at specific cancer driver gene loci may be of importance in onset/progression of the disease. Of particular interest are loss-of-function (LOF) of tumor suppressor gene (TSGs) alleles. While LOF tumor suppressor mutations are typically considered to be recessive, if these mutant alleles can be significantly differentially expressed relative to wild-type alleles in heterozygotes, the clinical consequences could be significant. LOF TSG alleles are shown to be segregating at high frequencies in world-wide populations of normal/healthy individuals. Matched sets of normal and tumor tissues isolated from 233 cancer patients representing four diverse tumor types demonstrate functionally important changes in patterns of ASE in individuals heterozygous for LOF TSG alleles associated with cancer onset/progression. While a variety of molecular mechanisms were identified as potentially contributing to changes in ASE patterns in cancer, changes in DNA copy number and allele-specific alternative splicing possibly mediated by antisense RNA emerged as predominant factors. In conclusion, LOF TSGs are segregating in human populations at significant frequencies indicating that many otherwise healthy individuals are at elevated risk of developing cancer. Changes in ASE between normal and cancer tissues indicates that LOF TSG alleles may contribute to cancer onset/progression even when heterozygous with wild-type functional alleles.
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Affiliation(s)
- Evan A. Clayton
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shareef Khalid
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dongjo Ban
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lu Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
| | - I. King Jordan
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- PanAmerican Bioinformatics Institute, Cali, Colombia
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - John F. McDonald
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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Zhang L, Li X, Quan X, Tian W, Yang X, Zhou B. A Case/Control Study: AGBL1 Polymorphism Related to Lung Cancer Risk in Chinese Nonsmoking Females. DNA Cell Biol 2019; 38:1452-1459. [PMID: 31603707 DOI: 10.1089/dna.2019.4851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
ATP/GTP binding protein like 1 (AGBL1) plays a role in controlling the length of polyglutamate side chains. Polymorphism rs4513061 in AGBL1 is suspected to influence the risk of lung cancer. A case/control study was performed involving 556 cases and 563 controls from a hospital participating in donation. The relationship between rs4513061 and the risk of lung cancer and the interaction between rs4513061 and environmental exposure were determined by the chi-square tests, logistic regression analysis, and crossover analysis. The survival analysis was conducted by Cox proportional hazard regression. The results showed that rs4513061 polymorphism is associated with the risk of lung cancer. The stratified analysis suggested the protective effect of rs4513061 to different histological types of lung cancer, including lung adenocarcinoma (AA vs. GG: odds ratio [OR] = 0.505, 95% confidence interval [CI] = 0.337-0.756, p < 0.001), squamous cell lung cancer (AG vs. GG: OR = 0.488, 95% CI = 0.269-0.883, p = 0.018), and small-cell lung cancer (AA vs. GG: OR = 0.421, 95% CI = 0.216-0.819, p = 0.011). Nevertheless, there was no significant interaction between rs4513061 and cooking oil fume. Significant impact was not observed between the rs4513061 polymorphism and survival time of lung cancer. Our study indicated that rs4513061 in AGBL1 decreases the risk of lung cancer in nonsmoking females from northeast China.
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Affiliation(s)
- Ludan Zhang
- Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,Department of Clinical Medicine, China Medical University, Shenyang, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Xiaowei Quan
- Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Wen Tian
- Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Xianglin Yang
- Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Baosen Zhou
- Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
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11
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Yin L, Wang Y, Lin Y, Yu G, Xia Q. Explorative analysis of the gene expression profile during liver regeneration of mouse: a microarray-based study. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:1113-1121. [PMID: 30963776 DOI: 10.1080/21691401.2019.1593851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The liver is an amazing organ due to its powerful regenerative capacity. Although many studies on liver regeneration have been documented, the detailed mechanisms remain unclear. Two-third partial hepatectomy (PH) in rodents plays a crucial role in the study of liver regeneration. In this study, the time series data of gene expression during liver regeneration in mouse were analyzed using the gene set numbered GSE6998 in GEO. A variety of bioinformatics methods, including masigPro, Weighted Gene Co-expression Network Analysis (WGCNA), spatial analysis of functional enrichment (SAFE) and ingenuity canonical pathway analysis (IPA) were used to identify and compare the significantly changed pathways, potential upstream regulators and key genes during liver regeneration. Our study showed that liver regeneration in the mouse is a coordinated process, which cell-cycle-related progress are at the centre of the interaction network involved in liver regeneration. Several candidate upstream regulators including PPARA, NFE2L2, MAD1 and CNR1 and some key genes such as Cdk1, Plk1, Cdc20, Aurka, Racgap1, Cenpa, Rrm1, Rrm2 were identified. In conclusion, these findings could contribute to revealing the molecular mechanism of liver regeneration after PH, which could provide new ideas and treatment methods for regenerative medicine, oncological drug development and oncological treatment.
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Affiliation(s)
- Li Yin
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
| | - Yuanyuan Wang
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
| | - Yingzi Lin
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
| | - Guoying Yu
- b State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Engineering Laboratory for Bioengineering and Drug Development , Henan Normal University , Xinxiang , Henan , China
| | - Qianfeng Xia
- a Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine , Hainan Medical University , Haikou , Hainan , China
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12
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Jiang P, Li Y, Poleshko A, Medvedeva V, Baulina N, Zhang Y, Zhou Y, Slater CM, Pellegrin T, Wasserman J, Lindy M, Efimov A, Daly M, Katz RA, Chen X. The Protein Encoded by the CCDC170 Breast Cancer Gene Functions to Organize the Golgi-Microtubule Network. EBioMedicine 2017; 22:28-43. [PMID: 28687497 PMCID: PMC5552109 DOI: 10.1016/j.ebiom.2017.06.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 12/17/2022] Open
Abstract
Genome-Wide Association Studies (GWAS) and subsequent fine-mapping studies (>50) have implicated single nucleotide polymorphisms (SNPs) located at the CCDC170/C6ORF97-ESR1 locus (6q25.1) as being associated with the risk of breast cancer. Surprisingly, our analysis using genome-wide differential allele-specific expression (DASE), an indicator for breast cancer susceptibility, suggested that the genetic alterations of CCDC170, but not ESR1, account for GWAS-associated breast cancer risk at this locus. Breast cancer-associated CCDC170 nonsense mutations and rearrangements have also been detected, with the latter being specifically implicated in driving breast cancer. Here we report that the wild type CCDC170 protein localizes to the region of the Golgi apparatus and binds Golgi-associated microtubules (MTs), and that breast cancer-linked truncations of CCDC170 result in loss of Golgi localization. Overexpression of wild type CCDC170 triggers Golgi reorganization, and enhances Golgi-associated MT stabilization and acetyltransferase ATAT1-dependent α-tubulin acetylation. Golgi-derived MTs regulate cellular polarity and motility, and we provide evidence that dysregulation of CCDC170 affects polarized cell migration. Taken together, our findings demonstrate that CCDC170 plays an essential role in Golgi-associated MT organization and stabilization, and implicate a mechanism for how perturbations in the CCDC170 gene may contribute to the hallmark changes in cell polarity and motility seen in breast cancer.
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Affiliation(s)
- Pengtao Jiang
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Yueran Li
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Andrey Poleshko
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Valentina Medvedeva
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Natalia Baulina
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Yongchao Zhang
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Yan Zhou
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Carolyn M Slater
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Trinity Pellegrin
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Jason Wasserman
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Michael Lindy
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Andrey Efimov
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Mary Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Richard A Katz
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
| | - Xiaowei Chen
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, United States.
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13
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Jiang Z, Slater CM, Zhou Y, Devarajan K, Ruth KJ, Li Y, Cai KQ, Daly M, Chen X. LincIN, a novel NF90-binding long non-coding RNA, is overexpressed in advanced breast tumors and involved in metastasis. Breast Cancer Res 2017; 19:62. [PMID: 28558830 PMCID: PMC5450112 DOI: 10.1186/s13058-017-0853-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 05/05/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Recent genome-wide profiling by sequencing and distinctive chromatin signatures has identified thousands of long non-coding RNA (lncRNA) species (>200 nt). LncRNAs have emerged as important regulators of gene expression, involving in both developmental and pathological processes. While altered expression of lncRNAs has been observed in breast cancer development, their roles in breast cancer progression and metastasis are still poorly understood. METHODS To identify novel breast cancer-associated lncRNA candidates, we employed a high-density SNP array-based approach to uncover intergenic lncRNA genes that are aberrantly expressed in breast cancer. We first evaluated the potential value as a breast cancer prognostic biomarker for one breast cancer-associated lncRNA, LincIN, using a breast cancer cohort retrieved from The Cancer Genome Atlas (TCGA) Data Portal. Then we characterized the role of LincIN in breast cancer progression and metastasis by in vitro invasion assay and a mouse tail vein injection metastasis model. To study the action of LincIN, we identified LincIN-interacting protein partner(s) by RNA pull-down experiments followed with protein identification by mass spectrometry. RESULTS High levels of LincIN expression are frequently observed in tumors compared to adjacent normal tissues, and are strongly associated with aggressive breast cancer. Importantly, analysis of TCGA data further suggest that high expression of LincIN is associated with poor overall survival in patients with breast cancer (P = 0.044 and P = 0.011 after adjustment for age). The functional experiments demonstrate that knockdown of LincIN inhibits tumor cell migration and invasion in vitro, which is supported by the results of transcriptome analysis in the LincIN-knockdown cells. Furthermore, knockdown of LincIN diminishes lung metastasis in a mouse tail vein injection model. We also identified a LincIN-binding protein, NF90, through which overexpression of LincIN may repress p21 protein expression by inhibiting its translation, and upregulation of p21 by LincIN knockdown may be associated with less aggressive metastasis phenotypes. CONCLUSIONS Our studies provide clear evidence to support LincIN as a new regulator of tumor progression-metastasis at both transcriptional and translational levels and as a promising prognostic biomarker for breast cancer.
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Affiliation(s)
- Zhengyu Jiang
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.,Present Address: Department of Medicine, Irving Cancer Research Center, Columbia University, New York, NY, 10032, USA
| | - Carolyn M Slater
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Yan Zhou
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Karthik Devarajan
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Karen J Ruth
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Yueran Li
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.,Present Address: The Third Xiangya Hospital of Central South University, Changsha, China
| | - Kathy Q Cai
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Mary Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Xiaowei Chen
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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14
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Sato T, Cesaroni M, Chung W, Panjarian S, Tran A, Madzo J, Okamoto Y, Zhang H, Chen X, Jelinek J, Issa JPJ. Transcriptional Selectivity of Epigenetic Therapy in Cancer. Cancer Res 2016; 77:470-481. [PMID: 27879268 DOI: 10.1158/0008-5472.can-16-0834] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 09/26/2016] [Accepted: 10/21/2016] [Indexed: 12/22/2022]
Abstract
A central challenge in the development of epigenetic cancer therapy is the ability to direct selectivity in modulating gene expression for disease-selective efficacy. To address this issue, we characterized by RNA-seq, DNA methylation, and ChIP-seq analyses the epigenetic response of a set of colon, breast, and leukemia cancer cell lines to small-molecule inhibitors against DNA methyltransferases (DAC), histone deacetylases (Depsi), histone demethylases (KDM1A inhibitor S2101), and histone methylases (EHMT2 inhibitor UNC0638 and EZH2 inhibitor GSK343). We also characterized the effects of DAC as combined with the other compounds. Averaged over the cancer cell models used, we found that DAC affected 8.6% of the transcriptome and that 95.4% of the genes affected were upregulated. DAC preferentially regulated genes that were silenced in cancer and that were methylated at their promoters. In contrast, Depsi affected the expression of 30.4% of the transcriptome but showed little selectivity for gene upregulation or silenced genes. S2101, UNC0638, and GSK343 affected only 2% of the transcriptome, with UNC0638 and GSK343 preferentially targeting genes marked with H3K9me2 or H3K27me3, respectively. When combined with histone methylase inhibitors, the extent of gene upregulation by DAC was extended while still maintaining selectivity for DNA-methylated genes and silenced genes. However, the genes upregulated by combination treatment exhibited limited overlap, indicating the possibility of targeting distinct sets of genes based on different epigenetic therapy combinations. Overall, our results demonstrated that DNA methyltransferase inhibitors preferentially target cancer-relevant genes and can be combined with inhibitors targeting histone methylation for synergistic effects while still maintaining selectivity. Cancer Res; 77(2); 470-81. ©2016 AACR.
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Affiliation(s)
- Takahiro Sato
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania.
| | - Matteo Cesaroni
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Shoghag Panjarian
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Anthony Tran
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Jozef Madzo
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Yasuyuki Okamoto
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Hanghang Zhang
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Xiaowei Chen
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania
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15
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Lin W, Lin HD, Guo XY, Lin Y, Su FX, Jia WH, Tang LY, Zheng W, Long JR, Ren ZF. Allelic expression imbalance polymorphisms in susceptibility chromosome regions and the risk and survival of breast cancer. Mol Carcinog 2016; 56:300-311. [DOI: 10.1002/mc.22493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/02/2016] [Accepted: 04/13/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Wei Lin
- Department of Statistics and Epidemiology; Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment; The School of Public Health; Sun Yat-sen University Guangzhou China
| | - Hong-Da Lin
- Department of Statistics and Epidemiology; Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment; The School of Public Health; Sun Yat-sen University Guangzhou China
| | - Xing-Yi Guo
- Division of Epidemiology; Department of Medicine; Vanderbilt University School of Medicine; Nashville Tennessee
| | - Ying Lin
- The First Affiliated Hospital; Sun Yat-sen University; Guangzhou China
| | - Feng-Xi Su
- The Second Affiliated Hospital; Sun Yat-sen University; Guangzhou China
| | - Wei-Hua Jia
- The Sun Yat-sen University Cancer Center; Guangzhou China
| | - Lu-Ying Tang
- The Third Affiliated Hospital; Sun Yat-sen University; Guangzhou China
| | - Wei Zheng
- Division of Epidemiology; Department of Medicine; Vanderbilt University School of Medicine; Nashville Tennessee
| | - Ji-Rong Long
- Division of Epidemiology; Department of Medicine; Vanderbilt University School of Medicine; Nashville Tennessee
| | - Ze-Fang Ren
- Department of Statistics and Epidemiology; Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment; The School of Public Health; Sun Yat-sen University Guangzhou China
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16
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Pontillo A, Bricher P, Leal V, Lima S, Souza P, Crovella S. Role of inflammasome genetics in susceptibility to HPV infection and cervical cancer development. J Med Virol 2016; 88:1646-51. [DOI: 10.1002/jmv.24514] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2016] [Indexed: 12/19/2022]
Affiliation(s)
- A. Pontillo
- Laboratory of Immunogenetics, Department of Immunology; Institute of Biomedical Sciences, University of Sao Paulo; Sao Paulo SP Brazil
| | - P. Bricher
- Laboratory of Immunogenetics, Department of Immunology; Institute of Biomedical Sciences, University of Sao Paulo; Sao Paulo SP Brazil
| | - V.N.C. Leal
- Laboratory of Immunogenetics, Department of Immunology; Institute of Biomedical Sciences, University of Sao Paulo; Sao Paulo SP Brazil
| | - S. Lima
- Laboratory of Immunopathology “Keiko Azami”; Federal University of Pernambuco; Recife PE Brazil
| | - P.R.E. Souza
- Department of Biology, Genetic Area; Federal Rural University of Pernambuco; Recife PE Brazil
| | - S. Crovella
- Department of Genetics; Federal University of Pernambuco; Recife PE Brazil
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17
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Chamberlain AJ, Vander Jagt CJ, Hayes BJ, Khansefid M, Marett LC, Millen CA, Nguyen TTT, Goddard ME. Extensive variation between tissues in allele specific expression in an outbred mammal. BMC Genomics 2015; 16:993. [PMID: 26596891 PMCID: PMC4657355 DOI: 10.1186/s12864-015-2174-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/31/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Allele specific gene expression (ASE), with the paternal allele more expressed than the maternal allele or vice versa, appears to be a common phenomenon in humans and mice. In other species the extent of ASE is unknown, and even in humans and mice there are several outstanding questions. These include; to what extent is ASE tissue specific? how often does the direction of allele expression imbalance reverse between tissues? how often is only one of the two alleles expressed? is there a genome wide bias towards expression of the paternal or maternal allele; and finally do genes that are nearby on a chromosome share the same direction of ASE? Here we use gene expression data (RNASeq) from 18 tissues from a single cow to investigate each of these questions in turn, and then validate some of these findings in two tissues from 20 cows. RESULTS Between 40 and 100 million sequence reads were generated per tissue across three replicate samples for each of the eighteen tissues from the single cow (the discovery dataset). A bovine gene expression atlas was created (the first from RNASeq data), and differentially expressed genes in each tissue were identified. To analyse ASE, we had access to unambiguously phased genotypes for all heterozygous variants in the cow's whole genome sequence, where these variants were homozygous in the whole genome sequence of her sire, and as a result we were able to map reads to parental genomes, to determine SNP and genes showing ASE in each tissue. In total 25,251 heterozygous SNP within 7985 genes were tested for ASE in at least one tissue. ASE was pervasive, 89 % of genes tested had significant ASE in at least one tissue. This large proportion of genes displaying ASE was confirmed in the two tissues in a validation dataset. For individual tissues the proportion of genes showing significant ASE varied from as low as 8-16 % of those tested in thymus to as high as 71-82 % of those tested in lung. There were a number of cases where the direction of allele expression imbalance reversed between tissues. For example the gene SPTY2D1 showed almost complete paternal allele expression in kidney and thymus, and almost complete maternal allele expression in the brain caudal lobe and brain cerebellum. Mono allelic expression (MAE) was common, with 1349 of 4856 genes (28 %) tested with more than one heterozygous SNP showing MAE. Across all tissues, 54.17 % of all genes with ASE favoured the paternal allele. Genes that are closely linked on the chromosome were more likely to show higher expression of the same allele (paternal or maternal) than expected by chance. We identified several long runs of neighbouring genes that showed either paternal or maternal ASE, one example was five adjacent genes (GIMAP8, GIMAP7 copy1, GIMAP4, GIMAP7 copy 2 and GIMAP5) that showed almost exclusive paternal expression in brain caudal lobe. CONCLUSIONS Investigating the extent of ASE across 18 bovine tissues in one cow and two tissues in 20 cows demonstrated 1) ASE is pervasive in cattle, 2) the ASE is often MAE but ranges from MAE to slight overexpression of the major allele, 3) the ASE is most often tissue specific and that more than half the time displays divergent allele specific expression patterns across tissues, 4) across all genes there is a slight bias towards expression of the paternal allele and 5) genes expressing the same parental allele are clustered together more than expected by chance, and there are several runs of large numbers of genes expressing the same parental allele.
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Affiliation(s)
- Amanda J Chamberlain
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
| | - Christy J Vander Jagt
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
| | - Benjamin J Hayes
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- La Trobe University, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
| | - Majid Khansefid
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Institute of Land and Food, University of Melbourne, Royal Parade, Parkville, Australia.
| | - Leah C Marett
- Department of Economic Development, Jobs, Transport and Resources, 1301 Hazeldean Rd, Ellinbank, Australia.
| | - Catriona A Millen
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Institute of Land and Food, University of Melbourne, Royal Parade, Parkville, Australia.
| | - Thuy T T Nguyen
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
| | - Michael E Goddard
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Institute of Land and Food, University of Melbourne, Royal Parade, Parkville, Australia.
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18
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Alterations in Salivary Proteome following Single Twenty-Minute Session of Yogic Breathing. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015; 2015:376029. [PMID: 25873979 PMCID: PMC4383272 DOI: 10.1155/2015/376029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/05/2014] [Accepted: 12/22/2014] [Indexed: 11/18/2022]
Abstract
Yogic breathing (YB) has been suggested to reduce stress and blood pressure and increase cognitive processes. However, alterations after YB at the molecular level are not well established. Twenty healthy volunteers were randomized into two groups (N = 10 per group): YB or attention controls (AC). The YB group performed two YB exercises, each for ten minutes, for a total of twenty minutes in a single session. AC group read a text of their choice for 20 minutes. Saliva was collected at baseline and at 5, 10, 15, and 20 minutes. Using Mass Spectrometry (MS), we initially found that 22 proteins were differentially expressed and then validated deleted in malignant brain tumor-1 (DMBT1) and Ig lambda-2 chain C region (IGLC2) using Western Blotting. DMBT1 was elevated in 7 of YB group by 10-fold and 11-fold at 10 and 15 minutes, respectively, whereas it was undetectable in the time-matched AC group (P < 0.05). There was a significant interaction between groups and time assessed by two-way ANOVA (P < 0.001). IGLC2 also showed a significant increase in YB group as measured by Western Blotting. These data are the first to demonstrate the feasibility of stimulating and detecting salivary protein biomarkers in response to an acute Yoga exercise. This trial is registered with ClincalTrials.gov NCT02108769.
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19
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AGUIAR DEREK, WONG WENDYS, ISTRAIL SORIN. Tumor haplotype assembly algorithms for cancer genomics. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2014:3-14. [PMID: 24297529 PMCID: PMC4051221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The growing availability of inexpensive high-throughput sequence data is enabling researchers to sequence tumor populations within a single individual at high coverage. But, cancer genome sequence evolution and mutational phenomena like driver mutations and gene fusions are difficult to investigate without first reconstructing tumor haplotype sequences. Haplotype assembly of single individual tumor populations is an exceedingly difficult task complicated by tumor haplotype heterogeneity, tumor or normal cell sequence contamination, polyploidy, and complex patterns of variation. While computational and experimental haplotype phasing of diploid genomes has seen much progress in recent years, haplotype assembly in cancer genomes remains uncharted territory. In this work, we describe HapCompass-Tumor a computational modeling and algorithmic framework for haplotype assembly of copy number variable cancer genomes containing haplotypes at different frequencies and complex variation. We extend our polyploid haplotype assembly model and present novel algorithms for (1) complex variations, including copy number changes, as varying numbers of disjoint paths in an associated graph, (2) variable haplotype frequencies and contamination, and (3) computation of tumor haplotypes using simple cycles of the compass graph which constrain the space of haplotype assembly solutions. The model and algorithm are implemented in the software package HapCompass-Tumor which is available for download from http://www.brown.edu/Research/Istrail_Lab/.
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Affiliation(s)
- DEREK AGUIAR
- Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - WENDY S.W. WONG
- Inova Translational Medicine Institute, Inova Health Systems, Falls Church, VA 22042, USA
| | - SORIN ISTRAIL
- Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
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20
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Smith RM, Webb A, Papp AC, Newman LC, Handelman SK, Suhy A, Mascarenhas R, Oberdick J, Sadee W. Whole transcriptome RNA-Seq allelic expression in human brain. BMC Genomics 2013; 14:571. [PMID: 23968248 PMCID: PMC3765493 DOI: 10.1186/1471-2164-14-571] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/16/2013] [Indexed: 01/27/2023] Open
Abstract
Background Measuring allelic RNA expression ratios is a powerful approach for detecting cis-acting regulatory variants, RNA editing, loss of heterozygosity in cancer, copy number variation, and allele-specific epigenetic gene silencing. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying allelic expression imbalance (AEI), but numerous factors bias allelic RNA ratio measurements. Here, we compare RNA-Seq allelic ratios measured in nine different human brain regions with a highly sensitive and accurate SNaPshot measure of allelic RNA ratios, identifying factors affecting reliable allelic ratio measurement. Accounting for these factors, we subsequently surveyed the variability of RNA editing across brain regions and across individuals. Results We find that RNA-Seq allelic ratios from standard alignment methods correlate poorly with SNaPshot, but applying alternative alignment strategies and correcting for observed biases significantly improves correlations. Deploying these methods on a transcriptome-wide basis in nine brain regions from a single individual, we identified genes with AEI across all regions (SLC1A3, NHP2L1) and many others with region-specific AEI. In dorsolateral prefrontal cortex (DLPFC) tissues from 14 individuals, we found evidence for frequent regulatory variants affecting RNA expression in tens to hundreds of genes, depending on stringency for assigning AEI. Further, we find that the extent and variability of RNA editing is similar across brain regions and across individuals. Conclusions These results identify critical factors affecting allelic ratios measured by RNA-Seq and provide a foundation for using this technology to screen allelic RNA expression on a transcriptome-wide basis. Using this technology as a screening tool reveals tens to hundreds of genes harboring frequent functional variants affecting RNA expression in the human brain. With respect to RNA editing, the similarities within and between individuals leads us to conclude that this post-transcriptional process is under heavy regulatory influence to maintain an optimal degree of editing for normal biological function.
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Affiliation(s)
- Ryan M Smith
- Department of Pharmacology, Program in Pharmacogenomics; College of Medicine, The Ohio State University Wexner Medical Center, 5184A Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, USA.
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