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Swisher EM, Aghajanian C, O'Malley DM, Fleming GF, Kaufmann SH, Levine DA, Birrer MJ, Moore KN, Spirtos NM, Shahin MS, Reid TJ, Friedlander M, Steffensen KD, Okamoto A, Sehgal V, Ansell PJ, Dinh MH, Bookman MA, Coleman RL. Impact of homologous recombination status and responses with veliparib combined with first-line chemotherapy in ovarian cancer in the Phase 3 VELIA/GOG-3005 study. Gynecol Oncol 2021; 164:245-253. [PMID: 34906376 DOI: 10.1016/j.ygyno.2021.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/16/2021] [Accepted: 12/01/2021] [Indexed: 11/18/2022]
Abstract
OBJECTIVE In the Phase 3 VELIA trial (NCT02470585), PARP inhibitor (PARPi) veliparib was combined with first-line chemotherapy and continued as maintenance for patients with ovarian carcinoma enrolled regardless of chemotherapy response or biomarker status. Here, we report exploratory analyses of the impact of homologous recombination deficient (HRD) or proficient (HRP) status on progression-free survival (PFS) and objective response rates during chemotherapy. METHODS Women with Stage III-IV ovarian carcinoma were randomized to veliparib-throughout, veliparib-combination-only, or placebo. Stratification factors included timing of surgery and germline BRCA mutation status. HRD status was dichotomized at genomic instability score 33. During combination therapy, CA-125 levels were measured at baseline and each cycle; radiographic responses were assessed every 9 weeks. RESULTS Of 1140 patients randomized, 742 had BRCA wild type (BRCAwt) tumors (HRP, n = 373; HRD/BRCAwt, n = 329). PFS hazard ratios between veliparib-throughout versus control were similar in both BRCAwt populations (HRD/BRCAwt: 22.9 vs 19.8 months; hazard ratio 0.76; 95% confidence interval [CI] 0.53-1.09; HRP: 15.0 vs 11.5 months; hazard ratio 0.765; 95% CI 0.56-1.04). By Cycle 3, the proportion with ≥90% CA-125 reduction from baseline was higher in those receiving veliparib (pooled arms) versus control (34% vs 23%; P = 0.0004); particularly in BRCAwt and HRP subgroups. Complete response rates among patients with measurable disease after surgery were 24% with veliparib (pooled arms) and 18% with control. CONCLUSIONS These results potentially broaden opportunities for PARPi utilization among patients who would not qualify for frontline PARPi maintenance based on other trials.
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Affiliation(s)
- Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-6460, USA.
| | - Carol Aghajanian
- Memorial Sloan Kettering Cancer Center, 300 East 66th Street, New York, NY 10065, USA
| | - David M O'Malley
- The Ohio State University and James CCC, 460 W. 10th Avenue, Columbus, OH 43210, USA
| | - Gini F Fleming
- The University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, IL, USA
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | | | - Michael J Birrer
- Winthrop P Rockefeller Cancer Institute, 4301 W. Markham Street, Little Rock, AR 72205-7199, USA
| | - Kathleen N Moore
- Stephenson Cancer Center at the University of Oklahoma Health Sciences Center, 800 N.E. 10th Street, Oklahoma City, OK 73104, USA
| | - Nick M Spirtos
- Women's Cancer Center of Nevada, 2460 Augusta, Las Vegas NV89109, USA
| | - Mark S Shahin
- Abington Jefferson Hospital, Asplundh Cancer Center of Sidney Kimmel Cancer Center, 3941 Commerce Ave, Willow Grove, PA 19090, USA
| | - Thomas J Reid
- University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Michael Friedlander
- Prince of Wales Clinical School UNSW and Prince of Wales Hospital and ANZGOG, Corner High Street and Avoca Street, Randwick, NSW 2031, Australia
| | - Karina Dahl Steffensen
- Lillebaelt University Hospital of Southern Denmark, Winsløwparken 19, 3, DK-5000 Odense C, Vejle, Denmark
| | - Aikou Okamoto
- The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Vasudha Sehgal
- AbbVie Inc., 1 North Waukegan Road, North Chicago, IL 60064-6124, USA
| | - Peter J Ansell
- AbbVie Inc., 1 North Waukegan Road, North Chicago, IL 60064-6124, USA
| | - Minh H Dinh
- AbbVie Inc., 1 North Waukegan Road, North Chicago, IL 60064-6124, USA
| | - Michael A Bookman
- Kaiser Permanente Northern California, 2238 Geary Blvd, San Francisco, CA 94115, USA
| | - Robert L Coleman
- US Oncology Research, 9180 Pinecroft, The Woodlands, TX 77380, USA
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Perrin HJ, Currin KW, Vadlamudi S, Pandey GK, Ng KK, Wabitsch M, Laakso M, Love MI, Mohlke KL. Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci. PLoS Genet 2021; 17:e1009865. [PMID: 34699533 PMCID: PMC8570510 DOI: 10.1371/journal.pgen.1009865] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/05/2021] [Accepted: 10/07/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and mechanisms at genome-wide association study (GWAS) loci. To identify regulatory elements that display differential activity across adipocyte differentiation, we performed ATAC-seq and RNA-seq in a human cell model of preadipocytes and adipocytes at days 4 and 14 of differentiation. For comparison, we created a consensus map of ATAC-seq peaks in 11 human subcutaneous adipose tissue samples. We identified 58,387 context-dependent chromatin accessibility peaks and 3,090 context-dependent genes between all timepoint comparisons (log2 fold change>1, FDR<5%) with 15,919 adipocyte- and 18,244 preadipocyte-dependent peaks. Adipocyte-dependent peaks showed increased overlap (60.1%) with Roadmap Epigenomics adipocyte nuclei enhancers compared to preadipocyte-dependent peaks (11.5%). We linked context-dependent peaks to genes based on adipocyte promoter capture Hi-C data, overlap with adipose eQTL variants, and context-dependent gene expression. Of 16,167 context-dependent peaks linked to a gene, 5,145 were linked by two or more strategies to 1,670 genes. Among GWAS loci for cardiometabolic traits, adipocyte-dependent peaks, but not preadipocyte-dependent peaks, showed significant enrichment (LD score regression P<0.005) for waist-to-hip ratio and modest enrichment (P < 0.05) for HDL-cholesterol. We identified 659 peaks linked to 503 genes by two or more approaches and overlapping a GWAS signal, suggesting a regulatory mechanism at these loci. To identify variants that may alter chromatin accessibility between timepoints, we identified 582 variants in 454 context-dependent peaks that demonstrated allelic imbalance in accessibility (FDR<5%), of which 55 peaks also overlapped GWAS variants. At one GWAS locus for palmitoleic acid, rs603424 was located in an adipocyte-dependent peak linked to SCD and exhibited allelic differences in transcriptional activity in adipocytes (P = 0.003) but not preadipocytes (P = 0.09). These results demonstrate that context-dependent peaks and genes can guide discovery of regulatory variants at GWAS loci and aid identification of regulatory mechanisms. Cardiovascular and metabolic diseases are widespread, and an increased understanding of genetic mechanisms behind these diseases could improve treatment. Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and genetic mechanisms for disease traits. A relevant context for cardiovascular and metabolic disease traits is adipocyte differentiation. To identify regulatory elements and genes that display differences in activity during adipocyte differentiation, we profiled chromatin accessibility and gene expression in a human cell model of preadipocytes and adipocytes. We identified chromatin regions that change accessibility during differentiation and predicted genes they may affect. We also linked these chromatin regions to genetic variants associated with risk of disease. At one genomic region linked to fatty acids, a chromatin region more accessible in adipocytes linked to a fatty acid synthesis gene and exhibited allelic differences in transcriptional activity in adipocytes but not preadipocytes. These results demonstrate that chromatin regions and genes that change during cell context can guide discovery of regulatory variants and aid identification of disease mechanisms.
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Affiliation(s)
- Hannah J. Perrin
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kevin W. Currin
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Gautam K. Pandey
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kenneth K. Ng
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Ulm University Hospital, Ulm, Germany
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Michael I. Love
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Larsson AJM, Ziegenhain C, Hagemann-Jensen M, Reinius B, Jacob T, Dalessandri T, Hendriks GJ, Kasper M, Sandberg R. Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance. PLoS Comput Biol 2021; 17:e1008772. [PMID: 33690599 PMCID: PMC7978379 DOI: 10.1371/journal.pcbi.1008772] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/19/2021] [Accepted: 02/03/2021] [Indexed: 12/02/2022] Open
Abstract
Transcriptional bursts render substantial biological noise in cellular transcriptomes. Here, we investigated the theoretical extent of allelic expression resulting from transcriptional bursting and how it compared to the amount biallelic, monoallelic and allele-biased expression observed in single-cell RNA-sequencing (scRNA-seq) data. We found that transcriptional bursting can explain the allelic expression patterns observed in single cells, including the frequent observations of autosomal monoallelic gene expression. Importantly, we identified that the burst frequency largely determined the fraction of cells with monoallelic expression, whereas the burst size had little effect on monoallelic observations. The high consistency between the bursting model predictions and scRNA-seq observations made it possible to assess the heterogeneity of a group of cells as their deviation in allelic observations from the expected. Finally, both burst frequency and size contributed to allelic imbalance observations and reinforced that studies of allelic imbalance can be confounded from the inherent noise in transcriptional bursting. Altogether, we demonstrate that allele-level transcriptional bursting renders widespread, although predictable, amounts of monoallelic and biallelic expression in single cells and cell populations. Genes are transcribed into RNA and further translated into proteins. The maternal and paternal copy of each gene are typically transcribed independently, and transcription itself occur in discrete stochastic bursts (transcriptional bursts). Pioneering single-cell analysis of RNA across cells revealed abundant fluctuations in the amounts of maternal and paternal RNA in cells, with frequent observations of RNA from only the maternal or paternal gene copy (monoallelic expression). In this study, we investigated to which extent the observed monoallelic expression across single cells can be explained by transcriptional bursting. We demonstrate that the process of transcriptional bursting is sufficient to explain the amount of monoallelic expression, and we further demonstrate that the frequency of bursts mainly determines the frequency of monoallelic observations. Furthermore, we show that transcriptional bursts may lead to false positive observations of monoallelic expression across cell populations. Therefore, stochastic transcription renders large fluctuations in allelic origin of RNA in cells over time, including frequent monoallelic observations when profiling single cells.
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Affiliation(s)
- Anton J. M. Larsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tina Jacob
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Tim Dalessandri
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gert-Jan Hendriks
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria Kasper
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Lee C, Kang EY, Gandal MJ, Eskin E, Geschwind DH. Profiling allele-specific gene expression in brains from individuals with autism spectrum disorder reveals preferential minor allele usage. Nat Neurosci 2019; 22:1521-1532. [PMID: 31455884 PMCID: PMC6750256 DOI: 10.1038/s41593-019-0461-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/09/2019] [Indexed: 12/21/2022]
Abstract
One fundamental but understudied mechanism of gene regulation in disease is allele-specific expression (ASE), the preferential expression of one allele. We leveraged RNA-sequencing data from human brain to assess ASE in autism spectrum disorder (ASD). When ASE is observed in ASD, the allele with lower population frequency (minor allele) is preferentially more highly expressed than the major allele, opposite to the canonical pattern. Importantly, genes showing ASE in ASD are enriched in those downregulated in ASD postmortem brains and in genes harboring de novo mutations in ASD. Two regions, 14q32 and 15q11, containing all known orphan C/D box small nucleolar RNAs (snoRNAs), are particularly enriched in shifts to higher minor allele expression. We demonstrate that this allele shifting enhances snoRNA-targeted splicing changes in ASD-related target genes in idiopathic ASD and 15q11-q13 duplication syndrome. Together, these results implicate allelic imbalance and dysregulation of orphan C/D box snoRNAs in ASD pathogenesis.
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Affiliation(s)
- Changhoon Lee
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eun Yong Kang
- Department of Computer Science, Henry Samueli School of Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Computer Science, Henry Samueli School of Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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Gådin JR, Buil A, Colantuoni C, Jaffe AE, Nielsen J, Shin JH, Hyde TM, Kleinman JE, Plath N, Eriksson P, Brunak S, Didriksen M, Weinberger DR, Folkersen L. Comparison of quantitative trait loci methods: Total expression and allelic imbalance method in brain RNA-seq. PLoS One 2019; 14:e0217765. [PMID: 31206532 PMCID: PMC6576752 DOI: 10.1371/journal.pone.0217765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/17/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Of the 108 Schizophrenia (SZ) risk-loci discovered through genome-wide association studies (GWAS), 96 are not altering the sequence of any protein. Evidence linking non-coding risk-SNPs and genes may be established using expression quantitative trait loci (eQTL). However, other approaches such allelic expression quantitative trait loci (aeQTL) also may be of use. METHODS We applied both the eQTL and aeQTL analysis to a biobank of deeply sequenced RNA from 680 dorso-lateral pre-frontal cortex (DLPFC) samples. For each of 340 genes proximal to the SZ risk-SNPs, we asked how much SNP-genotype affected total expression (eQTL), as well as how much the expression ratio between the two alleles differed from 1:1 as a consequence of the risk-SNP genotype (aeQTL). RESULTS We analyzed overlap with comparable eQTL-findings: 16 of the 30 risk-SNPs known to have gene-level eQTL also had gene-level aeQTL effects. 6 of 21 risk-SNPs with known splice-eQTL had exon-aeQTL effects. 12 novel potential risk genes were identified with the aeQTL approach, while 55 tested SNP-pairs were found as eQTL but not aeQTL. Of the tested 108 loci we could find at least one gene to be associated with 21 of the risk-SNPs using gene-level aeQTL, and with an additional 18 risk-SNPs using exon-level aeQTL. CONCLUSION Our results suggest that the aeQTL strategy complements the eQTL approach to susceptibility gene identification.
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Affiliation(s)
- Jesper R. Gådin
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | | | - Carlo Colantuoni
- Lieber Institute for Brain Development, Baltimore, United States of America
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, Baltimore, United States of America
| | | | - Joo-Heon Shin
- Lieber Institute for Brain Development, Baltimore, United States of America
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Baltimore, United States of America
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Baltimore, United States of America
| | | | | | - Per Eriksson
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Søren Brunak
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Lasse Folkersen
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
- Roskilde Hospital, Roskilde, Denmark
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den Hollander W, Pulyakhina I, Boer C, Bomer N, van der Breggen R, Arindrarto W, Couthino de Almeida R, Lakenberg N, Sentner T, Laros JFJ, ‘t Hoen PAC, Slagboom EPE, Nelissen RGHH, van Meurs J, Ramos YFM, Meulenbelt I. Annotating Transcriptional Effects of Genetic Variants in Disease-Relevant Tissue: Transcriptome-Wide Allelic Imbalance in Osteoarthritic Cartilage. Arthritis Rheumatol 2019; 71:561-570. [PMID: 30298554 PMCID: PMC6593438 DOI: 10.1002/art.40748] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/02/2018] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Multiple single-nucleotide polymorphisms (SNPs) conferring susceptibility to osteoarthritis (OA) mark imbalanced expression of positional genes in articular cartilage, reflected by unequally expressed alleles among heterozygotes (allelic imbalance [AI]). We undertook this study to explore the articular cartilage transcriptome from OA patients for AI events to identify putative disease-driving genetic variation. METHODS AI was assessed in 42 preserved and 5 lesioned OA cartilage samples (from the Research Arthritis and Articular Cartilage study) for which RNA sequencing data were available. The count fraction of the alternative alleles among the alternative and reference alleles together (φ) was determined for heterozygous individuals. A meta-analysis was performed to generate a meta-φ and P value for each SNP with a false discovery rate (FDR) correction for multiple comparisons. To further validate AI events, we explored them as a function of multiple additional OA features. RESULTS We observed a total of 2,070 SNPs that consistently marked AI of 1,031 unique genes in articular cartilage. Of these genes, 49 were found to be significantly differentially expressed (fold change <0.5 or >2, FDR <0.05) between preserved and paired lesioned cartilage, and 18 had previously been reported to confer susceptibility to OA and/or related phenotypes. Moreover, we identified notable highly significant AI SNPs in the CRLF1, WWP2, and RPS3 genes that were related to multiple OA features. CONCLUSION We present a framework and resulting data set for researchers in the OA research field to probe for disease-relevant genetic variation that affects gene expression in pivotal disease-affected tissue. This likely includes putative novel compelling OA risk genes such as CRLF1, WWP2, and RPS3.
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Affiliation(s)
| | - Irina Pulyakhina
- Radboud University Medical Center Nijmegen, The Netherlands, and Wellcome Trust Centre for Human GeneticsOxfordUK
| | - Cindy Boer
- Erasmus Medical CenterRotterdamThe Netherlands
| | - Nils Bomer
- Leiden University Medical CenterLeidenThe Netherlands
| | | | | | | | | | - Thom Sentner
- Leiden University Medical CenterLeidenThe Netherlands
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7
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Falkenberg KD, Braverman NE, Moser AB, Steinberg SJ, Klouwer FCC, Schlüter A, Ruiz M, Pujol A, Engvall M, Naess K, van Spronsen F, Körver-Keularts I, Rubio-Gozalbo ME, Ferdinandusse S, Wanders RJA, Waterham HR. Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder. Am J Hum Genet 2017; 101:965-976. [PMID: 29220678 DOI: 10.1016/j.ajhg.2017.11.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/14/2017] [Indexed: 01/14/2023] Open
Abstract
Zellweger spectrum disorders (ZSDs) are autosomal-recessive disorders that are caused by defects in peroxisome biogenesis due to bi-allelic mutations in any of 13 different PEX genes. Here, we identified seven unrelated individuals affected with an apparent dominant ZSD in whom a heterozygous mutant PEX6 allele (c.2578C>T [p.Arg860Trp]) was overrepresented due to allelic expression imbalance (AEI). We demonstrated that AEI of PEX6 is a common phenomenon and is correlated with heterozygosity for a frequent variant in the 3' untranslated region (UTR) of the mutant allele, which disrupts the most distal of two polyadenylation sites. Asymptomatic parents, who were heterozygous for PEX c.2578C>T, did not show AEI and were homozygous for the 3' UTR variant. Overexpression models confirmed that the overrepresentation of the pathogenic PEX6 c.2578T variant compared to wild-type PEX6 c.2578C results in a peroxisome biogenesis defect and thus constitutes the cause of disease in the affected individuals. AEI promoting the overrepresentation of a mutant allele might also play a role in other autosomal-recessive disorders, in which only one heterozygous pathogenic variant is identified.
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Affiliation(s)
- Kim D Falkenberg
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Nancy E Braverman
- Department of Pediatrics and Human Genetics, Research Institute of the McGill University Health Center and McGill University, Montreal, QC H4A 3J1, Canada
| | - Ann B Moser
- Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Steven J Steinberg
- Institute of Genetic Medicine and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Femke C C Klouwer
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Pediatric Neurology, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, Barcelona 08908, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Valencia 46010, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, Barcelona 08908, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Valencia 46010, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, Barcelona 08908, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Valencia 46010, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Martin Engvall
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 171 77, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 76, Sweden
| | - Karin Naess
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 171 77, Sweden; Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 171 77, Sweden
| | - FrancJan van Spronsen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen 9700 RB, the Netherlands
| | - Irene Körver-Keularts
- Department of Pediatrics, Maastricht University Medical Center, Maastricht 6211 LK, the Netherlands
| | - M Estela Rubio-Gozalbo
- Department of Pediatrics, Maastricht University Medical Center, Maastricht 6211 LK, the Netherlands; Laboratory Genetic Metabolic Diseases, Maastricht University Medical Center, Maastricht 6211 LK, the Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
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Li J, Woods SL, Healey S, Beesley J, Chen X, Lee JS, Sivakumaran H, Wayte N, Nones K, Waterfall JJ, Pearson J, Patch AM, Senz J, Ferreira MA, Kaurah P, Mackenzie R, Heravi-Moussavi A, Hansford S, Lannagan TRM, Spurdle AB, Simpson PT, da Silva L, Lakhani SR, Clouston AD, Bettington M, Grimpen F, Busuttil RA, Di Costanzo N, Boussioutas A, Jeanjean M, Chong G, Fabre A, Olschwang S, Faulkner GJ, Bellos E, Coin L, Rioux K, Bathe OF, Wen X, Martin HC, Neklason DW, Davis SR, Walker RL, Calzone KA, Avital I, Heller T, Koh C, Pineda M, Rudloff U, Quezado M, Pichurin PN, Hulick PJ, Weissman SM, Newlin A, Rubinstein WS, Sampson JE, Hamman K, Goldgar D, Poplawski N, Phillips K, Schofield L, Armstrong J, Kiraly-Borri C, Suthers GK, Huntsman DG, Foulkes WD, Carneiro F, Lindor NM, Edwards SL, French JD, Waddell N, Meltzer PS, Worthley DL, Schrader KA, Chenevix-Trench G. Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. Am J Hum Genet 2016; 98:830-842. [PMID: 27087319 DOI: 10.1016/j.ajhg.2016.03.001] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/02/2016] [Indexed: 12/15/2022] Open
Abstract
Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is an autosomal-dominant cancer-predisposition syndrome with a significant risk of gastric, but not colorectal, adenocarcinoma. We mapped the gene to 5q22 and found loss of the wild-type allele on 5q in fundic gland polyps from affected individuals. Whole-exome and -genome sequencing failed to find causal mutations but, through Sanger sequencing, we identified point mutations in APC promoter 1B that co-segregated with disease in all six families. The mutations reduced binding of the YY1 transcription factor and impaired activity of the APC promoter 1B in luciferase assays. Analysis of blood and saliva from carriers showed allelic imbalance of APC, suggesting that these mutations lead to decreased allele-specific expression in vivo. Similar mutations in APC promoter 1B occur in rare families with familial adenomatous polyposis (FAP). Promoter 1A is methylated in GAPPS and sporadic FGPs and in normal stomach, which suggests that 1B transcripts are more important than 1A in gastric mucosa. This might explain why all known GAPPS-affected families carry promoter 1B point mutations but only rare FAP-affected families carry similar mutations, the colonic cells usually being protected by the expression of the 1A isoform. Gastric polyposis and cancer have been previously described in some FAP-affected individuals with large deletions around promoter 1B. Our finding that GAPPS is caused by point mutations in the same promoter suggests that families with mutations affecting the promoter 1B are at risk of gastric adenocarcinoma, regardless of whether or not colorectal polyps are present.
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Affiliation(s)
- Jun Li
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Susan L Woods
- School of Medicine, University of Adelaide and Cancer Theme, SAHMRI, Adelaide, SA 5000, Australia
| | - Sue Healey
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Xiaoqing Chen
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Jason S Lee
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Haran Sivakumaran
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Nicci Wayte
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Katia Nones
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Joshua J Waterfall
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - John Pearson
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Anne-Marie Patch
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Janine Senz
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Manuel A Ferreira
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Pardeep Kaurah
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Robertson Mackenzie
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | | | - Samantha Hansford
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Tamsin R M Lannagan
- School of Medicine, University of Adelaide and Cancer Theme, SAHMRI, Adelaide, SA 5000, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Peter T Simpson
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; School of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Leonard da Silva
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; School of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Sunil R Lakhani
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; School of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia; Anatomical Pathology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029, Australia
| | - Andrew D Clouston
- Centre for Liver Disease Research, TRI Building, University of Queensland, Woolloongabba, QLD 4102, Australia; Envoi Specialist Pathologists, Bishop Street, Kelvin Grove, QLD 4059, Australia
| | - Mark Bettington
- School of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia; Envoi Specialist Pathologists, Bishop Street, Kelvin Grove, QLD 4059, Australia; The Conjoint Gastroenterology Laboratory, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Florian Grimpen
- Departments of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Brisbane, QLD 4006, Australia
| | - Rita A Busuttil
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, Melbourne, VIC 8006, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Natasha Di Costanzo
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, Melbourne, VIC 8006, Australia
| | - Alex Boussioutas
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, Melbourne, VIC 8006, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Marie Jeanjean
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - George Chong
- Molecular Pathology Centre, Department of Pathology, Jewish General Hospital - McGill University, Montreal, QC H3T 1E2, Canada
| | - Aurélie Fabre
- AP-HM Timone, Medical Genetics Department, 13385 Marseille, France; Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385 Marseille, France; Oncology Unit, Generale de Sante, Clairval Hospital, 13009 Marseille, France
| | - Sylviane Olschwang
- AP-HM Timone, Medical Genetics Department, 13385 Marseille, France; Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385 Marseille, France; Oncology Unit, Generale de Sante, Clairval Hospital, 13009 Marseille, France
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Evangelos Bellos
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; Department of Genomics of Common Disease, Imperial College London, London W12 0NN, UK
| | - Lachlan Coin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kevin Rioux
- Department of Medicine, Division of Gastroenterology, Department of Microbiology and Infectious Diseases, Gastrointestinal Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Oliver F Bathe
- Departments of Surgery and Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada; Division of Surgical Oncology, Tom Baker Cancer Centre, 1331 29(th) St NW, Calgary, AB T2N 4N1, Canada
| | - Xiaogang Wen
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP)/Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; Centro Hospitalar Vila Nova de Gaia/Espinho, Porto 4430-027, Portugal
| | - Hilary C Martin
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Deborah W Neklason
- Department of Internal Medicine, Huntsman Cancer Institute at University of Utah, Salt Lake City, UT 84112, USA
| | - Sean R Davis
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Robert L Walker
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Kathleen A Calzone
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Itzhak Avital
- Department of Surgery, Saint Peter's University Hospital, Rutgers University, New Brunswick, NJ 08901, USA
| | - Theo Heller
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Disease (NIDDK), NIH, Bethesda, MD 20892, USA
| | - Christopher Koh
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Disease (NIDDK), NIH, Bethesda, MD 20892, USA
| | - Marbin Pineda
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Udo Rudloff
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Pavel N Pichurin
- Department of Medical Genetics, Mayo Clinic, Rochester, MN 55905, USA
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | | | - Anna Newlin
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Wendy S Rubinstein
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), NIH, Bethesda, MD 20892, USA
| | - Jone E Sampson
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kelly Hamman
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - David Goldgar
- Department of Dermatology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nicola Poplawski
- Adult Genetics Unit, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA 5006, Australia; University Department of Paediatrics, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kerry Phillips
- Adult Genetics Unit, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA 5006, Australia; University Department of Paediatrics, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lyn Schofield
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA 6008, Australia
| | - Jacqueline Armstrong
- Adult Genetics Unit, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA 6008, Australia
| | - Graeme K Suthers
- University Department of Paediatrics, University of Adelaide, Adelaide, SA 5005, Australia
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC V6Z 2K5, Canada
| | - William D Foulkes
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Fatima Carneiro
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP)/Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; Medical Faculty of the University of Porto/Centro Hospitalar São João, Porto 4200-319, Portugal
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Stacey L Edwards
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Juliet D French
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Daniel L Worthley
- School of Medicine, University of Adelaide and Cancer Theme, SAHMRI, Adelaide, SA 5000, Australia
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia.
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9
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Halabi NM, Martinez A, Al-Farsi H, Mery E, Puydenus L, Pujol P, Khalak HG, McLurcan C, Ferron G, Querleu D, Al-Azwani I, Al-Dous E, Mohamoud YA, Malek JA, Rafii A. Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer. PLoS Genet 2016; 12:e1005755. [PMID: 26735499 PMCID: PMC4703369 DOI: 10.1371/journal.pgen.1005755] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 11/30/2015] [Indexed: 01/24/2023] Open
Abstract
Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. Identifying genes that contribute to cancer biology is complicated partly because cancers can have dozens of somatic mutations and thousands of germline variants. Somatic mutations are gene variants that arise after conception in an organism while germline variants are gene variants present at conception in an organism. Most methods to identify cancer drivers have focused on determining somatic mutations. In this study we attempt to identify, from a tumor sample, important germline and somatic variants by determining if a variant is expressed (made into RNA) more than expected from the amount of the variant in the genome. The preferred expression of a variant could benefit cancer cells. When applying our analysis to ovarian cancer samples we found that despite the apparent heterogeneity, different patients frequently share the same genes with preferentially expressed variants. These genes in many cases are known to affect cancer processes such as DNA repair, cell adhesion and cell signaling and are targetable with known drugs. We therefore conclude that our analysis can identify germline and somatic gene variants that contribute to cancer biology and can potentially guide individualized therapies.
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Affiliation(s)
- Najeeb M. Halabi
- Department of Genetic Medicine, Weill-Cornell Medical College, New York, United States of America
| | | | - Halema Al-Farsi
- Department of Genetic Medicine, Weill-Cornell Medical College, New York, United States of America
| | - Eliane Mery
- Pathology Department, Institute Claudius Regaud, Toulouse, France
| | | | - Pascal Pujol
- Oncogenetics, Centre Hospitalier Regional Universitaire de Montpellier, Montpellier, France
| | - Hanif G. Khalak
- Advanced Computing, Weill-Cornell Medical College in Qatar, Doha, Qatar
| | - Cameron McLurcan
- Biosciences Department, University of Birmingham, Birmingham, United Kingdom
| | - Gwenael Ferron
- Surgery Department, Institute Claudius Regaud, Toulouse, France
| | - Denis Querleu
- Surgery Department, Institute Claudius Regaud, Toulouse, France
| | - Iman Al-Azwani
- Genomics Core, Weill-Cornell Medical in Qatar, Doha, Qatar
| | - Eman Al-Dous
- Genomics Core, Weill-Cornell Medical in Qatar, Doha, Qatar
| | | | - Joel A. Malek
- Department of Genetic Medicine, Weill-Cornell Medical College, New York, United States of America
- Genomics Core, Weill-Cornell Medical in Qatar, Doha, Qatar
| | - Arash Rafii
- Department of Genetic Medicine, Weill-Cornell Medical College, New York, United States of America
- Stem Cells and Microenvironment Laboratory, Weill-Cornell Medical College in Qatar, Doha, Qatar
- * E-mail:
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10
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Xia R, Vattathil S, Scheet P. Identification of allelic imbalance with a statistical model for subtle genomic mosaicism. PLoS Comput Biol 2014; 10:e1003765. [PMID: 25166618 PMCID: PMC4148184 DOI: 10.1371/journal.pcbi.1003765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/22/2014] [Indexed: 11/18/2022] Open
Abstract
Genetic heterogeneity in a mixed sample of tumor and normal DNA can confound characterization of the tumor genome. Numerous computational methods have been proposed to detect aberrations in DNA samples from tumor and normal tissue mixtures. Most of these require tumor purities to be at least 10-15%. Here, we present a statistical model to capture information, contained in the individual's germline haplotypes, about expected patterns in the B allele frequencies from SNP microarrays while fully modeling their magnitude, the first such model for SNP microarray data. Our model consists of a pair of hidden Markov models--one for the germline and one for the tumor genome--which, conditional on the observed array data and patterns of population haplotype variation, have a dependence structure induced by the relative imbalance of an individual's inherited haplotypes. Together, these hidden Markov models offer a powerful approach for dealing with mixtures of DNA where the main component represents the germline, thus suggesting natural applications for the characterization of primary clones when stromal contamination is extremely high, and for identifying lesions in rare subclones of a tumor when tumor purity is sufficient to characterize the primary lesions. Our joint model for germline haplotypes and acquired DNA aberration is flexible, allowing a large number of chromosomal alterations, including balanced and imbalanced losses and gains, copy-neutral loss-of-heterozygosity (LOH) and tetraploidy. We found our model (which we term J-LOH) to be superior for localizing rare aberrations in a simulated 3% mixture sample. More generally, our model provides a framework for full integration of the germline and tumor genomes to deal more effectively with missing or uncertain features, and thus extract maximal information from difficult scenarios where existing methods fail.
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Affiliation(s)
- Rui Xia
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, United States of America
- * E-mail:
| | - Selina Vattathil
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Human & Molecular Genetics Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, United States of America
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, United States of America
- Human & Molecular Genetics Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, United States of America
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11
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Czarnecka KH, Migdalska-Sęk M, Antczak A, Pastuszak-Lewandoska D, Kordiak J, Nawrot E, Domańska D, Kaleta D, Górski P, Brzeziańska EB. Allelic imbalance in 1p, 7q, 9p, 11p, 12q and 16q regions in non-small cell lung carcinoma and its clinical association: a pilot study. Mol Biol Rep 2013; 40:6671-84. [PMID: 24091944 PMCID: PMC3835956 DOI: 10.1007/s11033-013-2782-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 09/14/2013] [Indexed: 11/29/2022]
Abstract
In lung cancer pathogenesis, genetic instability, i.e., loss of heterozygosity (LOH) and microsatellite instability (MSI) is a frequent molecular event, occurring at an early stage of cancerogenesis. The presence of LOH/MSI in non-small cell lung carcinoma (NSCLC) was found in many chromosomal regions, but exclusive of 3p their diagnostic value remains controversial. In this study we focused on other than 3p regions-1p31.2, 7q32.2, 9p21.3, 11p15.5, 12q23.2 and 16q22-the loci of many oncogenes and tumour suppressor genes. To analyze the potential role of LOH/MSI involved in NSCLC pathogenesis we allelotyped a panel of 13 microsatellite markers in a group of 56 cancer specimens. Our data demonstrate the presence of allelic loss for all (13) analyzed markers. Total LOH/MSI frequency in NSCLC was the highest for chromosomal region 11p15.5 (25.84 %), followed by 9p21.3 and 1p31.2 (19.87 and 16.67 % respectively). A statistically significant increase of total LOH/MSI frequency was detected for the 11p15.5 region (p = 0.0301; χ(2) test). The associations of total LOH/MSI frequency: 1) increase in 11p15.5 region (p = 0.047; χ(2) test) and 2) decrease in 7q32.2 region (p = 0.037; χ(2) test) have been statistically significant in AJCC III (American Joint Committee on Cancer Staging). In Fractional Allele Loss (FAL) index analysis, the correlation with cigarette addiction has been statistically significant. The increased amount of cigarettes smoked (pack years) in a lifetime correlates with increasing FAL (p = 0.024; Kruskal-Wallis test). These results demonstrate that LOH/MSI alternation in studied chromosomal regions is strongly influenced by tobacco smoking but do not seem to be pivotal NSCLC diagnostic marker with prognostic impact.
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Affiliation(s)
- Karolina H. Czarnecka
- Department of Molecular Bases of Medicine, Medical University of Lodz, Pomorska Str. 251, 92-213 Łódź, Poland
| | - Monika Migdalska-Sęk
- Department of Molecular Bases of Medicine, Medical University of Lodz, Pomorska Str. 251, 92-213 Łódź, Poland
| | - Adam Antczak
- Department of General and Oncological Pneumology, Medical University of Lodz, Kopcińskiego 22, 90-153 Łódź, Poland
| | - Dorota Pastuszak-Lewandoska
- Department of Molecular Bases of Medicine, Medical University of Lodz, Pomorska Str. 251, 92-213 Łódź, Poland
| | - Jacek Kordiak
- Department of Thoracic Surgery, General and Oncologic Surgery, Medical University of Lodz, Żeromskiego 113, 90-710 Łódź, Poland
| | - Ewa Nawrot
- Department of Molecular Bases of Medicine, Medical University of Lodz, Pomorska Str. 251, 92-213 Łódź, Poland
| | - Daria Domańska
- Department of Molecular Bases of Medicine, Medical University of Lodz, Pomorska Str. 251, 92-213 Łódź, Poland
| | - Dorota Kaleta
- Department of Preventive Medicine, Medical University of Lodz, Żeligowskiego 7/9, 90-643 Łódź, Poland
| | - Paweł Górski
- Department of Pneumology and Allergology, Medical University of Lodz, Kopcińskiego 22, 90-153 Łódź, Poland
| | - Ewa Barbara Brzeziańska
- Department of Molecular Bases of Medicine, Medical University of Lodz, Pomorska Str. 251, 92-213 Łódź, Poland
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12
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Piazza R, Magistroni V, Pirola A, Redaelli S, Spinelli R, Redaelli S, Galbiati M, Valletta S, Giudici G, Cazzaniga G, Gambacorti-Passerini C. CEQer: a graphical tool for copy number and allelic imbalance detection from whole-exome sequencing data. PLoS One 2013; 8:e74825. [PMID: 24124457 PMCID: PMC3790773 DOI: 10.1371/journal.pone.0074825] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 08/06/2013] [Indexed: 11/24/2022] Open
Abstract
Copy number alterations (CNA) are common events occurring in leukaemias and solid tumors. Comparative Genome Hybridization (CGH) is actually the gold standard technique to analyze CNAs; however, CGH analysis requires dedicated instruments and is able to perform only low resolution Loss of Heterozygosity (LOH) analyses. Here we present CEQer (Comparative Exome Quantification analyzer), a new graphical, event-driven tool for CNA/allelic-imbalance (AI) coupled analysis of exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. This data is used to build mixed statistical/heuristic models allowing the identification of CNA/AI events. To test our tool, we initially used in silico generated data, then we performed whole-exome sequencing from 20 leukemic specimens and corresponding matched controls and we analyzed the results using CEQer. Taken globally, these analyses showed that the combined use of comparative digital exon quantification and LOH/AI allows generating very accurate CNA data. Therefore, we propose CEQer as an efficient, robust and user-friendly graphical tool for the identification of CNA/AI in the context of whole-exome sequencing data.
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Affiliation(s)
- Rocco Piazza
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
- * E-mail:
| | - Vera Magistroni
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Alessandra Pirola
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Sara Redaelli
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Roberta Spinelli
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Serena Redaelli
- Department of Neurosciences and Biomedical Technologies, University of Milano-Bicocca, Monza, Italy
| | - Marta Galbiati
- Tettamanti Research Center, University of Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Simona Valletta
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Giovanni Giudici
- Tettamanti Research Center, University of Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Giovanni Cazzaniga
- Tettamanti Research Center, University of Milano-Bicocca, San Gerardo Hospital, Monza, Italy
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Costa-Guda J, Imanishi Y, Palanisamy N, Kawamata N, Phillip Koeffler H, Chaganti RSK, Arnold A. Allelic imbalance in sporadic parathyroid carcinoma and evidence for its de novo origins. Endocrine 2013; 44:489-95. [PMID: 23435613 PMCID: PMC3683451 DOI: 10.1007/s12020-013-9903-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 02/07/2013] [Indexed: 12/26/2022]
Abstract
Parathyroid cancer is a rare, clinically aggressive cause of primary hyperparathyroidism, and whether these malignancies generally evolve from pre-existing benign adenomas or arise de novo is unclear. Furthermore, while inactivation of the CDC73 (HRPT2) tumor suppressor gene, encoding parafibromin, is a major contributor, other genes essential to parathyroid carcinogenesis remain unknown. We sought to identify genomic regions potentially harboring such oncogenes or tumor suppressor genes, and to gain insight into the origins and molecular relationship of malignant versus benign parathyroid tumors. We performed genome-wide copy-number and loss of heterozygosity analysis using Affymetrix 50K SNP mapping arrays and/or comparative genomic hybridization on 16 primary parathyroid carcinomas, local recurrences or distant metastases, and matched normal controls, from 10 individuals. Recurrent regions of allelic loss were observed on chromosomes 1p, 3, and 13q suggesting that key parathyroid tumor suppressor genes are located in these chromosomal locations. Recurrent allelic gains were seen on chromosomes 1q and 16, suggesting the presence of parathyroid oncogenes on these chromosomes. Importantly, the most common alteration in benign parathyroid adenomas, loss of 11q, was not found as a recurrent change in the malignant parathyroid tissues. Molecular allelotyping using highly polymorphic microsatellite markers provided further confirmation that the prevalence of 11q loss is markedly and significantly lower in carcinomas as compared with adenomas. Our observations provide molecular support for the concept that sporadic parathyroid cancer usually arises de novo, rather than evolving from a pre-existing typical benign adenoma. Furthermore, these results help direct future investigation to ultimately determine which of the candidate genes in these chromosomal locations make significant contributions to the molecular pathogenesis of parathyroid cancer.
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Nemtsova MV, Bykov II, Udilova AA, Zaletaev DV, Khorobrykh TV. [Allelic imbalance of loci 17p13.1 (TP53), 1p36.1 (RUNX3), 16p22 (CDH1) and microsatellite instability in gastric cancer]. Mol Biol (Mosk) 2013; 47:835-841. [PMID: 25509356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We examined allelic imbalance (AI) on loci 17p13.1 (TP53), 1p36.1 (RUNX) and 16p22 (CDHI) and microsatellite instability (MI) with BAT26 in 78 patients with gastric cancer. We have shown a significant difference in the frequency of allelic imbalance of the studied loci among different types of gastric cancer. Frequency of AI in 16p22.1 (CDH1) (p = 0.023), 17p13.1 (TP53) (p = 0.038), microsatellite instability (p = 0.047) and AD two and more loci in a single sample (p = 0.0176) was significantly higher in the intestinal type of gastric cancer than in the diffuse type. We have shown, that, frequency of AI in 16p22.1 (CDH1), and AD two and more loci in a single sample, was higher in thetumors with high or moderate type of tumor cells differentiation (p = 0.0414, p = 0.0057 respectively). We found no significant differences in the groups with metastases in regional lymph nodes, different tumor stage, localization of tumors and the generalization process.
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Syddall CM, Reynard LN, Young DA, Loughlin J. The identification of trans-acting factors that regulate the expression of GDF5 via the osteoarthritis susceptibility SNP rs143383. PLoS Genet 2013; 9:e1003557. [PMID: 23825960 PMCID: PMC3694828 DOI: 10.1371/journal.pgen.1003557] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 04/24/2013] [Indexed: 02/03/2023] Open
Abstract
rs143383 is a C to T transition SNP located in the 5′untranslated region (5′UTR) of the growth differentiation factor 5 gene GDF5. The T allele of the SNP is associated with increased risk of osteoarthritis (OA) in Europeans and in Asians. This susceptibility is mediated by the T allele producing less GDF5 transcript relative to the C allele, a phenomenon known as differential allelic expression (DAE). The aim of this study was to identify trans-acting factors that bind to rs143383 and which regulate this GDF5 DAE. Protein binding to the gene was investigated by two experimental approaches: 1) competition and supershift electrophoretic mobility shift assays (EMSAs) and 2) an oligonucleotide pull down assay followed by quantitative mass spectrometry. Binding was then confirmed in vivo by chromatin immunoprecipitation (ChIP), and the functional effects of candidate proteins investigated by RNA interference (RNAi) and over expression. Using these approaches the trans-acting factors Sp1, Sp3, P15, and DEAF-1 were identified as interacting with the GDF5 5′UTR. Knockdown and over expression of the factors demonstrated that Sp1, Sp3, and DEAF-1 are repressors of GDF5 expression. Depletion of DEAF-1 modulated the DAE of GDF5 and this differential allelic effect was confirmed following over expression, with the rs143383 T allele being repressed to a significantly greater extent than the rs143383 C allele. In combination, Sp1 and DEAF-1 had the greatest repressive activity. In conclusion, we have identified four trans-acting factors that are binding to GDF5, three of which are modulating GDF5 expression via the OA susceptibility locus rs143383. GDF5 is an important growth factor that plays a vital role in the development and repair of articulating joints. rs143383 is a polymorphism within the regulatory region of the GDF5 gene and has two allelic forms, C and T. Genetic studies have demonstrated that the T allele is associated with an increased risk of osteoarthritis in a range of ethnic populations whilst previous functional studies revealed that this allele mediates its effect by producing less GDF5 transcript than the C allele. In this study, we sought to identify transcription factors that are binding to rs143383 and that are responsible for mediating this differential level of expression. Using two different approaches we have identified four factors and our functional studies have revealed that three of these factors repress GDF5 expression and that DEAF-1 modulates the differential expression of the two rs143383 alleles. The factors that we have identified could serve as novel therapeutic targets, with their depletion restoring the expression levels of GDF5 in patients with the osteoarthritis susceptibility T allele. The relevance of our results extends beyond osteoarthritis, since the T allele of rs143383 is also a risk factor for a number of other musculoskeletal diseases.
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Affiliation(s)
- Catherine M. Syddall
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Louise N. Reynard
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David A. Young
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John Loughlin
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
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Luca F, Di Rienzo A. Allelic imbalance assays to quantify allele-specific gene expression and transcription factor binding. Methods Mol Biol 2013; 1015:201-211. [PMID: 23824858 DOI: 10.1007/978-1-62703-435-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A growing number of noncoding variants are found to influence the susceptibility to common diseases and interindividual variation in drug response. However, the mechanisms by which noncoding variation affects cellular and clinical phenotypes remain to be elucidated. Allele-specific assays allow testing directly the differential properties of the alleles at a regulatory variant, which are detected as an allelic imbalance. Two widely used allelic imbalance assays target cDNA and DNA from chromatin immunoprecipitation (ChIP) experiments, and therefore revealing allele-specific gene expression and transcription factor binding, respectively. The throughput of allelic imbalance assays ranges from single variant to the genome scale, which are made possible by the recent advances in genotyping and sequencing technologies (e.g., genome-wide quantitative cDNA genotyping, ChIP-seq).
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Affiliation(s)
- Francesca Luca
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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Massouras A, Waszak SM, Albarca-Aguilera M, Hens K, Holcombe W, Ayroles JF, Dermitzakis ET, Stone EA, Jensen JD, Mackay TFC, Deplancke B. Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS Genet 2012. [PMID: 23189034 PMCID: PMC3499359 DOI: 10.1371/journal.pgen.1003055] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Understanding the relationship between genetic and phenotypic variation is one of the great outstanding challenges in biology. To meet this challenge, comprehensive genomic variation maps of human as well as of model organism populations are required. Here, we present a nucleotide resolution catalog of single-nucleotide, multi-nucleotide, and structural variants in 39 Drosophila melanogaster Genetic Reference Panel inbred lines. Using an integrative, local assembly-based approach for variant discovery, we identify more than 3.6 million distinct variants, among which were more than 800,000 unique insertions, deletions (indels), and complex variants (1 to 6,000 bp). While the SNP density is higher near other variants, we find that variants themselves are not mutagenic, nor are regions with high variant density particularly mutation-prone. Rather, our data suggest that the elevated SNP density around variants is mainly due to population-level processes. We also provide insights into the regulatory architecture of gene expression variation in adult flies by mapping cis-expression quantitative trait loci (cis-eQTLs) for more than 2,000 genes. Indels comprise around 10% of all cis-eQTLs and show larger effects than SNP cis-eQTLs. In addition, we identified two-fold more gene associations in males as compared to females and found that most cis-eQTLs are sex-specific, revealing a partial decoupling of the genomic architecture between the sexes as well as the importance of genetic factors in mediating sex-biased gene expression. Finally, we performed RNA-seq-based allelic expression imbalance analyses in the offspring of crosses between sequenced lines, which revealed that the majority of strong cis-eQTLs can be validated in heterozygous individuals. One of the principal challenges in current biology is to understand the relationship between genetic and phenotypic variation. The increasing availability of genomic variation maps of human as well as of model organism populations (mouse and Arabidopsis) constitutes an important step towards meeting this challenge. However, despite its excellent track record as a premier model to understand genome function, no genome-wide variation data beyond single-nucleotide variants and microsatellites are currently available for D. melanogaster. Here, we present a comprehensive, nucleotide-resolution catalogue of variants of various types (single-nucleotide, multi-nucleotide, and structural variants) for 39 wild-derived inbred D. melanogaster lines based on high-throughput sequencing. This catalogue confirms that non–SNP variants account for more than half of genomic variation, allowing us to provide new insights into the non-random distribution of variants in the Drosophila genome. We further present genome-wide cis-associations with gene expression based on whole adult fly microarray data, revealing significant associations for about 2,000 genes. Most associations are sex-specific, providing evidence for a decoupling of the genomic, regulatory architecture between males and females.
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Affiliation(s)
- Andreas Massouras
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sebastian M. Waszak
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Monica Albarca-Aguilera
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Korneel Hens
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Wiebke Holcombe
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien F. Ayroles
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Eric A. Stone
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jeffrey D. Jensen
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Trudy F. C. Mackay
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- * E-mail:
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Lefebvre JF, Vello E, Ge B, Montgomery SB, Dermitzakis ET, Pastinen T, Labuda D. Genotype-based test in mapping cis-regulatory variants from allele-specific expression data. PLoS One 2012; 7:e38667. [PMID: 22685595 PMCID: PMC3369843 DOI: 10.1371/journal.pone.0038667] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 05/13/2012] [Indexed: 12/20/2022] Open
Abstract
Identifying and understanding the impact of gene regulatory variation is of considerable importance in evolutionary and medical genetics; such variants are thought to be responsible for human-specific adaptation and to have an important role in genetic disease. Regulatory variation in cis is readily detected in individuals showing uneven expression of a transcript from its two allelic copies, an observation referred to as allelic imbalance (AI). Identifying individuals exhibiting AI allows mapping of regulatory DNA regions and the potential to identify the underlying causal genetic variant(s). However, existing mapping methods require knowledge of the haplotypes, which make them sensitive to phasing errors. In this study, we introduce a genotype-based mapping test that does not require haplotype-phase inference to locate regulatory regions. The test relies on partitioning genotypes of individuals exhibiting AI and those not expressing AI in a 2×3 contingency table. The performance of this test to detect linkage disequilibrium (LD) between a potential regulatory site and a SNP located in this region was examined by analyzing the simulated and the empirical AI datasets. In simulation experiments, the genotype-based test outperforms the haplotype-based tests with the increasing distance separating the regulatory region from its regulated transcript. The genotype-based test performed equally well with the experimental AI datasets, either from genome-wide cDNA hybridization arrays or from RNA sequencing. By avoiding the need of haplotype inference, the genotype-based test will suit AI analyses in population samples of unknown haplotype structure and will additionally facilitate the identification of cis-regulatory variants that are located far away from the regulated transcript.
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Affiliation(s)
- Jean Francois Lefebvre
- Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Emilio Vello
- Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Bing Ge
- McGill University and Genome Québec Innovation Centre, Montréal, Québec, Canada
| | - Stephen B. Montgomery
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Tomi Pastinen
- McGill University and Genome Québec Innovation Centre, Montréal, Québec, Canada
- Department of Human Genetics, McGill University Health Centre, McGill University, Montréal, Québec, Canada
- Department of Medical Genetics, McGill University Health Centre, McGill University, Montréal, Québec, Canada
| | - Damian Labuda
- Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
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Tang F, Barbacioru C, Nordman E, Bao S, Lee C, Wang X, Tuch BB, Heard E, Lao K, Surani MA. Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS One 2011; 6:e21208. [PMID: 21731673 PMCID: PMC3121735 DOI: 10.1371/journal.pone.0021208] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 05/23/2011] [Indexed: 01/14/2023] Open
Abstract
Stochastic and deterministic allele specific gene expression (ASE) might influence single cell phenotype, but the extent and nature of the phenomenon at the onset of early mouse development is unknown. Here we performed single cell RNA-Seq analysis of single blastomeres of mouse embryos, which revealed significant changes in the transcriptome. Importantly, over half of the transcripts with detectable genetic polymorphisms exhibit ASE, most notably, individual blastomeres from the same two-cell embryo show similar pattern of ASE. However, about 6% of them exhibit stochastic expression, indicated by altered expression ratio between the two alleles. Thus, we demonstrate that ASE is both deterministic and stochastic in early blastomeres. Furthermore, we also found that 1,718 genes express two isoforms with different lengths of 3'UTRs, with the shorter one on average 5-6 times more abundant in early blastomeres compared to the transcripts in epiblast cells, suggesting that microRNA mediated regulation of gene expression acquires increasing importance as development progresses.
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Affiliation(s)
- Fuchou Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
- Biodynamic Optical Imaging Center, School of Life Sciences, Peking University, Beijing, China
| | - Catalin Barbacioru
- Genetic Systems, Applied Biosystems, Life Technologies, Foster City, California, United States of America
| | - Ellen Nordman
- Genetic Systems, Applied Biosystems, Life Technologies, Foster City, California, United States of America
| | - Siqin Bao
- Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
| | - Caroline Lee
- Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
| | - Xiaohui Wang
- Genetic Systems, Applied Biosystems, Life Technologies, Foster City, California, United States of America
| | - Brian B. Tuch
- Genetic Systems, Applied Biosystems, Life Technologies, Foster City, California, United States of America
| | - Edith Heard
- CNRS UMR3215, INSERM U934, Institut Curie, Paris, France
| | - Kaiqin Lao
- Genetic Systems, Applied Biosystems, Life Technologies, Foster City, California, United States of America
- * E-mail: (MAS); (KL)
| | - M. Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (MAS); (KL)
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Hashemi J, Worrall C, Vasilcanu D, Fryknäs M, Sulaiman L, Karimi M, Weng WH, Lui WO, Rudduck C, Axelson M, Jernberg-Wiklund H, Girnita L, Larsson O, Larsson C. Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP). PLoS One 2011; 6:e14757. [PMID: 21423728 PMCID: PMC3056661 DOI: 10.1371/journal.pone.0014757] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 02/06/2011] [Indexed: 11/18/2022] Open
Abstract
Background Picropodophyllin (PPP) is a promising novel anti-neoplastic agent that efficiently kills tumor cells in vitro and causes tumor regression and increased survival in vivo. We have previously reported that PPP treatment induced moderate tolerance in two out of 10 cell lines only, and here report the acquired genomic and expression alterations associated with PPP selection over 1.5 years of treatment. Methodology/Principal Findings Copy number alterations monitored using metaphase and array-based comparative genomic hybridization analyses revealed largely overlapping alterations in parental and maximally tolerant cells. Gain/ amplification of the MYC and PVT1 loci in 8q24.21 were verified on the chromosome level. Abnormalities observed in connection to PPP treatment included regular gains and losses, as well as homozygous losses in 10q24.1-q24.2 and 12p12.3-p13.2 in one of the lines and amplification at 5q11.2 in the other. Abnormalities observed in both tolerant derivatives include amplification/gain of 5q11.2, gain of 11q12.1-q14.3 and gain of 13q33.3-qter. Using Nexus software analysis we combined the array-CGH data with data from gene expression profilings and identified genes that were altered in both inputs. A subset of genes identified as downregulated (ALDH1A3, ANXA1, TLR4 and RAB5A) or upregulated (COX6A1, NFIX, ME1, MAPK and TAP2) were validated by siRNA in the tolerant or parental cells to alter sensitivity to PPP and confirmed to alter sensitivity to PPP in further cell lines. Conclusions Long-term PPP selection lead to altered gene expression in PPP tolerant cells with increase as well as decrease of genes involved in cell death such as PTEN and BCL2. In addition, acquired genomic copy number alterations were observed that were often reflected by altered mRNA expression levels for genes in the same regions.
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Affiliation(s)
- Jamileh Hashemi
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, CMM L8:01, Stockholm, Sweden.
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Braga E, Loginov W, Khodyrev D, Pronina I, Kazubskaya T, Bogatyrova O, Kashuba VI, Senchenko VN, Klein G, Lerman MI, Kisselev LL, Zabarovsky ER. A novel MECA3 region in human 3p21.3 harboring putative tumor suppressor genes and oncogenes. Exp Oncol 2011; 33:33-41. [PMID: 21423093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
BACKGROUND Human chromosome arm 3p is often affected in various epithelial tumors, and several tumor suppressor genes were recently identified in this region. The most affected is 3p21 region that is 50-100% rearranged in more than 30 types of malignancies, mostly in epithelial cancers: lung, breast, ovarian, cervical, kidney, head and neck, nasopharyngeal, colon etc. These cancers are responsible for 90% of cancer deaths. AIM To perform the detailed analysis of 3p (especially 3p21 region) to discover novel potential oncogenes and/or tumor suppressors. METHODS To find novel "hot spots" and genes involved in major cancers, dense 3p microsatellite markers (altogether 24 ) were allelotyped in four epithelial carcinomas (272 patients in total): breast (BC), renal cell (RCC), non-small cell lung (NSCLC) and epithelial ovarian (EOC) cancers. RESULTS As a main result, a novel region, frequently affected in BC, RCC, NSCLC and EOC was localized between markers D3S2409 and D3S3667 in the 3p21.3. This region (MECA3, major epithelial cancers affected region No. 3) covers numerous UniGene clusters, including genes involved in vital cell functions and carcinogenesis (e.g. MST1, MSTR1/RON, GPX1 and RHOA). The homozygous deletions were detected in the GPX1 in RCC (12%, 6 of 50 cases) and BC (1 of 37 cases). At the same time, amplifications and multiplications within the RHOA putative oncogene were identified in BC and RCC. CONCLUSIONS The data suggest that genes with potential oncogenic features are located in the close proximity to putative tumor suppressor gene(s) (TSG(s)) in the MECA3. Multiplication of the RHOA was not reported before. Significant correlation of allelic alterations in the, AP20, MECA3 and LUCA regions with tumor progression was found for some common histological tumor subtypes (e.g. clear cell RCC, and serous EOC).
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Affiliation(s)
- E Braga
- Russian State Genetics Center, Moscow 117545 Russia.
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Dworkin AM, Ridd K, Bautista D, Allain DC, Iwenofu OH, Roy R, Bastian BC, Toland AE. Germline variation controls the architecture of somatic alterations in tumors. PLoS Genet 2010; 6:e1001136. [PMID: 20885788 PMCID: PMC2944791 DOI: 10.1371/journal.pgen.1001136] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 08/24/2010] [Indexed: 11/19/2022] Open
Abstract
Studies have suggested that somatic events in tumors can depend on an individual's constitutional genotype. We used squamous cell carcinomas (SCC) of the skin, which arise in high multiplicity in organ transplant recipients, as a model to compare the pattern of somatic alterations within and across individuals. Specifically, we performed array comparative genomic hybridization on 104 tumors from 25 unrelated individuals who each had three or more independently arisen SCCs and compared the profiles occurring within patients to profiles of tumors across a larger set of 135 patients. In general, chromosomal aberrations in SCCs were more similar within than across individuals (two-sided exact-test p-value<1x10(-7)), consistent with the notion that the genetic background was affecting the pattern of somatic changes. To further test this possibility, we performed allele-specific imbalance studies using microsatellite markers mapping to 14 frequently aberrant regions of multiple independent tumors from 65 patients. We identified nine loci which show evidence of preferential allelic imbalance. One of these loci, 8q24, corresponded to a region in which multiple single nucleotide polymorphisms have been associated with increased cancer risk in genome-wide association studies (GWAS). We tested three implicated variants and identified one, rs13281615, with evidence of allele-specific imbalance (p-value=0.012). The finding of an independently identified cancer susceptibility allele with allele-specific imbalance in a genomic region affected by recurrent DNA copy number changes suggest that it may also harbor risk alleles for SCC. Together these data provide strong evidence that the genetic background is a key driver of somatic events in cancer, opening an opportunity to expand this approach to identify cancer risk alleles.
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Affiliation(s)
- Amy M. Dworkin
- Integrated Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
| | - Katie Ridd
- Department of Dermatology and UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | | | - Dawn C. Allain
- Clinical Cancer Genetics Program and Human Cancer Genetics Program, Department of Internal Medicine, Division of Human Genetics, Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University Medical Center, Columbus, Ohio, United States of America
| | - O. Hans Iwenofu
- Department of Pathology and Laboratory Medicine, The Ohio State University Medical Center, Columbus, Ohio, United States of America
| | - Ritu Roy
- Biostatistics Core Facility, UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Boris C. Bastian
- Departments of Dermatology and Pathology and UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (AET); (BCB)
| | - Amanda Ewart Toland
- Departments of Internal Medicine and Molecular Virology, Immunology, and Medical Genetics, Divison of Human Cancer Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (AET); (BCB)
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Sun C, Southard C, Witonsky DB, Olopade OI, Di Rienzo A. Allelic imbalance (AI) identifies novel tissue-specific cis-regulatory variation for human UGT2B15. Hum Mutat 2010; 31:99-107. [PMID: 19847790 PMCID: PMC2922057 DOI: 10.1002/humu.21145] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Allelic imbalance (AI) is a powerful tool to identify cis-regulatory variation for gene expression. UGT2B15 is an important enzyme involved in the metabolism of multiple endobiotics and xenobiotics. In this study, we measured the relative expression of two alleles at this gene by using SNP rs1902023:G>T. An excess of the G over the T allele was consistently observed in liver (P<0.001), but not in breast (P=0.06) samples, suggesting that SNPs in strong linkage disequilibrium with G253T regulate UGT2B15 expression in liver. Seven such SNPs were identified by resequencing the promoter and exon 1, which define two distinct haplotypes. Reporter gene assays confirmed that one haplotype displayed approximately 20% higher promoter activity compared to the other major haplotype in liver HepG2 (P<0.001), but not in breast MCF-7 (P=0.540) cells. Reporter gene assays with additional constructs pointed to rs34010522:G>T and rs35513228:C>T as the cis-regulatory variants; both SNPs were also evaluated in LNCaP and Caco-2 cells. By ChIP, we showed that the transcription factor Nrf2 binds to the region spanning rs34010522:G>T in all four cell lines. Our results provide a good example for how AI can be used to identify cis-regulatory variation and gain insights into the tissue specific regulation of gene expression.
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Affiliation(s)
- Chang Sun
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | | | - David B. Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | | | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
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Kanber D, Berulava T, Ammerpohl O, Mitter D, Richter J, Siebert R, Horsthemke B, Lohmann D, Buiting K. The human retinoblastoma gene is imprinted. PLoS Genet 2009; 5:e1000790. [PMID: 20041224 PMCID: PMC2791201 DOI: 10.1371/journal.pgen.1000790] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 11/25/2009] [Indexed: 11/18/2022] Open
Abstract
Genomic imprinting is an epigenetic process leading to parent-of-origin–specific DNA methylation and gene expression. To date, ∼60 imprinted human genes are known. Based on genome-wide methylation analysis of a patient with multiple imprinting defects, we have identified a differentially methylated CpG island in intron 2 of the retinoblastoma (RB1) gene on chromosome 13. The CpG island is part of a 5′-truncated, processed pseudogene derived from the KIAA0649 gene on chromosome 9 and corresponds to two small CpG islands in the open reading frame of the ancestral gene. It is methylated on the maternal chromosome 13 and acts as a weak promoter for an alternative RB1 transcript on the paternal chromosome 13. In four other KIAA0649 pseudogene copies, which are located on chromosome 22, the two CpG islands have deteriorated and the CpG dinucleotides are fully methylated. By analysing allelic RB1 transcript levels in blood cells, as well as in hypermethylated and 5-aza-2′-deoxycytidine–treated lymphoblastoid cells, we have found that differential methylation of the CpG island skews RB1 gene expression in favor of the maternal allele. Thus, RB1 is imprinted in the same direction as CDKN1C, which operates upstream of RB1. The imprinting of two components of the same pathway indicates that there has been strong evolutionary selection for maternal inhibition of cell proliferation. Genomic imprinting is an epigenetic process leading to parent-of-origin–specific DNA methylation and gene expression. Defects in this process lead to abnormal development, growth, or behavior. It is still unclear why and how imprinting evolved and how many human genes are imprinted. Based on genome-wide DNA methylation analysis in a patient with a generalized imprinting defect, we have found that the paradigmatic retinoblastoma 1 (RB1) gene on chromosome 13 is imprinted. Imprinting of RB1 is linked to the insertion of a DNA sequence derived by retrotransposition from a gene on chromosome 9. Part of the inserted DNA sequence has evolved into a differentially methylated alternative RB1 promoter. Differential methylation of this sequence skews expression of the RB1 gene in favour of the maternal allele. The direction of the imprint imposed on the RB1 gene is the same as of the maternally expressed CDKN1C gene, which operates upstream of RB1. The imprinting of two components of the same pathway indicates that there has been strong evolutionary selection for maternal inhibition of cell proliferation.
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Affiliation(s)
- Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Tea Berulava
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Ole Ammerpohl
- Institut für Humangenetik, Christian-Albrechts Universität zu Kiel, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Diana Mitter
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Julia Richter
- Institut für Humangenetik, Christian-Albrechts Universität zu Kiel, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Reiner Siebert
- Institut für Humangenetik, Christian-Albrechts Universität zu Kiel, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
- * E-mail:
| | - Dietmar Lohmann
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Karin Buiting
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
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Auvin S, Holder-Espinasse M, Lamblin MD, Andrieux J. Array-CGH detection of a de novo 0.7-Mb deletion in 19p13.13 including CACNA1A associated with mental retardation and epilepsy with infantile spasms. Epilepsia 2009; 50:2501-3. [PMID: 19874387 DOI: 10.1111/j.1528-1167.2009.02189.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lopez-Escamez JA, Moreno A, Bernal M, Perez-Garrigues H, Santos-Perez S, Soto-Varela A, Aran I, Fernandez-Sanfrancisco O, Lopez-Nevot A, Lopez-Nevot MA. Poly(ADP-ribose) polymerase-1 (PARP-1) longer alleles spanning the promoter region may confer protection to bilateral Meniere's disease. Acta Otolaryngol 2009; 129:1222-5. [PMID: 19863315 DOI: 10.3109/00016480802684080] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
CONCLUSION The longer alleles (CA)17-20 of the promoter region of PARP-1 gene may confer some protection against bilateral Meniere's disease (BMD). OBJECTIVE To analyze microsatellite (CA)(n) polymorphisms in the promoter region of PARP-1 gene and seek out risk and protective variants for BMD. SUBJECTS AND METHODS Eighty patients from two ethnically defined groups with definite BMD, according to the diagnostic scale of the American Academy of Otolaryngology Head and Neck Surgery, were compared with a group of 371 normal controls from the same origin in a prospective multicenter study. We developed a specific amplification protocol to determine the PARP1-promotor CA microsatellite polymorphisms. RESULTS We found that the longer alleles (CA)17-20 had a very low frequency in BMD (2/160, 1.3%, OR=7.33 (1.77-30.37, 95% CI), corrected p=0.012), suggesting that it may confer some protection against BMD.
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Affiliation(s)
- Jose A Lopez-Escamez
- Otology & Neurotology Group, Department of Otolaryngology, Hospital de Poniente de Almería, Ctra. de Almerimar s/n, El Ejido, Almería.
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Tung J, Fédrigo O, Haygood R, Mukherjee S, Wray GA. Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation. Mol Biol Evol 2009; 26:2047-59. [PMID: 19506001 PMCID: PMC2734157 DOI: 10.1093/molbev/msp113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2009] [Indexed: 12/29/2022] Open
Abstract
Variation in gene expression is an important contributor to phenotypic diversity within and between species. Although this variation often has a genetic component, identification of the genetic variants driving this relationship remains challenging. In particular, measurements of gene expression usually do not reveal whether the genetic basis for any observed variation lies in cis or in trans to the gene, a distinction that has direct relevance to the physical location of the underlying genetic variant, and which may also impact its evolutionary trajectory. Allelic imbalance measurements identify cis-acting genetic effects by assaying the relative contribution of the two alleles of a cis-regulatory region to gene expression within individuals. Identification of patterns that predict commonly imbalanced genes could therefore serve as a useful tool and also shed light on the evolution of cis-regulatory variation itself. Here, we show that sequence motifs, polymorphism levels, and divergence levels around a gene can be used to predict commonly imbalanced genes in a human data set. Reduction of this feature set to four factors revealed that only one factor significantly differentiated between commonly imbalanced and nonimbalanced genes. We demonstrate that these results are consistent between the original data set and a second published data set in humans obtained using different technical and statistical methods. Finally, we show that variation in the single allelic imbalance-associated factor is partially explained by the density of genes in the region of a target gene (allelic imbalance is less probable for genes in gene-dense regions), and, to a lesser extent, the evenness of expression of the gene across tissues and the magnitude of negative selection on putative regulatory regions of the gene. These results suggest that the genomic distribution of functional cis-regulatory variants in the human genome is nonrandom, perhaps due to local differences in evolutionary constraint.
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Affiliation(s)
- Jenny Tung
- Department of Biology, Duke University, Durham, NC, USA.
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Lacy S, Lopez-Beltran A, MacLennan GT, Foster SR, Montironi R, Cheng L. Molecular pathogenesis of urothelial carcinoma: the clinical utility of emerging new biomarkers and future molecular classification of bladder cancer. Anal Quant Cytol Histol 2009; 31:5-16. [PMID: 19320188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Bladder cancer remains one of the most common and expensive cancers to treat worldwide. Numerous molecular markers are being investigated as possible ways to decrease health care costs, increase patient survival and prognosis, and increase sensitivity in screening tests. Several genetic markers have emerged as potential therapeutic targets and have provided new theories concerning the origins and progression of these tumors. Future classifications of bladder tumors should be based on the understanding of disease processes and should incorporate these emerging biomarkers for stratification of tumors into different prognostic groups.
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Affiliation(s)
- Shanon Lacy
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
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Lavi S, McConnell JP, Lavi R, Barsness GW, Rihal CS, Novak GD, Lerman LO, Lerman A. Association between the paraoxonase-1 192Q>R allelic variant and coronary endothelial dysfunction in patients with early coronary artery disease. Mayo Clin Proc 2008; 83:158-64. [PMID: 18241625 DOI: 10.4065/83.2.158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To test the hypothesis that allelic variants of the paraoxonase-1 gene are associated with endothelial dysfunction, an early stage of atherosclerosis. PATIENTS AND METHODS We assessed 192Q>R and 55L>M allelic variants of the paraoxonase gene and coronary endothelial function in response to intracoronary acetylcholine in 99 patients (52 with homozygous QQ, 47 with homozygous RR or heterozygous QR). The study was conducted from September 1, 2002, through November 30, 2004. RESULTS Of 52 homozygous QQ patients, 39 (75%) had endothelial dysfunction vs 20 (43%) of the 47 RR/QR patients (P=.001), and this association remained significant after adjustment in a multivariable linear regression model (P=.005). In homozygous QQ vs RR/QR patients, epicardial arterial diameter decreased more (% change in diameter, -22%+/-21% vs -9%+/-16%, respectively, P=.002), coronary blood flow increased less (+37%+/-77% vs +75%+/-75%, P=.02) in response to acetylcholine, and oxidized LDL levels were higher. The 55L>M allelic variant was not significantly associated with endothelial dysfunction and had no effect on the association between endothelial dysfunction and the 192Q>R allelic variant. CONCLUSION The 192Q>R allelic variant of the paraoxonase-1 gene is associated with coronary endothelial dysfunction. The current study provides further information regarding the potential mechanisms by which this allelic variant contributes to early atherosclerosis in humans.
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Affiliation(s)
- Shahar Lavi
- Division of Cardiovascular Diseases, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
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Mohamedali A, Gäken J, Twine NA, Ingram W, Westwood N, Lea NC, Hayden J, Donaldson N, Aul C, Gattermann N, Giagounidis A, Germing U, List AF, Mufti GJ. Prevalence and prognostic significance of allelic imbalance by single-nucleotide polymorphism analysis in low-risk myelodysplastic syndromes. Blood 2007; 110:3365-73. [PMID: 17634407 DOI: 10.1182/blood-2007-03-079673] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Abstract
Low-risk myelodysplastic syndrome (MDS) with normal cytogenetics accounts for approximately 50% of MDS patients. There are no pathognomonic markers in these cases and the diagnosis rests on cytomorphologic abnormalities in bone marrow and/or peripheral blood. Affymetrix high-resolution single-nucleotide polymorphism (SNP) genotyping microarrays allow detection of cytogenetically cryptic genomic aberrations. We have studied 119 low-risk MDS patients (refractory anemia [RA] = 22; refractory cytopenia with multilineage dysplasia [RCMD] = 51; refractory anemia with ringed sideroblasts [RARS] = 12; refractory cytopenia with multilineage dysplasia with ringed sideroblasts [RCMD-RS] = 12; 5q− syndrome = 16; refractory anemia with excess blasts [RAEB] = 6) using SNP microarrays to seek chromosomal markers undetected by conventional cytogenetics. Loss of heterozygosity (LOH) detected by 50K arrays was verified using 250K and 500K arrays. We demonstrate the presence of uniparental disomy (UPD) in 46%, deletions in 10%, and amplifications in 8% of cases. Copy number (CN) changes were acquired, whereas UPDs were also detected in constitutional DNA. UPD on 4q was identified in 25% of RARS, 12% of RCMD with normal cytogenetics, 17% of RAEB, and 6% of 5q− syndrome cases. Univariate analysis showed deletions (P = .04) and International Prognostic Scoring System (IPSS; P < .001) scores correlated with overall survival; however, on multivariate analysis only IPSS scores retained prognostic significance (P < .001). We show, for the first time, that SNP microarray analysis in low-risk MDS patients reveals hitherto unrecognized UPD and CN changes that may allow stratification of these patients for early therapeutic interventions.
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Affiliation(s)
- Azim Mohamedali
- Department of Haematological Medicine, King's College Hospital, King's College London School of Medicine, Denmark Hill, London, United Kingdom
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Callaghan KA, Becker TE, Ellsworth DL, Hooke JA, Ellsworth RE, Shriver CD. Genomic instability and the development of metastatic lymph node tumors. Ann Surg Oncol 2007; 14:3125-32. [PMID: 17653592 DOI: 10.1245/s10434-007-9504-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2007] [Revised: 05/24/2007] [Accepted: 05/25/2007] [Indexed: 11/18/2022]
Abstract
BACKGROUND Although recent data suggest that cells with metastatic potential disseminate from the primary breast tumor early in tumor development, the mechanism by which disseminated breast cancer cells proliferate within foreign tissues is not well understood. Here, we examined levels and patterns of allelic imbalance (AI) in metastatic lymph node (LN) tumors to identify molecular signals that promote the survival and growth of disseminated breast tumor cells. METHODS DNA from 106 metastatic LN tumors from 25 patients was isolated after laser microdissection of pure tumor cell populations. AI was assessed at 26 chromosomal regions frequently altered in breast cancer. Tumor burden was calculated by dividing the area of the metastatic tumor in the node by the area of the entire LN. RESULTS Metastatic tumor burden ranged from focal to complete replacement of the LN with tumor. Grouping the nodes as < 25% tumor, 25-50% tumor, 50-75% tumor, and > or = 75% tumor replacement revealed the average frequency of AI ranged from 0.13 (+/-0.11) in the < 25% group to 0.17 (+/-0.13) in LNs with > or = 75% tumor burden. The range of AI in both the < 25% and > 75% replacement group was 0.00-0.48. Allelic losses at chromosomal regions 1p36.1-36.2, 5q21.1-21.3, 6q15, 10q23.31-23.33, and 17p13.1 were significantly higher in metastatic LNs with > 75% compared with < 25% tumor burden. CONCLUSIONS In metastatic LNs, levels of AI were not associated with tumor burden, suggesting that accumulation of genetic changes is not coincidental with tumor growth; rather the accumulation of specific genetic changes is a prerequisite to the transformation of disseminated breast cells into metastatic LN tumors.
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Affiliation(s)
- Karen A Callaghan
- Clinical Breast Care Project, Walter Reed Army Medical Center, Washington, DC, USA.
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Abstract
Single-nucleotide polymorphisms (SNPs) are common in the human genome, with more than 11 million SNPs having frequencies greater than 1%. The challenge is to identify the minority of functional SNPs from the large number of SNPs that are expected to be silent. Whereas coding variants are unusual, and functional (nonsynonymous) coding SNPs likely rare, regulatory SNPs appear to be common. Traditional methods to identify these SNPs in vitro are time consuming and challenging. An alternative method is to examine the allele-specific expression in the cDNA from tissues expressing the genes of interest and in individuals heterozygous for a transcribed SNP. This method permits expression to be evaluated in the context of the same trans-acting factors and to identify genes with likely cis-acting regulatory variants or parent of origin (imprinting) effects. Such studies require a method to reliably quantify the expression from each allele. Pyrosequencing offers such capabilities, and given the relatively low cost and high throughput, it offers a sensitive method to determine allelic imbalance in the cDNA from tissues expressing genes of interest.
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Affiliation(s)
- Hua Wang
- Division of Endocrinology, Department of Internal Medicine, Central Arkansas Veterans Healthcare System and College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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Chuensumran U, Wongkham S, Pairojkul C, Chauin S, Petmitr S. Prognostic value of DNA alterations on chromosome 17p13.2 for intrahepatic cholangiocarcinoma. World J Gastroenterol 2007; 13:2986-91. [PMID: 17589952 PMCID: PMC4171154 DOI: 10.3748/wjg.v13.i21.2986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 04/12/2007] [Accepted: 04/28/2007] [Indexed: 02/06/2023] Open
Abstract
AIM To characterize and evaluate DNA alterations among intrahepatic cholangiocarcinoma (ICC) patients. METHODS DNA from tumor and corresponding normal tissues of 52 patients was amplified with 33 arbitrary primers. The DNA fragment that alters most frequently in ICC was cloned, sequenced, and identified by comparison with known nucleotide sequences in the genome database (www.ncbi.nlm.nih.gov). The DNA copy numbers of the allelic alterations in cholangiocarcinoma were determined by quantitative real-time PCR and interpreted as allelic loss or DNA amplification by comparison with the reference gene. Associations between allelic imbalance and clinicopathological parameters of ICC patients were evaluated by chi2-test. The Kaplan-Meier method was used to analyze survival rates. RESULTS From 33 primers, an altered DNA fragment (518 bp) amplified from BC17 random primer was found frequently in the tumors analyzed and mapped to chromosome 17p13.2. Sixteen of 52 (31%) cases showed DNA amplification, while 7 (13%) showed allelic loss. Interestingly, DNA amplification on chromosome 17p13.2 was associated with a good prognosis, median survival time (wk) of amp vs no amp was 44.14 vs 24.14, P = 0.002; whereas allelic loss of this DNA sequence corresponded with a poor prognosis, median survival time (wk) of loss vs no loss was 18.00 vs 28.71, P = 0.019). Moreover, Kaplan-Meier curves comparing the DNA alterations with survival depicted highly significant separation that the median survival time equal to DNA amplification, allelic loss, and normal was 44.14 wk, 18.00 wk, and 24.29 wk, respectively (P = 0.005). CONCLUSION Alterations in the DNA sequence on chromosome 17p13.2 may be involved in cholangio-carcinogenesis, and could be used as a prognostic marker in the treatment of ICC patients.
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Affiliation(s)
- Ubol Chuensumran
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
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Heaphy CM, Hines WC, Butler KS, Haaland CM, Heywood G, Fischer EG, Bisoffi M, Griffith JK. Assessment of the frequency of allelic imbalance in human tissue using a multiplex polymerase chain reaction system. J Mol Diagn 2007; 9:266-71. [PMID: 17384220 PMCID: PMC1867446 DOI: 10.2353/jmoldx.2007.060115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Genomic instability can generate chromosome breakage and fusion randomly throughout the genome, frequently resulting in allelic imbalance, a deviation from the normal 1:1 ratio of maternal and paternal alleles. Allelic imbalance reflects the karyotypic complexity of the cancer genome. Therefore, it is reasonable to speculate that tissues with more sites of allelic imbalance have a greater likelihood of having disruption of any of the numerous critical genes that cause a cancerous phenotype and thus may have diagnostic or prognostic significance. For this reason, it is desirable to develop a robust method to assess the frequency of allelic imbalance in any tissue. To address this need, we designed an economical and high-throughput method, based on the Applied Biosystems AmpFlSTR Identifiler multiplex polymerase chain reaction system, to evaluate allelic imbalance at 16 unlinked, microsatellite loci located throughout the genome. This method provides a quantitative comparison of the extent of allelic imbalance between samples that can be applied to a variety of frozen and archival tissues. The method does not require matched normal tissue, requires little DNA (the equivalent of approximately 150 cells) and uses commercially available reagents, instrumentation, and analysis software. Greater than 99% of tissue specimens with >or=2 unbalanced loci were cancerous.
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Affiliation(s)
- Christopher M Heaphy
- Department of Biochemistry and Molecular Biology, MSC08 4670, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
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Martin J, Cleak J, Willis-Owen SAG, Flint J, Shifman S. Mapping regulatory variants for the serotonin transporter gene based on allelic expression imbalance. Mol Psychiatry 2007; 12:421-2. [PMID: 17453058 DOI: 10.1038/sj.mp.4001952] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Abstract
Tryptophan hydroxylase isoform 2 (TPH2) is expressed in serotonergic neurons in the raphe nuclei, where it catalyzes the rate-limiting step in the synthesis of the neurotransmitter serotonin. In search for functional polymorphisms within the TPH2 gene locus, we measured allele-specific expression of TPH2 mRNA in sections of human pons containing the dorsal and median raphe nuclei. Differences in allelic mRNA expression--referred to as allelic expression imbalance (AEI)--are a measure of cis-acting regulation of gene expression and mRNA processing. Two marker SNPs, located in exons 7 and 9 of TPH2 (rs7305115 and rs4290270, respectively), served for quantitative allelic mRNA measurements in pons RNA samples from 27 individuals heterozygous for one or both SNPs. Significant AEI (ranging from 1.2- to 2.5-fold) was detected in 19 out of the 27 samples, implying the presence of cis-acting polymorphisms that differentially affect TPH2 mRNA levels in pons. For individuals heterozygous for both marker SNPs, the results correlated well (r=0.93), validating the AEI analysis. AEI is tightly associated with the exon 7 marker SNP, in 17 of 18 subjects. Remarkably, expression from the minor allele exceeded that of the major allele in each case, possibly representing a gain-of-function. Genotyping of 20 additional TPH2 SNPs identified a haplotype block of five tightly linked SNPs for which heterozygosity is highly correlated with AEI and overall expression of TPH2 mRNA. These results reveal the presence of a functional cis-acting polymorphism, with high frequency in normal human subjects, resulting in increased TPH2 expression levels. The SNPs that correlate with AEI are closely linked to TPH2 SNPs previously shown to associate with major depression and suicide.
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Affiliation(s)
- J-E Lim
- Department of Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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Abstract
Aneuploidy, the relative excess or deficiency of specific chromosome types, results in gene dosage imbalance. Plants can produce viable and fertile aneuploid individuals, while most animal aneuploids are inviable or developmentally abnormal. The swarms of aneuploid progeny produced by Arabidopsis triploids constitute an excellent model to investigate the mechanisms governing dosage sensitivity and aneuploid syndromes. Indeed, genotype alters the frequency of aneuploid types within these swarms. Recombinant inbred lines that were derived from a triploid hybrid segregated into diploid and tetraploid individuals. In these recombinant inbred lines, a single locus, which we call SENSITIVE TO DOSAGE IMBALANCE (SDI), exhibited segregation distortion in the tetraploid subpopulation only. Recent progress in quantitative genotyping now allows molecular karyotyping and genetic analysis of aneuploid populations. In this study, we investigated the causes of the ploidy-specific distortion at SDI. Allele frequency was distorted in the aneuploid swarms produced by the triploid hybrid. We developed a simple quantitative measure for aneuploidy lethality and using this measure demonstrated that distortion was greatest in the aneuploids facing the strongest viability selection. When triploids were crossed to euploids, the progeny, which lack severe aneuploids, exhibited no distortion at SDI. Genetic characterization of SDI in the aneuploid swarm identified a mechanism governing aneuploid survival, perhaps by buffering the effects of dosage imbalance. As such, SDI could increase the likelihood of retaining genomic rearrangements such as segmental duplications. Additionally, in species where triploids are fertile, aneuploid survival would facilitate gene flow between diploid and tetraploid populations via a triploid bridge and prevent polyploid speciation. Our results demonstrate that positional cloning of loci affecting traits in populations containing ploidy and chromosome number variants is now feasible using quantitative genotyping approaches.
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Affiliation(s)
- Isabelle M Henry
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Brian P Dilkes
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Luca Comai
- Department of Biology, University of Washington, Seattle, Washington, United States of America
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Nordlander C, Karlsson S, Karlsson A, Sjöling A, Winnes M, Klinga-Levan K, Behboudi A. Analysis of chromosome 10 aberrations in rat endometrial cancer-evidence for a tumor suppressor locus distal to Tp53. Int J Cancer 2007; 120:1472-81. [PMID: 17245700 DOI: 10.1002/ijc.22533] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have recently shown in the BDII rat model of human endometrial adenocarcinoma (EAC), rat chromosome 10 (RNO10) is frequently involved in chromosomal aberrations. In the present study, we investigated the association between RNO10 deletions, allelic imbalance (AI) at RNO10q24 and Tp53 mutation in 27 rat EAC tumors. We detected chromosomal breakage accompanied by loss of proximal and/or gain of distal parts of RNO10 in approximately 2/3 of the tumors. This finding is suggestive of a tumor suppressor activity encoded from the proximal RNO10. Given the fact that Tp53 is located at RNO10q24-q25, we then performed Tp53 mutation analysis. However, we could not find a strong correlation between AI/deletions at RNO10q24 and Tp53 mutation. Instead, the observed patterns for AI, chromosomal breaks and deletions suggest that major selection was directed against a region located close to, but distal of Tp53. In different human malignancies a similar situation of AI at chromosome band 17p13.3 (HSA17p13.3) unassociated with TP53 mutation has been observed. Although RNO10 is largely homologous to HSA17, the conservation with respect to gene order among them is not extensive. We utilized publicly available draft DNA sequences to study intrachromosomal rearrangement during the divergence between HSA17 and RNO10. By using reciprocal comparison of rat and human genome data, we could substantially narrow down the candidate tumor suppressor region in rat from 3 Mb to a chromosomal segment of about 0.5 Mb in size. These results provide scientific groundwork for identification of the putative tumor suppressor gene(s) at 17p13.3 in human tumors.
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Affiliation(s)
- Carola Nordlander
- CMB-Genetics, Lundberg Laboratory, Göteborg University, SE 40530 Gothenburg, Sweden
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Abstract
Autism is a neurodevelopmental disorder characterized by impairments in social interactions, communication, and behavior. Multiple lines of evidence support the notion that most cases of autism likely have an underlying genetic cause or predisposition. Like mental retardation, autism is likely to be caused by many different genetic mechanisms and genes rather than a single, or few, major genes or environmental effects. In this review, we will focus on the cytogenetic contribution to uncovering regions of the genome involved in autism. Some common cytogenetic imbalances already known to cause autism will be highlighted. Routine genetic testing in clinical (CLIA-certified) diagnostic laboratories can identify the specific etiology and recurrence risk in 10% to 15% of autism cases and is clinically indicated for any child with autism. Powerful new methods for identifying novel regions of the genome causing or contributing to autism also will be discussed and will start to explain the etiology for some percentage of the remaining 85% to 90% of autism cases.
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MESH Headings
- Adolescent
- Adult
- Allelic Imbalance/genetics
- Asperger Syndrome/diagnosis
- Asperger Syndrome/genetics
- Asperger Syndrome/psychology
- Autistic Disorder/diagnosis
- Autistic Disorder/genetics
- Autistic Disorder/psychology
- Child
- Child Development Disorders, Pervasive/diagnosis
- Child Development Disorders, Pervasive/genetics
- Child Development Disorders, Pervasive/psychology
- Child, Preschool
- Chromosome Deletion
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 22/genetics
- Fragile X Syndrome/diagnosis
- Fragile X Syndrome/genetics
- Fragile X Syndrome/psychology
- Gene Duplication
- Genetic Testing
- Genotype
- Humans
- Oligonucleotide Array Sequence Analysis
- Phenotype
- Social Environment
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Affiliation(s)
- Christa Lese Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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40
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Lu X, Shaw CA, Patel A, Li J, Cooper ML, Wells WR, Sullivan CM, Sahoo T, Yatsenko SA, Bacino CA, Stankiewicz P, Ou Z, Chinault AC, Beaudet AL, Lupski JR, Cheung SW, Ward PA. Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases. PLoS One 2007; 2:e327. [PMID: 17389918 PMCID: PMC1828620 DOI: 10.1371/journal.pone.0000327] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 03/05/2007] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Array Comparative Genomic Hybridization (a-CGH) is a powerful molecular cytogenetic tool to detect genomic imbalances and study disease mechanism and pathogenesis. We report our experience with the clinical implementation of this high resolution human genome analysis, referred to as Chromosomal Microarray Analysis (CMA). METHODS AND FINDINGS CMA was performed clinically on 2513 postnatal samples from patients referred with a variety of clinical phenotypes. The initial 775 samples were studied using CMA array version 4 and the remaining 1738 samples were analyzed with CMA version 5 containing expanded genomic coverage. Overall, CMA identified clinically relevant genomic imbalances in 8.5% of patients: 7.6% using V4 and 8.9% using V5. Among 117 cases referred for additional investigation of a known cytogenetically detectable rearrangement, CMA identified the majority (92.5%) of the genomic imbalances. Importantly, abnormal CMA findings were observed in 5.2% of patients (98/1872) with normal karyotypes/FISH results, and V5, with expanded genomic coverage, enabled a higher detection rate in this category than V4. For cases without cytogenetic results available, 8.0% (42/524) abnormal CMA results were detected; again, V5 demonstrated an increased ability to detect abnormality. Improved diagnostic potential of CMA is illustrated by 90 cases identified with 51 cryptic microdeletions and 39 predicted apparent reciprocal microduplications in 13 specific chromosomal regions associated with 11 known genomic disorders. In addition, CMA identified copy number variations (CNVs) of uncertain significance in 262 probands; however, parental studies usually facilitated clinical interpretation. Of these, 217 were interpreted as familial variants and 11 were determined to be de novo; the remaining 34 await parental studies to resolve the clinical significance. CONCLUSIONS This large set of clinical results demonstrates the significantly improved sensitivity of CMA for the detection of clinically relevant genomic imbalances and highlights the need for comprehensive genetic counseling to facilitate accurate clinical correlation and interpretation.
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Affiliation(s)
- Xinyan Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jiangzhen Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - M. Lance Cooper
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - William R. Wells
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Cathy M. Sullivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Trilochan Sahoo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Svetlana A. Yatsenko
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zhishu Ou
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - A. Craig Chinault
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sau W. Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Patricia A. Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
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41
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Carr J, Bown NP, Case MC, Hall AG, Lunec J, Tweddle DA. High-resolution analysis of allelic imbalance in neuroblastoma cell lines by single nucleotide polymorphism arrays. ACTA ACUST UNITED AC 2007; 172:127-38. [PMID: 17213021 DOI: 10.1016/j.cancergencyto.2006.08.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 08/04/2006] [Accepted: 08/15/2006] [Indexed: 12/15/2022]
Abstract
Genomic copy number changes are detectable in many malignancies, including neuroblastoma, using techniques such as comparative genomic hybridization (CGH), microsatellite analysis, conventional karyotyping, and fluorescence in situ hybridization (FISH). We report the use of 10K single nucleotide polymorphism (SNP) microarrays to detect copy number changes and allelic imbalance in six neuroblastoma cell lines (IMR32, SHEP, NBL-S, SJNB-1, LS, and SKNBE2c). SNP data were generated using the GeneChip DNA Analysis and GeneChip chromosome copy number software (Affymetrix). SNP arrays confirmed the presence of all previously reported cytogenetic abnormalities in the cell lines, including chromosome 1p deletion, MYCN amplification, gain of 17q and 11q, and 14q deletions. In addition, the SNP arrays revealed several chromosome gains and losses not detected by CGH or karyotyping; these included gain of 8q21.1 approximately 24.3 and gain of chromosome 12 in IMR-32 cells; loss at 4p15.3 approximately 16.1 and loss at 16p12.3 approximately 13.2, 11q loss with loss of heterozygosity (LOH) at 11q14.3 approximately 23.3 in SJNB-1 cells; and loss at 8p21.2 approximately 23.3 and 9p21.3 approximately 22.1 with corresponding LOH in SHEP cells. The SNP arrays refined the mapping of the 2p amplicons in LS, BE2c, and IMR-32 cell lines, the 12q amplicon in LS cells, and also identified an 11q13 amplicon in LS cells. There was good concordance among SNP arrays, CGH, and karyotyping. SNP array analysis is a powerful tool for the detection of allelic imbalance in neuroblastoma and also allows identification of LOH without changes in copy number (uniparental disomy).
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Affiliation(s)
- Jane Carr
- Northern Institute for Cancer Research, Paul O'Gorman Building, Framlington Place, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
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42
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Zhao J, Yart A, Frigerio S, Perren A, Schraml P, Weisstanner C, Stallmach T, Krek W, Moch H. Sporadic human renal tumors display frequent allelic imbalances and novel mutations of the HRPT2 gene. Oncogene 2006; 26:3440-9. [PMID: 17130827 DOI: 10.1038/sj.onc.1210131] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inactivation of the HRPT2 gene encoding parafibromin was recently linked to the familial hyperparathyroidism-jaw tumor syndrome. Patients with this syndrome carry an increased risk of parathyroid and renal tumors. To determine the relevance of HRPT2 for sporadic renal tumors, clear cell, papillary and chromophobe renal cell carcinomas as well as oncocytomas and Wilms tumors were analysed for HRPT2 gene alterations. Loss of heterozygosity (LOH) of HRPT2 was found in seven of 56 (12.5%) clear cell, three of 14 (21%) papillary, six of 10 (60%) chromophobe renal cell carcinomas, three of eight (38%) oncocytomas and four of 10 (40%) Wilms tumors. In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively. These tumors displayed LOH of the remaining wild-type allele, but interestingly no von Hippel-Lindau (VHL) mutation. Functional analysis revealed that the K34Q mutant species of parafibromin is, unlike wild-type protein, defective in suppressing cyclin D1 expression in vivo. Taken together, these results suggest that renal cancer-associated mutations in parafibromin occur in the absence of VHL mutation, which in turn may contribute to constitutively elevated cyclin D1 expression and abnormal cell proliferation.
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Affiliation(s)
- J Zhao
- Department of Pathology, Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland.
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43
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Song YS, Song JS. Analytic computation of the expectation of the linkage disequilibrium coefficient r2. Theor Popul Biol 2006; 71:49-60. [PMID: 17069867 DOI: 10.1016/j.tpb.2006.09.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 06/25/2006] [Accepted: 09/13/2006] [Indexed: 11/19/2022]
Abstract
The squared correlation coefficient r(2) (sometimes denoted Delta(2)) is a measure of linkage disequilibrium that is widely used, but computing its expectation E[r(2)] in the population has remained an intriguing open problem. The expectation E[r(2)] is often approximated by the standard linkage deviation sigma(d)(2), which is a ratio of two expectations amenable to analytic computation. In this paper, a method of computing the population-wide E[r(2)] is introduced for a model with recurrent mutation, genetic drift and recombination. The approach is algebraic and is based on the diffusion process approximation. In the limit as the population-scaled recombination rate rho approaches infinity, it is shown rigorously that the asymptotic behavior of E[r(2)] is given by 1/rho+O(rho(-2)), which, incidentally, is the same as that of sigma(d)(2). A computer software that computes E[r(2)] numerically is available upon request.
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Affiliation(s)
- Yun S Song
- Department of Computer Science, University of California at Davis, 2063 Kemper Hall, One Shields Avenue, Davis, CA 95616, USA.
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44
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Teare MD, Heighway J, Santibáñez Koref MF. An expectation-maximization algorithm for the analysis of allelic expression imbalance. Am J Hum Genet 2006; 79:539-43. [PMID: 16909391 PMCID: PMC1559538 DOI: 10.1086/506968] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 06/12/2006] [Indexed: 11/03/2022] Open
Abstract
A significant proportion of the variation between individuals in gene expression levels is genetic, and it is likely that these differences correlate with phenotypic differences or with risk of disease. Cis-acting polymorphisms are important in determining interindividual differences in gene expression that lead to allelic expression imbalance, which is the unequal expression of homologous alleles in individuals heterozygous for such a polymorphism. This expression imbalance can be detected using a transcribed polymorphism, and, once it is established, the next step is to identify the polymorphisms that are responsible for or predictive of allelic expression levels. We present an expectation-maximization algorithm for such analyses, providing a formal statistical framework to test whether a candidate polymorphism is associated with allelic expression differences.
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Affiliation(s)
- M D Teare
- Division of Genomic Medicine, University of Sheffield, United Kingdom
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45
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Wełnicka-Jaśkiewicz M, Zaczek A, Brandt B, Bielawski KP, Jaśkiewicz J, Konopa K, Jassem J. (CA)n Microsatellite polymorphism of ERBB-1 in breast cancer. Eur J Cancer 2006; 42:1698-701. [PMID: 16765588 DOI: 10.1016/j.ejca.2006.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 03/15/2006] [Accepted: 03/22/2006] [Indexed: 11/24/2022]
Abstract
The aim of this study was to determine polymorphism of repeated sequences (CA)(n) in the ERBB-1 gene. The study group included 197 breast cancer patients and 180 healthy women. DNA was isolated from fresh-frozen tumour tissue and from peripheral blood. ERBB-1 (CA)(n) microsatellite polymorphism was examined by polymerase chain reaction (PCR). A polymorphic simple sequence repeat region of 9-23 CA repeats was detected in both groups. Homozygotes comprised 22% and 34% of breast cancer patients and controls, respectively (P=0.009). An allelic imbalance (AI), mostly in the shorter allele, was found in 27% of breast cancer patients. AI occurrence was associated with the lack of oestrogen receptors in tumour cells (P=0.05); otherwise, there were no correlations between histoclinical features and (CA)(n) microsatellite polymorphism of ERBB-1. It was concluded that an allelic imbalance is a common feature in breast cancer patients and may coincide with the lack of oestrogen receptors in tumour cells. The clinical relevance of ERBB-1 microsatellite polymorphism in breast cancer remains to be established.
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Affiliation(s)
- Marzena Wełnicka-Jaśkiewicz
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, ul. Debinki 7, 80-211 Gdańsk, Poland.
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46
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Xinarianos G, McRonald FE, Risk JM, Bowers NL, Nikolaidis G, Field JK, Liloglou T. Frequent genetic and epigenetic abnormalities contribute to the deregulation of cytoglobin in non-small cell lung cancer. Hum Mol Genet 2006; 15:2038-44. [PMID: 16698880 DOI: 10.1093/hmg/ddl128] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Lung cancer demonstrates the highest mortality in the UK. Previous studies have implicated allelic loss at chromosome 17q in the development of non-small cell lung carcinoma (NSCLC), and a number of known and putative tumour-suppressor genes reside within this region. One candidate tumour-suppressor gene is cytoglobin (CYGB), which is contained entirely within the 42.5 kb tylosis with oesophageal cancer (TOC) minimal region. CYGB abnormalities have been demonstrated only in sporadic head and neck cancers. In this study, we investigated the expression, promoter methylation and allelic imbalance status of this gene in 52 paired (normal/tumour) surgically excised lung tissue samples from patients with NSCLC. CYGB expression in tumour tissue was significantly reduced compared with corresponding adjacent normal in 54% of the examined cases (paired t-test, P<0.001). The CYGB promoter was shown by pyrosequencing to be significantly hypermethylated [2-fold increase of methylation index (MtI) in tumours] in 25/52 (48%) tumour samples compared with normal samples. MtI of the CYGB promoter was associated with CYGB mRNA expression (linear regression analysis, P=0.009), suggesting a primary role for the epigenetic events in CYGB silencing. In addition, frequent LOH was detected at the locus 17q25 in 32/48 (67%) tumours examined. It is of note that the loss of expression intensified when both LOH and hypermethylation coincided in samples (Mann-Whitney, P=0.049). These findings provide the first evidence to suggest the implication of CYGB in the pathogenesis of NSCLCs.
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MESH Headings
- Aged
- Aged, 80 and over
- Allelic Imbalance/genetics
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Cell Line
- Cell Line, Tumor
- Chromosomes, Human, Pair 17/genetics
- Cytoglobin
- DNA Methylation
- Epigenesis, Genetic/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Gene Frequency/genetics
- Globins/genetics
- Humans
- Linear Models
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Male
- Middle Aged
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
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Affiliation(s)
- George Xinarianos
- University of Liverpool Cancer Research Center, Roy Castle Lung Cancer Research Programme, Liverpool, UK
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47
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Bott SRJ, Masters JRW, Parkinson MC, Kirby RS, Feneley M, Hooper J, Williamson M. Allelic imbalance and biochemical outcome after radical prostatectomy. Prostate Cancer Prostatic Dis 2006; 9:160-8. [PMID: 16534511 DOI: 10.1038/sj.pcan.4500862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To compare the incidence of allelic imbalance (AI) in men with rapid disease progression with those who remained disease free after radical prostatectomy, with the aim of identifying genetic markers to predict prognosis and guide further treatment. PATIENTS AND METHODS Tumour and normal DNA were extracted from two matched groups of 31 men with extracapsular node-negative (pT3N0) prostate cancer who had undergone radical prostatectomy. One group comprised men who developed biochemical recurrence within 2 years of surgery and one group were prostate-specific antigen (PSA) free for at least 3 years. Men were matched for Gleason grade, preoperative PSA and pathological stage. Analysis was performed by genotyping. RESULTS Allelic imbalance was analysed using 30 markers, and was seen in at least one marker in 57 (92%) of the cases. Deletion at marker D10S211 (10p12.1) was significantly more common in the relapse group than the non-relapse group (35 vs 5%, P=0.03). CONCLUSIONS This study demonstrates significant association between AI on chromosome 10 and biochemical progression after radical prostatectomy.
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Affiliation(s)
- S R J Bott
- Prostate Cancer Research Centre, Institute of Urology, London, UK.
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48
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Lam CW, To KF, Tong SF. Genome-wide detection of allelic imbalance in renal cell carcinoma using high-density single-nucleotide polymorphism microarrays. Clin Biochem 2006; 39:187-90. [PMID: 16513104 DOI: 10.1016/j.clinbiochem.2006.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 12/09/2005] [Accepted: 01/02/2006] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Renal cell carcinoma (RCC) appears in both a sporadic form and a hereditary form. Eighty-five percent of sporadic RCCs are of the clear-cell histologic type. The cytogenetic analysis of RCCs has revealed several recurring sites of chromosomal aberrations (non-disjunction, deletion or mitotic recombination) including segments of loss of heterozygosity (LOH) identifiable by polymorphic markers. In this pilot study, we performed a comprehensive genome-wide scan to identify LOH sites of RCCs in three Chinese patients using high-density single-nucleotide polymorphism microarrays (HuSNP arrays). DESIGN AND METHODS Three sporadic clear-cell RCCs specimens were diagnosed histologically. Tumor genomic DNA was extracted from paraffin-embedded sections after microdissection to avoid gross contamination by non-tumor cells. Germline DNA was obtained from paired normal adjacent tissues. Affymetrix HuSNP mapping assay was performed according to the manufacturer's instructions. RESULTS Using high-density single-nucleotide polymorphism microarrays, we were able to identify the previously described and new LOH sites in RCCs of the three Chinese patients. CONCLUSION The high-density single-nucleotide polymorphism microarrays and assays offer significant operating cost benefits in sample preparation, processing, and data analysis for identification of LOH sites in cancer samples. In contrast to the typical microsatellite genotyping strategy, the entire genome scan is completed in one experiment taking less than 2 days.
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Affiliation(s)
- Ching-Wan Lam
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.
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49
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Fischer S, Lüdecke HJ, Wieczorek D, Böhringer S, Gillessen-Kaesbach G, Horsthemke B. Histone acetylation dependent allelic expression imbalance of BAPX1 in patients with the oculo-auriculo-vertebral spectrum. Hum Mol Genet 2006; 15:581-7. [PMID: 16407370 DOI: 10.1093/hmg/ddi474] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The oculo-auriculo-vertebral spectrum (OAVS) (OMIM % 164210) is a common developmental disorder characterized by hemifacial microsomia, epibulbar tumours, ear malformation and vertebral anomalies. Although rare familial cases suggest that OAVS has a genetic basis, no genetic defect has been identified so far. In a patient with OAVS and a chromosomal translocation t(4;8) we have found that the chromosome 4 breakpoint is 76.4 kb distal to the BAPX1 gene, which plays an essential role in craniofacial development. We did not detect any BAPX1 mutation in 105 patients, but observed a strong allelic expression imbalance (sAEI) in fibroblasts from five of 12 patients, but not in nine normal controls (Fisher's exact test, P=0.038). sAEI was de novo in one patient and inherited in two other patients. Prolonged cell culture or treatment with the histone deacetylase inhibitor Trichostatin A led to reactivation of the downregulated allele. We propose that epigenetic dysregulation of BAPX1 plays an important role in OAVS.
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Affiliation(s)
- Sven Fischer
- Institut für Humangenetik, Universitätsklinikum Essen, 45122 Essen, Germany
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50
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Abstract
BACKGROUND A fraction of head and neck squamous cell carcinomas (HNSCC) reveal overexpression of the p53 protein although sequence analysis failed to detect mutations in the core region of the protein. The functional and clinical status of p53 in these tumors is unclear. METHODS In 31 HNSCC, allelic imbalances (AI) at TP53 and other chromosome 17 loci were analyzed by microsatellite marker analysis. Expression of p16(INK4a) protein was analyzed by immunohistochemistry. Seven tumors were re-examined for sequence alterations by the Affymetrix p53 GeneChip. RESULTS About 54.8% of these tumors showed AI at TP53; 41.9% showed loss of p16, an overlapping fraction of 35.5% demonstrated AI and p16 loss. Six of seven such tumors revealed heterozygous missense mutations. CONCLUSIONS A large proportion of HNSCC with presumed wild-type p53 overexpression are false-negative cases. These results strengthen the established strong association of p53 protein overexpression with missense mutations. AI at TP53 and p16 loss are useful surrogate markers for genetic alterations of TP53 in HNSCC.
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Affiliation(s)
- Katharina Leng
- Molekularbiologisches Labor, Universitäts-HNO-Klinik, Heidelberg, Germany
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