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Saleh M, Cassier PA, Eberst L, Naik G, Morris VK, Pant S, Terret C, Gao L, Long A, Mao H, McNeely S, Wagner EK, Carlesi RM, Fu S. Phase I Study of Ramucirumab Plus Merestinib in Previously Treated Metastatic Colorectal Cancer: Safety, Preliminary Efficacy, and Pharmacokinetic Findings. Oncologist 2020; 25:e1628-e1639. [PMID: 32537847 PMCID: PMC7648328 DOI: 10.1634/theoncologist.2020-0520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/30/2020] [Indexed: 11/17/2022] Open
Abstract
LESSONS LEARNED The combination of the antivascular endothelial growth factor receptor 2 monoclonal antibody, ramucirumab, and the type II MET kinase inhibitor, merestinib, is tolerable. Preliminary efficacy data suggest that the combination may provide clinical benefit to patients with metastatic colorectal cancer (mCRC). Further development of this combination would likely necessitate the identification of subsets of patients with mCRC where the clinical benefit is of clinical relevance. BACKGROUND This study evaluated safety, preliminary efficacy, and pharmacokinetics of ramucirumab plus merestinib in patients with MCR previously treated with oxaliplatin and/or irinotecan. METHODS Open-label phase Ia/b study comprising 3+3 dose-limiting toxicity (DLT) observation and expansion parts. Treatment was ramucirumab 8 mg/kg on days 1 and 15 and merestinib 80 mg once daily (QD; 28-day cycle). Primary objective was safety and tolerability. Secondary objectives were pharmacokinetics and preliminary antitumor activity. Exploratory objective was biomarker associations. RESULTS Safety findings: DLT (proteinuria) of 7 phase Ia patients (the expansion part started at the initial recommended dose level); 16 patients (70%) with grade ≥3 treatment-emergent adverse events (TEAEs); 10 patients (43%) with grade ≥3 treatment-related TEAEs. The most common grade ≥3 treatment-related TEAEs were fatigue (4 patients [17%]) and increased blood alkaline phosphatase, diarrhea, and hypertension (2 patients each [9%]). One patient discontinued treatment because of cholestatic hepatitis. Geometric mean trough concentrations at cycle 1, day 15, were ramucirumab, 24.8 μg/mL; merestinib, 130 ng/mL. No complete or partial response was seen; 12 patients (52%) achieved stable disease. Median progression-free survival was 3.3 months (95% confidence interval [CI]: 1.6-4.4). Median overall survival was 8.9 months (95% CI: 3.5-12.7). There were no associations between genetic alterations and efficacy. CONCLUSION Ramucirumab plus merestinib is tolerable and may have clinical benefit in biomarker-unselected, heavily pretreated patients with mCRC.
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Affiliation(s)
- Mansoor Saleh
- O'Neal Comprehensive Cancer Center of University of Alabama at BirminghamBirminghamAlabamaUSA
| | | | - Lauriane Eberst
- Centre Léon Bérard, Department of Medical OncologyLyonFrance
- Université Claude Bernard Lyon 1LyonFrance
| | - Gurudatta Naik
- O'Neal Comprehensive Cancer Center of University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Van K. Morris
- University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Shubham Pant
- University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | | | - Ling Gao
- Eli Lilly and CompanyIndianapolisIndianaUSA
| | | | | | | | | | | | - Siqing Fu
- University of Texas MD Anderson Cancer CenterHoustonTexasUSA
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Abstract
Open data sharing and access has the potential to promote transparency and reproducibility in research, contribute to education and training, and prompt innovative secondary research. Yet, there are many reasons why researchers don't share their data. These include, among others, time and resource constraints, patient data privacy issues, lack of access to appropriate funding, insufficient recognition of the data originators' contribution, and the concern that commercial or academic competitors may benefit from analyses based on shared data. Nevertheless, there is a positive interest within and across the research and patient communities to create shared data resources. In this perspective, we will try to highlight the spectrum of "openness" and "data access" that exists at present and highlight the strengths and weakness of current data access platforms, present current examples of data sharing platforms, and propose guidelines to revise current data sharing practices going forward.
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Affiliation(s)
- Frank Rockhold
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | | | | | - Marc Buyse
- International Drug Development Institute (IDDI), San Francisco, CA, USA
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Wagner EK, Raje S, Amos L, Kurata J, Badve AS, Li Y, Busby B. Extending TCGA queries to automatically identify analogous genomic data from dbGaP. F1000Res 2017; 6:319. [PMID: 28794857 PMCID: PMC5538035 DOI: 10.12688/f1000research.9837.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/15/2016] [Indexed: 11/26/2022] Open
Abstract
Data sharing is critical to advance genomic research by reducing the demand to collect new data by reusing and combining existing data and by promoting reproducible research. The Cancer Genome Atlas (TCGA) is a popular resource for individual-level genotype-phenotype cancer related data. The Database of Genotypes and Phenotypes (dbGaP) contains many datasets similar to those in TCGA. We have created a software pipeline that will allow researchers to discover relevant genomic data from dbGaP, based on matching TCGA metadata. The resulting research provides an easy to use tool to connect these two data sources.
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Affiliation(s)
| | - Satyajeet Raje
- National Library of Medicine, National Institutes of Health, Bethesda, USA
| | - Liz Amos
- National Library of Medicine, National Institutes of Health, Bethesda, USA
| | - Jessica Kurata
- Department of Molecular and Cellular Biology, City of Hope, Duarte, USA
| | | | - Yingquan Li
- Corporate Executive Board (CEB), Arlington, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
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Yu Y, Wagner EK, Souied EH, Seitsonen S, Immonen IJ, Häppölä P, Raychaudhuri S, Daly MJ, Seddon JM. Protective coding variants in CFH and PELI3 and a variant near CTRB1 are associated with age-related macular degeneration†. Hum Mol Genet 2016; 25:5276-5285. [PMID: 28011711 PMCID: PMC6078639 DOI: 10.1093/hmg/ddw336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 01/26/2016] [Revised: 09/16/2016] [Accepted: 09/29/2016] [Indexed: 12/17/2022] Open
Abstract
Although numerous common age-related macular degeneration (AMD) alleles have been discovered using genome-wide association studies, substantial disease heritability remains unexplained. We sought to identify additional common and rare variants associated with advanced AMD. A total of 4,332 cases and 25,268 controls of European ancestry from three different populations were genotyped using the Illumina Infinium HumanExome BeadChip. We performed meta-analyses to identify associations with common variants, and single variant and gene-based burden tests to identify rare variants. Two protective, low-frequency, non-synonymous variants were significantly associated with a decrease in AMD risk: A307V in PELI3 (odds ratio [OR] = 0.14, P = 4.3 × 10-10) and N1050Y in CFH (OR = 0.76, P = 6.2 × 10-12). The new variants have a large effect size, similar to some rare mutations we reported previously in a targeted sequencing study, which remain significant in this analysis: CFH R1210C (OR = 18.82, P = 3.5 × 10-07), C3 K155Q (OR = 3.27, P = 1.5 × 10-10) and C9 P167S (OR = 2.04, P = 2.8 × 10-07). We also identified a strong protective signal for a common variant (rs8056814) near CTRB1 associated with a decrease in AMD risk (logistic regression: OR = 0.71, P = 1.8 × 10-07). Suggestive protective loci were identified in the COL4A3 and APOH genes. Our results support the involvement of common and low-frequency protective variants in this vision-threatening condition. This study expands the roles of the innate immune pathway as well as the extracellular matrix and high-density lipoprotein pathways in the aetiology of AMD.
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Affiliation(s)
- Yi Yu
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA, USA
| | - Erin K. Wagner
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA, USA
- Department of Ophthalmology, Tufts University School of Medicine, Boston, MA, USA
| | - Eric H. Souied
- Hôpital Intercommunal, Hôpital Henri Mondor, Créteil Université Paris Est, Paris, France
| | | | | | - Paavo Häppölä
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Soumya Raychaudhuri
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA and
| | - Johanna M. Seddon
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA, USA
- Department of Ophthalmology, Tufts University School of Medicine, Boston, MA, USA
- Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, USA
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Zhang Y, Wagner EK, Guo X, May I, Cai Q, Zheng W, He C, Long J. Long intergenic non-coding RNA expression signature in human breast cancer. Sci Rep 2016; 6:37821. [PMID: 27897201 PMCID: PMC5126689 DOI: 10.1038/srep37821] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/28/2016] [Indexed: 12/21/2022] Open
Abstract
Breast cancer is a complex disease, characterized by gene deregulation. There is less systematic investigation of the capacity of long intergenic non-coding RNAs (lincRNAs) as biomarkers associated with breast cancer pathogenesis or several clinicopathological variables including receptor status and patient survival. We designed a two-stage study, including 1,000 breast tumor RNA-seq data from The Cancer Genome Atlas (TCGA) as the discovery stage, and RNA-seq data of matched tumor and adjacent normal tissue from 50 breast cancer patients as well as 23 normal breast tissue from healthy women as the replication stage. We identified 83 lincRNAs showing the significant expression changes in breast tumors with a false discovery rate (FDR) < 1% in the discovery dataset. Thirty-seven out of the 83 were validated in the replication dataset. Integrative genomic analyses suggested that the aberrant expression of these 37 lincRNAs was probably related with the expression alteration of several transcription factors (TFs). We observed a differential co-expression pattern between lincRNAs and their neighboring genes. We found that the expression levels of one lincRNA (RP5-1198O20 with Ensembl ID ENSG00000230615) were associated with breast cancer survival with P < 0.05. Our study identifies a set of aberrantly expressed lincRNAs in breast cancer.
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Affiliation(s)
- Yanfeng Zhang
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Erin K Wagner
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN 46202, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Isaac May
- Bowdoin College, Brunswick, ME, 04011, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Chunyan He
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN 46202, USA.,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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Atkinson JP, Wagner EK, Raychaudhuri S, Villalonga MB, Java A, Triebwasser MP, Daly MJ, Seddon JM. Mapping rare, deleterious mutations in Factor H: Association with early onset, drusen burden, and lower antigenic levels in familial AMD. Immunobiology 2016. [DOI: 10.1016/j.imbio.2016.06.178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Wu W, Wagner EK, Hao Y, Rao X, Dai H, Han J, Chen J, Storniolo AMV, Liu Y, He C. Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer. Sci Rep 2016; 6:32731. [PMID: 27597120 PMCID: PMC5011741 DOI: 10.1038/srep32731] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 05/12/2016] [Accepted: 08/12/2016] [Indexed: 02/01/2023] Open
Abstract
Inference of the biological roles of lncRNAs in breast cancer development remains a challenge. Here, we analyzed RNA-seq data in tumor and normal breast tissue samples from 18 breast cancer patients and 18 healthy controls and constructed a functional lncRNA-mRNA co-expression network. We revealed two distinctive co-expression patterns associated with breast cancer, reflecting different underlying regulatory mechanisms: (1) 516 pairs of lncRNA-mRNAs have differential co-expression pattern, in which the correlation between lncRNA and mRNA expression differs in tumor and normal breast tissue; (2) 291 pairs have dose-response co-expression pattern, in which the correlation is similar, but the expression level of lncRNA or mRNA differs in the two tissue types. We further validated our findings in TCGA dataset and annotated lncRNAs using TANRIC. One novel lncRNA, AC145110.1 on 8p12, was found differentially co-expressed with 127 mRNAs (including TOX4 and MAEL) in tumor and normal breast tissue and also highly correlated with breast cancer clinical outcomes. Functional enrichment and pathway analyses identified distinct biological functions for different patterns of co-expression regulations. Our data suggested that lncRNAs might be involved in breast tumorigenesis through the modulation of gene expression in multiple pathologic pathways.
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Affiliation(s)
- Wenting Wu
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Erin K. Wagner
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Yangyang Hao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xi Rao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hongji Dai
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, National Clinical Research Center for Cancer, Tianjin & Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Jinhui Chen
- Spinal Cord and Brain Injury Research Group, Department of Neurosurgery, Stark Neuroscience Research Institute, Indiana University, Indianapolis, IN, USA
| | - Anna Maria V. Storniolo
- Susan G. Komen Tissue Bank at the Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University, Indianapolis, IN 46202, USA
| | - Chunyan He
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University, Indianapolis, IN 46202, USA
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8
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Wagner EK, Raychaudhuri S, Villalonga MB, Java A, Triebwasser MP, Daly MJ, Atkinson JP, Seddon JM. Mapping rare, deleterious mutations in Factor H: Association with early onset, drusen burden, and lower antigenic levels in familial AMD. Sci Rep 2016; 6:31531. [PMID: 27572114 PMCID: PMC5004131 DOI: 10.1038/srep31531] [Citation(s) in RCA: 40] [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: 01/08/2016] [Accepted: 07/21/2016] [Indexed: 02/02/2023] Open
Abstract
The genetic architecture of age-related macular degeneration (AMD) involves numerous genetic variants, both common and rare, in the coding region of complement factor H (CFH). While these variants explain high disease burden in some families, they fail to explain the pathology in all. We selected families whose AMD was unexplained by known variants and performed whole exome sequencing to probe for other rare, highly penetrant variants. We identified four rare loss-of-function variants in CFH associated with AMD. Missense variant CFH 1:196646753 (C192F) segregated perfectly within a family characterized by advanced AMD and drusen temporal to the macula. Two families, each comprising a pair of affected siblings with extensive extramacular drusen, carried essential splice site variant CFH 1:196648924 (IVS6+1G>A) or missense variant rs139360826 (R175P). In a fourth family, missense variant rs121913058 (R127H) was associated with AMD. Most carriers had early onset bilateral advanced AMD and extramacular drusen. Carriers tended to have low serum Factor H levels, especially carriers of the splice variant. One missense variant (R127H) has been previously shown not to be secreted. The two other missense variants were produced recombinantly: compared to wild type, one (R175P) had no functional activity and the other (C192F) had decreased secretion.
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Affiliation(s)
- Erin K. Wagner
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA 02111, USA
- Department of Ophthalmology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Soumya Raychaudhuri
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Mercedes B. Villalonga
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA 02111, USA
| | - Anuja Java
- Washington University School of Medicine, Department of Medicine, Division of Nephrology, Saint Louis, MO 63110, USA
| | - Michael P. Triebwasser
- Washington University School of Medicine, Department of Medicine, Division of Rheumatology, Saint Louis, MO 63110, USA
| | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA 02115, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John P. Atkinson
- Washington University School of Medicine, Department of Medicine, Division of Rheumatology, Saint Louis, MO 63110, USA
| | - Johanna M. Seddon
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA 02111, USA
- Department of Ophthalmology, Tufts University School of Medicine, Boston, MA 02111, USA
- Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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Triebwasser MP, Roberson EDO, Yu Y, Schramm EC, Wagner EK, Raychaudhuri S, Seddon JM, Atkinson JP. Rare Variants in the Functional Domains of Complement Factor H Are Associated With Age-Related Macular Degeneration. Invest Ophthalmol Vis Sci 2016; 56:6873-8. [PMID: 26501415 DOI: 10.1167/iovs.15-17432] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Age-related macular degeneration (AMD) has a substantial genetic risk component, as evidenced by the risk from common genetic variants uncovered in the first genome-wide association studies. More recently, it has become apparent that rare genetic variants also play an independent role in AMD risk. We sought to determine if rare variants in complement factor H (CFH) played a role in AMD risk. METHODS We had previously collected DNA from a large population of patients with advanced age-related macular degeneration (A-AMD) and controls for targeted deep sequencing of candidate AMD risk genes. In this analysis, we tested for an increased burden of rare variants in CFH in 1665 cases and 752 controls from this cohort. RESULTS We identified 65 missense, nonsense, or splice-site mutations with a minor allele frequency ≤ 1%. Rare variants with minor allele frequency ≤ 1% (odds ratio [OR] = 1.5, P = 4.4 × 10⁻²), 0.5% (OR = 1.6, P = 2.6 × 10⁻²), and all singletons (OR = 2.3, P = 3.3 × 10⁻²) were enriched in A-AMD cases. Moreover, we observed loss-of-function rare variants (nonsense, splice-site, and loss of a conserved cysteine) in 10 cases and serum levels of FH were decreased in all 5 with an available sample (haploinsufficiency). Further, rare variants in the major functional domains of CFH were increased in cases (OR = 3.2; P = 1.4 × 10⁻³) and the magnitude of the effect correlated with the disruptive nature of the variant, location in an active site, and inversely with minor allele frequency. CONCLUSIONS In this large A-AMD cohort, rare variants in the CFH gene were enriched and tended to be located in functional sites or led to low serum levels. These data, combined with those indicating a similar, but even more striking, increase in rare variants found in CFI, strongly implicate complement activation in A-AMD etiopathogenesis as CFH and CFI interact to inhibit the alternative pathway.
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Affiliation(s)
- Michael P Triebwasser
- Washington University School of Medicine Department of Internal Medicine, Division of Rheumatology, St. Louis, Missouri, United States
| | - Elisha D O Roberson
- Washington University School of Medicine Department of Internal Medicine, Division of Rheumatology, St. Louis, Missouri, United States 2Washington University School of Medicine, Department of Genetics, St. Louis, Missouri, United States
| | - Yi Yu
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, Massachusetts, United States
| | - Elizabeth C Schramm
- Washington University School of Medicine Department of Internal Medicine, Division of Rheumatology, St. Louis, Missouri, United States
| | - Erin K Wagner
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, Massachusetts, United States 4Department of Ophthalmology, Tufts University School of Medicine, Sackler School of Graduate Medical Sciences, Tufts Universi
| | - Soumya Raychaudhuri
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, Massachusetts, United States 4Department of Ophthalmology, Tufts University School of Medicine, Sackler School of Graduate Medical Sciences, Tufts Universi
| | - Johanna M Seddon
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, Massachusetts, United States 4Department of Ophthalmology, Tufts University School of Medicine, Sackler School of Graduate Medical Sciences, Tufts Universi
| | - John P Atkinson
- Washington University School of Medicine Department of Internal Medicine, Division of Rheumatology, St. Louis, Missouri, United States
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Kavanagh D, Yu Y, Schramm EC, Triebwasser M, Wagner EK, Raychaudhuri S, Daly MJ, Atkinson JP, Seddon JM. Rare genetic variants in the CFI gene are associated with advanced age-related macular degeneration and commonly result in reduced serum factor I levels. Hum Mol Genet 2015; 24:3861-70. [PMID: 25788521 PMCID: PMC4459386 DOI: 10.1093/hmg/ddv091] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 03/09/2015] [Indexed: 12/13/2022] Open
Abstract
To assess a potential diagnostic and therapeutic biomarker for age-related macular degeneration (AMD), we sequenced the complement factor I gene (CFI) in 2266 individuals with AMD and 1400 without, identifying 231 individuals with rare genetic variants. We evaluated the functional impact by measuring circulating serum factor I (FI) protein levels in individuals with and without rare CFI variants. The burden of very rare (frequency <1/1000) variants in CFI was strongly associated with disease (P = 1.1 × 10−8). In addition, we examined eight coding variants with counts ≥5 and saw evidence for association with AMD in three variants. Individuals with advanced AMD carrying a rare CFI variant had lower mean FI compared with non-AMD subjects carrying a variant (P < 0.001). Further new evidence that FI levels drive AMD risk comes from analyses showing individuals with a CFI rare variant and low FI were more likely to have advanced AMD (P = 5.6 × 10−5). Controlling for covariates, low FI increased the risk of advanced AMD among those with a variant compared with individuals without advanced AMD with a rare CFI variant (OR 13.6, P = 1.6 × 10−4), and also compared with control individuals without a rare CFI variant (OR 19.0, P = 1.1 × 10−5). Thus, low FI levels are strongly associated with rare CFI variants and AMD. Enhancing FI activity may be therapeutic and measuring FI provides a screening tool for identifying patients who are most likely to benefit from complement inhibitory therapy.
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Affiliation(s)
- David Kavanagh
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Yi Yu
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA, USA
| | - Elizabeth C Schramm
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael Triebwasser
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Erin K Wagner
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA, USA
| | - Soumya Raychaudhuri
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA, Division of Genetics, Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Mark J Daly
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - John P Atkinson
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Johanna M Seddon
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA, USA, Department of Ophthalmology, Tufts University School of Medicine, Boston, MA, USA and Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, USA
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Abstract
PURPOSE Previous studies have identified novel genetic variants associated with age at menarche in females of European descent. The pubertal growth effects of these variants have not been carefully evaluated in non-European descent groups. We aimed to examine the effects of 31 newly identified menarche-related single-nucleotide polymorphisms (SNPs) on growth outcomes in African-American (AA) and European-American (EA) children in a prospective cohort. METHODS We analyzed longitudinal data collected from 263 AAs and 338 EAs enrolled between ages 5 and 17 years; the subjects were followed semiannually for an average of 6 years. The associations between the SNPs and growth-related outcomes, including weight, height, and body mass index (BMI), were examined using mixed-effect models. RESULTS Longitudinal analyses revealed that 4 (near or in genes VGLL3, PEX2, CA10, and SKOR2) of the 14 menarche-only-related SNPs were associated with changes in weight and BMI in EA and AA (p ≤ .0032), but none of them was associated with changes in height. Of the eight menarche-timing and BMI-related SNPs, none was associated with changes in height, but three (in or near genes NEGR1, ETV5, and FTO) were associated with more rapid increases in weight and/or BMI in EA (p ≤ .0059). Among the nine menarche-timing and height-related SNPs, four (in or near genes ZBTB38, LOC728666, TBX2, and CABLES) were associated with changes in weight or height in EA and AA (p ≤ .0042). CONCLUSIONS Genetic variants related to age at menarche were found to be associated with various growth parameters in healthy adolescents. The identified associations were often race and sex specific.
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Affiliation(s)
- Wanzhu Tu
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Erin K Wagner
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, Indiana
| | - George J Eckert
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Zhangsheng Yu
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Tamara Hannon
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - J Howard Pratt
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana; The Veterans Affairs Medical Center, Indianapolis, Indiana
| | - Chunyan He
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, Indiana; Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana.
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12
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Tu W, Wagner EK, Eckert GJ, Yu Z, Hannon T, Pratt JH, He C. Associations between menarche-related genetic variants and pubertal growth in male and female adolescents. J Adolesc Health 2015; 56:66-72. [PMID: 25287989 PMCID: PMC4275397 DOI: 10.1016/j.jadohealth.2014.07.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/16/2014] [Accepted: 07/30/2014] [Indexed: 12/25/2022]
Abstract
PURPOSE Previous studies have identified novel genetic variants associated with age at menarche in females of European descent. The pubertal growth effects of these variants have not been carefully evaluated in non-European descent groups. We aimed to examine the effects of 31 newly identified menarche-related single-nucleotide polymorphisms (SNPs) on growth outcomes in African-American (AA) and European-American (EA) children in a prospective cohort. METHODS We analyzed longitudinal data collected from 263 AAs and 338 EAs enrolled between ages 5 and 17 years; the subjects were followed semiannually for an average of 6 years. The associations between the SNPs and growth-related outcomes, including weight, height, and body mass index (BMI), were examined using mixed-effect models. RESULTS Longitudinal analyses revealed that 4 (near or in genes VGLL3, PEX2, CA10, and SKOR2) of the 14 menarche-only-related SNPs were associated with changes in weight and BMI in EA and AA (p ≤ .0032), but none of them was associated with changes in height. Of the eight menarche-timing and BMI-related SNPs, none was associated with changes in height, but three (in or near genes NEGR1, ETV5, and FTO) were associated with more rapid increases in weight and/or BMI in EA (p ≤ .0059). Among the nine menarche-timing and height-related SNPs, four (in or near genes ZBTB38, LOC728666, TBX2, and CABLES) were associated with changes in weight or height in EA and AA (p ≤ .0042). CONCLUSIONS Genetic variants related to age at menarche were found to be associated with various growth parameters in healthy adolescents. The identified associations were often race and sex specific.
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Affiliation(s)
- Wanzhu Tu
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Erin K. Wagner
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, Indiana
| | - George J. Eckert
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Zhangsheng Yu
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Tamara Hannon
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - J. Howard Pratt
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana,The Veterans Affairs Medical Center, Indianapolis, Indiana
| | - Chunyan He
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, Indiana; Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana.
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13
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Perry JRB, Day F, Elks CE, Sulem P, Thompson DJ, Ferreira T, He C, Chasman DI, Esko T, Thorleifsson G, Albrecht E, Ang WQ, Corre T, Cousminer DL, Feenstra B, Franceschini N, Ganna A, Johnson AD, Kjellqvist S, Lunetta KL, McMahon G, Nolte IM, Paternoster L, Porcu E, Smith AV, Stolk L, Teumer A, Tšernikova N, Tikkanen E, Ulivi S, Wagner EK, Amin N, Bierut LJ, Byrne EM, Hottenga JJ, Koller DL, Mangino M, Pers TH, Yerges-Armstrong LM, Zhao JH, Andrulis IL, Anton-Culver H, Atsma F, Bandinelli S, Beckmann MW, Benitez J, Blomqvist C, Bojesen SE, Bolla MK, Bonanni B, Brauch H, Brenner H, Buring JE, Chang-Claude J, Chanock S, Chen J, Chenevix-Trench G, Collée JM, Couch FJ, Couper D, Coveillo AD, Cox A, Czene K, D’adamo AP, Smith GD, De Vivo I, Demerath EW, Dennis J, Devilee P, Dieffenbach AK, Dunning AM, Eiriksdottir G, Eriksson JG, Fasching PA, Ferrucci L, Flesch-Janys D, Flyger H, Foroud T, Franke L, Garcia ME, García-Closas M, Geller F, de Geus EEJ, Giles GG, Gudbjartsson DF, Gudnason V, Guénel P, Guo S, Hall P, Hamann U, Haring R, Hartman CA, Heath AC, Hofman A, Hooning MJ, Hopper JL, Hu FB, Hunter DJ, Karasik D, Kiel DP, Knight JA, Kosma VM, Kutalik Z, Lai S, Lambrechts D, Lindblom A, Mägi R, Magnusson PK, Mannermaa A, Martin NG, Masson G, McArdle PF, McArdle WL, Melbye M, Michailidou K, Mihailov E, Milani L, Milne RL, Nevanlinna H, Neven P, Nohr EA, Oldehinkel AJ, Oostra BA, Palotie A, Peacock M, Pedersen NL, Peterlongo P, Peto J, Pharoah PDP, Postma DS, Pouta A, Pylkäs K, Radice P, Ring S, Rivadeneira F, Robino A, Rose LM, Rudolph A, Salomaa V, Sanna S, Schlessinger D, Schmidt MK, Southey MC, Sovio U, Stampfer MJ, Stöckl D, Storniolo AM, Timpson NJ, Tyrer J, Visser JA, Vollenweider P, Völzke H, Waeber G, Waldenberger M, Wallaschofski H, Wang Q, Willemsen G, Winqvist R, Wolffenbuttel BHR, Wright MJ, Boomsma DI, Econs MJ, Khaw KT, Loos RJF, McCarthy MI, Montgomery GW, Rice JP, Streeten EA, Thorsteinsdottir U, van Duijn CM, Alizadeh BZ, Bergmann S, Boerwinkle E, Boyd HA, Crisponi L, Gasparini P, Gieger C, Harris TB, Ingelsson E, Järvelin MR, Kraft P, Lawlor D, Metspalu A, Pennell CE, Ridker PM, Snieder H, Sørensen TIA, Spector TD, Strachan DP, Uitterlinden AG, Wareham NJ, Widen E, Zygmunt M, Murray A, Easton DF, Stefansson K, Murabito JM, Ong KK. Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Nature 2014; 514:92-97. [PMID: 25231870 PMCID: PMC4185210 DOI: 10.1038/nature13545] [Citation(s) in RCA: 378] [Impact Index Per Article: 37.8] [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: 12/23/2013] [Accepted: 05/30/2014] [Indexed: 02/02/2023]
Abstract
Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P < 5 × 10(-8)) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1-WDR25, MKRN3-MAGEL2 and KCNK9) demonstrating parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and γ-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition.
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Affiliation(s)
- John RB Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- University of Exeter Medical School, University of Exeter, Exeter, UK EX1 2LU
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Felix Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Cathy E Elks
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | | | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chunyan He
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN 46202, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children’s Hospital, Boston, MA 02115, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, 140 Cambridge 02142, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Wei Q Ang
- School of Women’s and Infants’ Health, The University of Western Australia
| | - Tanguy Corre
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Diana L Cousminer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - Andrea Ganna
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Andrew D Johnson
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, MA
| | - Sanela Kjellqvist
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Kathryn L Lunetta
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, MA
- Boston University School of Public Health, Department of Biostatistics. Boston, MA
| | - George McMahon
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Eleonora Porcu
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Italy
- University of Sassari, Dept. Of Biomedical Sciences, Sassari, Italy
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Lisette Stolk
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Natalia Tšernikova
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Department of Biotechnology, University of Tartu, Tartu, 51010, Estonia
| | - Emmi Tikkanen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
- Hjelt Institute, University of Helsinki, Finland
| | - Sheila Ulivi
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo” – Trieste, Italy
| | - Erin K Wagner
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN 46202, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Najaf Amin
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Laura J Bierut
- Dept. of Psychiatry, Washington University, St. Louis, MO 63110
| | - Enda M Byrne
- The University of Queensland, Queensland Brain Institute, St.Lucia, QLD, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - Daniel L Koller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Tune H Pers
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children’s Hospital, Boston, MA 02115, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, 140 Cambridge 02142, MA, USA
- Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, US
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical 142 University of Denmark, Lyngby 2800, Denmark
| | - Laura M Yerges-Armstrong
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition - University of Maryland School of Medicine, USA. Baltimore, MD 21201
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Irene L Andrulis
- Ontario Cancer Genetics Network, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, California, USA
| | | | - Stefania Bandinelli
- Tuscany Regional Health Agency, Florence, Italy, I.O.T. and Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
- Geriatric Unit, Azienda Sanitaria di Firenze, Florence, Italy
| | - Matthias W Beckmann
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Javier Benitez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Milan, Italy
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart
- University of Tübingen, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jinhui Chen
- Departments of Anatomy and Neurological Surgery, Indiana University school of Medicine, Indianapolis, IN 46202, USA
- Stark Neuroscience Research Center, Indiana University school of Medicine, Indianapolis, IN 46202, USA
| | | | - J. Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - David Couper
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC
| | - Andrea D Coveillo
- Boston University School of Medicine, Department of Medicine, Sections of Preventive Medicine and Endocrinology, Boston, MA
| | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Adamo Pio D’adamo
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo” – Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, Italy
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minn., USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Peter Devilee
- Department of Human Genetics & Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Aida K Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, UK
| | | | - Johan G Eriksson
- National Institute for Health and Welfare, Finland
- Department of General Practice and Primary health Care, University of Helsinki, Finland
- Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland
- Folkhalsan Research Centre, Helsinki, Finland
| | - Peter A Fasching
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Luigi Ferrucci
- Longitudinal Studies Section, Clinical Research Branch, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland, United States of America
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry and Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Melissa E Garcia
- National Insitute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Montserrat García-Closas
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
- Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Eco EJ de Geus
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
- EMGO + Institute for Health and Care Research, VU University Medical Centre, Van der Boechorststraat 7, 1081 Bt, Amsterdam, The Netherlands
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Daniel F Gudbjartsson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Suiqun Guo
- Department of Obstetrics and Gynecology, Southern Medical University, Guangzhou, China
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Robin Haring
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Catharina A Hartman
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Andrew C Heath
- Washington University, Department of Psychiatry, St.Louis, Missouri, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdan, the Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Frank B Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
| | - David J Hunter
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, 140 Cambridge 02142, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David Karasik
- Harvard Medical School, Boston, MA 02115
- Hebrew SeniorLife Institute for Aging Research, Boston, MA
| | - Douglas P Kiel
- Hebrew SeniorLife Institute for Aging Research, Boston, MA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Zoltan Kutalik
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandra Lai
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Italy
| | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Patrik K Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Nicholas G Martin
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Patrick F McArdle
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition - University of Maryland School of Medicine, USA. Baltimore, MD 21201
| | - Wendy L McArdle
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
- Department of Medicine, Stanford School of Medicine, Stanford, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Department of Biotechnology, University of Tartu, Tartu, 51010, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Patrick Neven
- KULeuven (University of Leuven), Department of Oncology, Multidisciplinary Breast Center, University Hospitals Leuven, Belgium
| | - Ellen A Nohr
- Research Unit of Obstetrics & Gynecology, Institute of Clinical Research, University of Southern denmark, DK
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ben A Oostra
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Munro Peacock
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Paul DP Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, UK
| | - Dirkje S Postma
- University Groningen, University Medical Center Groningen, Department Pulmonary Medicine and Tuberculosis, GRIAC Research Institute, Groningen, The Netherlands
| | - Anneli Pouta
- National Institute for Health and Welfare, Finland
- Department of Obstetrics and Gynecology, Oulu University Hospital, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdan, the Netherlands
| | - Antonietta Robino
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo” – Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, Italy
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Serena Sanna
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Italy
| | - David Schlessinger
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Mellissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Ulla Sovio
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, United Kingdom
| | - Meir J Stampfer
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
| | - Doris Stöckl
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Obstetrics and Gynaecology, Campus Grosshadern, Ludwig-Maximilians- University, Munich, Germany
| | - Anna M Storniolo
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Jonathan Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, UK
| | - Jenny A Visser
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Peter Vollenweider
- Department of Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
| | - Gerard Waeber
- Department of Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Henri Wallaschofski
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Bruce HR Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Margaret J Wright
- Queensland Insitute of Medical Research, Brisbane, Queensland, Australia
| | - Australian Ovarian Cancer Study
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - The GENICA Network
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart
- University of Tübingen, Germany
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
- Institute of Pathology, Medical Faculty of the University of Bonn, Bonn, Germany
- Institute of Occupational Medicine and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - kConFab
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - Michael J Econs
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ruth JF Loos
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Genetics of Obesity and Related Metabolic Traits Program, The Charles Bronfman Institute for Personalized Medicine, The Mindich Child Health and Development Institute, Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1003, New York, NY 10029, USA
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
| | - Grant W Montgomery
- Queensland Insitute of Medical Research, Brisbane, Queensland, Australia
| | - John P Rice
- Dept. of Psychiatry, Washington University, St. Louis, MO 63110
| | - Elizabeth A Streeten
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition - University of Maryland School of Medicine, USA. Baltimore, MD 21201
- Geriatric Research and Education Clinical Center (GRECC) - Veterans Administration Medical Center, USA. Baltimore, MD 21201
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Cornelia M van Duijn
- Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- Centre of Medical Systems Biology, Leiden, the Netherlands
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sven Bergmann
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eric Boerwinkle
- Human Genetics Center and Div. of Epidemiology, University of Houston, TX
| | - Heather A Boyd
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Laura Crisponi
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Italy
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo” – Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, Italy
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Tamara B Harris
- National Insitute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Institute of Health Sciences, P.O.Box 5000, FI-90014 University of Oulu, Finland
- Biocenter Oulu, P.O.Box 5000, Aapistie 5A, FI-90014 University of Oulu, Finland
- Department of Children and Young People and Families, National Institute for Health and Welfare, Aapistie 1, Box 310, FI-90101 Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, P.O.Box 20, FI-90220 Oulu, 90029 OYS, Finland
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Debbie Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Department of Biotechnology, University of Tartu, Tartu, 51010, Estonia
| | - Craig E Pennell
- School of Women’s and Infants’ Health, The University of Western Australia
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Thorkild IA Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, The Capital Region, Copenhagen, Denmark
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - David P Strachan
- Division of Population Health Sciences and Education, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdan, the Netherlands
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - Marek Zygmunt
- Department of Obstetrics and Gynecology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Anna Murray
- University of Exeter Medical School, University of Exeter, Exeter, UK EX1 2LU
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Joanne M Murabito
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, MA
- Boston University School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA
| | - Ken K Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Department of Paediatrics,University of Cambridge,Cambridge,UK
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14
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Wagner EK, Shevate SK, Liu Y, He C. Abstract 2555: Tissue-specific regulation of alternative splicing by breast cancer associated genetic variants identified in recent GWAS. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-2555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent genome-wide association studies (GWAS) have identified more than 30 novel loci associated with breast cancer. However, the biological functions of these genetic variants have not been characterized yet. Alternative splicing is one mechanism through which genetic variants may act on gene expression. We hypothesize that the associated genetic variants influence tissue-specific regulation of alternative splicing leading to misregulation of specific isoforms involved in breast tumorigenesis. We performed an integrated analysis of genomic variation and transcriptome sequencing to elucidate alternatively spliced isoform expression quantitative trait loci (asQTL) and to identify breast cancer susceptibility genes whose isoform-specific expression were influenced by the candidate genetic variants. The current study utilized a unique source of paired blood and normal breast tissue from 20 healthy women free of diagnosed breast cancer. We genotyped 42 SNPs that were associated with breast cancer in previous GWAS reports, and assessed expression of approximately 35,000 known splicing variants in more than 24,000 gene transcripts in normal breast tissue using RNA sequencing data. Analysis of variance (ANOVA) was performed to assess the differences of isoform-specific expression across genotypes. After account of age, race and batch effects, we found 384 unique genes whose isoform-specific expressions in normal breast tissue were correlated with the 42 breast cancer candidate SNPs (Bonferroni corrected p < 0.05). The majority of the identified gene isoforms (>90%) were associated with the candidate SNPs in trans, i.e. isoform-specific expression were influenced by SNPs on a different chromosome. In addition, 27 out of the 384 identified genes also showed differential isoform-specific expression in breast tumor vs. normal tissue in our separate analyses. We have identified known cancer genes including SOD1, NPM1, FAU, GABARAP, and SMAD5, as well as novel putative breast cancer genes including PCBP2, SAP18, ATPF7IP, and N4BP2L2. An ingenuity pathway analysis of the 27 genes suggested three functional networks. Network 1, related to “Cell Death and Survival, Cell Cycle, and Gene Expression," includes genes EIF4A1, GABARAP, HARS, HNRNPC and USP33; network 2, related to “Organ Morphology, Reproductive
System Development of Function, and Embryonic Development," included genes ATF7IP, NPM1, RAB2A, SMAD5, and SOD1; network 3, related to “Cancer, Neurological Disease, Cell Death and Survival," includes gene FAM45A. Our results identify known and novel putative breast cancer susceptibility genes whose isoform-specific expression were influenced by breast cancer candidate SNPs from previous GWAS, showing the impact of germline variants on the regulation of alternative splicing in transcriptome.
Citation Format: Erin K. Wagner, Swapnil Kanifnath Shevate, Yunlong Liu, Chunyan He. Tissue-specific regulation of alternative splicing by breast cancer associated genetic variants identified in recent GWAS. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2555. doi:10.1158/1538-7445.AM2013-2555
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15
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He C, Eckert GJ, Wagner EK, Yu Z, Pratt JH, Tu W. Abstract 437: Reproductive Timing Related Genetic Variants from GWAS are Associated with Blood Pressure in Healthy Adolescents. Hypertension 2012. [DOI: 10.1161/hyp.60.suppl_1.a437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Blood pressure (BP) increases in an accelerated fashion during puberty. Previous studies have identified genetic variants that were associated with the timing of reproductive aging, namely menarche and menopause. But the effects of these genetic variations on BP have not been investigated. We examined the BP effects of 46 SNPs identified in genome-wide association studies (GWAS) that were linked to age of menarche or of menopause in women of European ancestry. The current analysis was based on longitudinal data collected from 601 adolescents (338 whites and 263 blacks). Subjects were enrolled between ages 4 and 17 and followed for an average of 6 years. After adjusting for multiple testing, we found 3 of the 16 menarche-related SNPs, rs10423674 in
CRTC1
, rs13187289 near
PHF15
and rs9635759 near
CA10
, were associated with a more rapid increase of BP in black males (all P< 0.0023); and two SNPs (rs17268785 in
CCDC85A
and rs7642134 near
VGLL3
) and one SNP (rs1079866 near
INHBA
) were associated with increased BP in black and white females, respectively (all P<0.0026). Of the 8 menarche and weight-related SNPs, rs7647305 near
ETV5
was associated with increased BP in whites (P=0.0028); and 3 of the 7 menarche and height-related NPs, rs10946808 near
HIST1H1D
, rs6440003 in
ZBTB38
and
rs757608
near
TBX2
, were positively associated with BP in white males, white females, and black males, respectively (all P<0.005). Except for one SNP, none of the 15 menopause-related SNPs were associated with BP. The one menopause-related SNP in gene
SYCP2L
, rs2153157, was associated with an increase of BP in whites (P= 0.0028). Most of the associations (9 of 11) were in the direction predicted by previously observed associations with menarche or menopause ages. Furthermore, these associations did not appear to be attenuated by weight and height. In conclusion, genetic variants from previous GWAS that were associated with a women’s reproductive aging showed significant associations with BP in healthy male and female adolescents. The genetic effects were independent of a subject’s sex, race or growth related factors such as weight, height, and BMI, and thus may represent novel candidates for BP genes.
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Affiliation(s)
| | | | | | | | | | - Wanzhu Tu
- Indiana Univeristy, Indianapolis, IN
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16
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Aguilar JS, Devi-Rao GV, Rice MK, Sunabe J, Ghazal P, Wagner EK. Quantitative comparison of the HSV-1 and HSV-2 transcriptomes using DNA microarray analysis. Virology 2006; 348:233-41. [PMID: 16448680 DOI: 10.1016/j.virol.2005.12.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [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: 11/09/2005] [Revised: 11/30/2005] [Accepted: 12/19/2005] [Indexed: 10/25/2022]
Abstract
The genomes of human herpes virus type-1 and type-2 share a high degree of sequence identity; yet, they exhibit important differences in pathology in their natural human host as well as in animal host and cell cultures. Here, we report the comparative analysis of the time and relative abundance profiles of the transcription of each virus type (their transcriptomes) using parallel infections and microarray analysis using HSV-1 probes which hybridize with high efficiency to orthologous HSV-2 transcripts. We have confirmed that orthologous transcripts belong to the same kinetic class; however, the temporal pattern of accumulation of 4 transcripts (U(L)4, U(L)29, U(L)30, and U(L)31) differs in infections between the two virus types. Interestingly, the protein products of these transcripts are all involved in nuclear organization and viral DNA localization. We discuss the relevance of these findings and whether they may have potential roles in the pathological differences of HSV-1 and HSV-2.
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Affiliation(s)
- J S Aguilar
- Department of Molecular Biology and Biochemistry and Center for Virus Research, University of California, Irvine, Irvine, CA 92697, USA.
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17
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Sun A, Devi-Rao GV, Rice MK, Gary LW, Bloom DC, Sandri-Goldin RM, Ghazal P, Wagner EK. Immediate-early expression of the herpes simplex virus type 1 ICP27 transcript is not critical for efficient replication in vitro or in vivo. J Virol 2004; 78:10470-8. [PMID: 15367613 PMCID: PMC516393 DOI: 10.1128/jvi.78.19.10470-10478.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 02/11/2004] [Accepted: 05/28/2004] [Indexed: 11/20/2022] Open
Abstract
We constructed a promoter mutation altering the immediate-early expression of the herpes simplex virus type 1 (HSV-1) ICP27 transcript and its cognate wild-type rescue viruses in order to assess the role of the ICP27 protein in the earliest stages of viral infection by global transcriptional analysis with a DNA microarray. This mutant, ICP27/VP16, replaces the whole ICP27 promoter/enhancer with the VP16 promoter. It demonstrates loss of immediate-early expression of ICP27 according to the criteria expression in the absence of de novo protein synthesis and earliest expression in the kinetic cascade. Significant differences in relative transcript abundances between the mutant and wild-type rescue viruses were limited at the earliest times measured and not evident at all by 4 h after infection. Consistent with this observation, levels of some critical proteins were reduced in the mutant as compared to rescue virus infections at the earliest times tested, but were equivalent by 8 h postinfection. Further, both single and multistep levels of virus replication were equivalent with both mutant and rescue viruses. Thus, altering the immediate-early kinetics of ICP27 leads to a suboptimal quantitative lag phase in gene expression but without consequence for replication fitness in vitro. Infections in vivo also revealed equivalent ability of mutant and rescue viruses to invade the central nervous system of mice following footpad injections. Limitations to an immediate-early role of ICP27 in the biology of HSV are discussed in light of these observations.
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MESH Headings
- Animals
- Blotting, Western
- Cells, Cultured
- Disease Models, Animal
- Ganglia, Spinal/virology
- Gene Expression Profiling
- Gene Expression Regulation, Viral
- Genes, Immediate-Early
- Herpes Simplex/virology
- Herpesvirus 1, Human/genetics
- Herpesvirus 1, Human/physiology
- Humans
- Immediate-Early Proteins/biosynthesis
- Immediate-Early Proteins/genetics
- Mice
- Mutation
- Oligonucleotide Array Sequence Analysis
- Promoter Regions, Genetic
- Transcription, Genetic
- Viral Plaque Assay
- Virus Replication
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Affiliation(s)
- Aixu Sun
- Department of Molecular Biology and Biochemistry and Center for Virus Research, University of California, Irvine, CA 92717-3900, USA
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18
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O'Neil JE, Loutsch JM, Aguilar JS, Hill JM, Wagner EK, Bloom DC. Wide variations in herpes simplex virus type 1 inoculum dose and latency-associated transcript expression phenotype do not alter the establishment of latency in the rabbit eye model. J Virol 2004; 78:5038-44. [PMID: 15113885 PMCID: PMC400357 DOI: 10.1128/jvi.78.10.5038-5044.2004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [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: 11/20/2022] Open
Abstract
The latency-associated transcript (LAT) is required for efficient reactivation of herpes simplex virus type 1 from latent infection in the rabbit eye model, but LAT's mechanism of action is unknown. In addition to reactivation, the LAT region seems to correspond to multiple functions, with some LAT deletion mutants exhibiting increased virulence, increased neuronal death, and restricted establishment of latency. While a LAT promoter deletion mutant (17DeltaPst) seems to be primarily restricted in reactivation in the rabbit, subtle effects on virulence or the establishment of latency cannot be precluded at the normal high levels of virus inoculum used in the rabbit model. Since such additional LAT phenotypes may be more evident with lower doses of virus, we evaluated the influence of initial viral inoculum and LAT expression on the progression of acute infection and the establishment of latency. We have assayed both virus recovery rates and viral genome loads in rabbit corneas and trigeminal ganglia. Our results show that (i) in the corneas and trigeminal ganglia, the maximum amount of virus present during acute infection is independent of the LAT genotype and inoculum dose, although greater viral yields are obtained earlier with higher inoculum doses, and (ii) the range in numbers of latent genomes detected in the ganglia is independent of the inoculum dose and the LAT genotype and therefore no difference in establishment of latency is observed.
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Affiliation(s)
- J E O'Neil
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL 32610-0266, USA
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19
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Aguilar JS, Roy D, Ghazal P, Wagner EK. Dimethyl sulfoxide blocks herpes simplex virus-1 productive infection in vitro acting at different stages with positive cooperativity. Application of micro-array analysis. BMC Infect Dis 2002; 2:9. [PMID: 12052246 PMCID: PMC116584 DOI: 10.1186/1471-2334-2-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [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: 01/16/2002] [Accepted: 05/24/2002] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Dimethyl sulfoxide (DMSO) is frequently used at a concentration of up to 95% in the formulation of antiherpetic agents because of its properties as a skin penetration enhancer. Here, we have analyzed the effect of DMSO on several parameters of Herpes Simplex Virus replication. METHODS Productive infection levels of HSV-1 were determined by plaque assay or by reporter gene activity, and its DNA replication was estimated by PCR. Transcript levels were evaluated with HSV-specific DNA micro-arrays. RESULTS DMSO blocks productive infection in vitro in different cell types with a 50% inhibitory concentration (IC50) from 0.7 to 2% depending upon the multiplicity of infection. The concentration dependence exhibits a Hill coefficient greater than 1, indicating that DMSO blocks productive infection by acting at multiple different points (mechanisms of action) with positive cooperativity. Consistently, we identified at least three distinct temporal target mechanisms for inhibition of virus growth by DMSO. At late stages of infection, DMSO reduces virion infectivity, and markedly inhibits viral DNA replication. A third mode of action was revealed using an oligonucleotide-based DNA microarray system for HSV. These experiments showed that DMSO reduced the transcript levels of many HSV-1 genes; including several genes coding for proteins involved in forming and assembling the virion. Also, DMSO markedly inhibited some but not all early transcripts indicating a previously unknown mode for inhibiting the early phase of HSV transcription-replication cycle. CONCLUSION These observations suggest that DMSO itself may have a role in the anti-herpetic activity of formulations utilizing it as a dispersant.
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Affiliation(s)
- JS Aguilar
- Dept. of Mol. Biol. & Biochem, U. Calif. Irvine, 19172 Jamboree Road, Irvine, CA 92697, USA
| | - D Roy
- Genomic Technology & Informatics Centre, University of Edinburgh, Summerhall EH9 1QH, UK
| | - P Ghazal
- Genomic Technology & Informatics Centre, University of Edinburgh, Summerhall EH9 1QH, UK
| | - EK Wagner
- Dept. of Mol. Biol. & Biochem, U. Calif. Irvine, 19172 Jamboree Road, Irvine, CA 92697, USA
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20
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Guzowski JF, Setlow B, Wagner EK, McGaugh JL. Experience-dependent gene expression in the rat hippocampus after spatial learning: a comparison of the immediate-early genes Arc, c-fos, and zif268. J Neurosci 2001; 21:5089-98. [PMID: 11438584 PMCID: PMC6762831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2001] [Revised: 04/30/2001] [Accepted: 05/01/2001] [Indexed: 02/20/2023] Open
Abstract
Neuronal immediate-early gene (IEG) expression is regulated by synaptic activity and plays an important role in the neuroplastic mechanisms critical to memory consolidation. IEGs can be divided into two functional classes: (1) regulatory transcription factors (RTFs), which can broadly influence cell function depending on the "downstream" genes they regulate, and (2) "effector" proteins, which may directly modulate specific cellular functions. The objective of the current study was to determine whether the expression of an effector IEG (Arc) was similar to, or different from, that of two well characterized RTF IEGs (c-fos and zif268) after learning. IEG RNA levels from rats trained in spatial and nonspatial water tasks were determined using RNase protection assays and in situ hybridization. Overall, the regulation of the three IEGs was similar in the hippocampus and the entorhinal and primary visual cortices. Consequently, IEG RNA levels were positively correlated within a structure. By contrast, Arc and zif268 RNA levels were not correlated or only weakly correlated across structures, although c-fos RNA levels were moderately correlated across structures. Arc RNA expression differed from that of zif268 and c-fos in two regards: (1) hippocampal Arc RNA levels were correlated with learning of the hippocampal-dependent spatial, but not hippocampal-independent cued response, water task, and (2) Arc RNA levels in the hippocampus and entorhinal cortex increased after spatial reversal learning relative to an asymptotic performance group. Thus, although the expression of Arc, zif268, and c-fos exhibited many similarities, Arc was most responsive to differences in behavioral task demands.
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Affiliation(s)
- J F Guzowski
- Arizona Research Laboratories, Division of Neural Systems, Memory and Aging, University of Arizona, Tucson, Arizona 85724-5115, USA.
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21
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Petroski MD, Devi-Rao GB, Rice MK, Wagner EK. The downstream activation sequence of the strict late Herpes Simplex Virus Type 1 U(L)38 promoter interacts with hTAF(II)70, a component of TFIID. Virus Genes 2001; 22:299-310. [PMID: 11450948 DOI: 10.1023/a:1011162106727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [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: 11/12/2022]
Abstract
A class of strict late Herpes Simplex Virus Type 1 (HSV-1) promoters contains a conserved sequence element (termed the downstream activation sequence, DAS) located downstream of the transcription start site. These DAS-containing promoters also require both a TATA box and an initiator element for maximal levels of transcription. In this communication, we demonstrate that the downstream promoter element (DPE) found on a class of Drosophila TATA-less promoters and known to bind the homologue of human TAF(II)70 (a component of TFIID), can functionally substitute for DAS in the context of the strict late UL38 promoter in spite of no obvious sequence similarity. Although Drosophila DPE-containing promoters do not require a TATA box, the element does not remove the requirement for a TATA box when functioning in the HSV promoter. Next, we demonstrate that hTAF(II)70, interacts in a sequence specific manner with DAS as predicted from the fact that DPE binds Drosophila TBP. These results suggest that multiple TFIID/promoter interactions are important in the activation of HSV-1 late gene expression upon viral DNA replication. We propose that such interactions could be favored upon viral DNA replication since TFIID concentrates to viral transcription foci that form during the later stages of infection.
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Affiliation(s)
- M D Petroski
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, USA
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22
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Stingley SW, Ramirez JJ, Aguilar SA, Simmen K, Sandri-Goldin RM, Ghazal P, Wagner EK. Global analysis of herpes simplex virus type 1 transcription using an oligonucleotide-based DNA microarray. J Virol 2000; 74:9916-27. [PMID: 11024119 PMCID: PMC102029 DOI: 10.1128/jvi.74.21.9916-9927.2000] [Citation(s) in RCA: 120] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
More than 100 transcripts of various abundances and kinetic classes are expressed during phases of productive and latent infections by herpes simplex virus (HSV) type 1. To carry out rapid global analysis of variations in such patterns as a function of perturbation of viral regulatory genes and cell differentiation, we have made DNA microchips containing sets of 75-mer oligonucleotides specific for individual viral transcripts. About half of these are unique for single transcripts, while others function for overlapping ones. We have also included probes for 57 human genes known to be involved in some aspect of stress response. The chips efficiently detect all viral transcripts, and analysis of those abundant under various conditions of infection demonstrates excellent correlation with known kinetics of mRNA accumulation. Further, quantitative sensitivity is high. We have further applied global analysis of transcription to an investigation of mRNA populations in cells infected with a mutant virus in which the essential immediate-early alpha27 (U(L)54) gene has been functionally deleted. Transcripts expressed at 6 h following infection with this mutant can be classified into three groups: those whose abundance is augmented (mainly immediate-early transcripts) or unaltered, those whose abundance is somewhat reduced, and those where there is a significant reduction in transcript levels. These do not conform to any particular kinetic class. Interestingly, levels of many cellular transcripts surveyed are increased. The high proportion of such transcripts suggests that the alpha27 gene plays a major role in the early decline in cellular gene expression so characteristic of HSV infection.
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Affiliation(s)
- S W Stingley
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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23
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Abstract
The HSV-1 VP5 and VP16 transcripts are expressed with leaky-late (gamma1) kinetics and reach maximal levels after viral DNA replication. While the minimal VP5 promoter includes only an Sp1 site at -48, a TATA box at -30, and an initiator (Inr) element at the cap site, here we show that elements upstream of -48 can functionally compensate for the mutational loss of the critical Sp1 site at -48. To determine whether this is a general feature of leaky-late promoters, we have carried out a detailed analysis of the VP16 promoter in the context of the viral genome at the gC locus. Sequence analysis suggests a great deal of similarity between the two. Despite this, however, mutational analysis revealed that the 5' boundary of the VP16 promoter extends to ca. -90. This region includes an Sp1 binding site at -46, CAAT box homology at -77, and "E box" (CACGTG) at -85. Mutational and deletional analyses demonstrate that the proximal Sp1 site plays little or no role in promoter strength; despite this it can be shown to bind Sp1 protein using DNA mobility shift assays. Like the VP5 promoter, the VP16 promoter also requires an initiator element at the cap site. The VP16 Inr element differs in sequence from that of the VP5 promoter, and its deletion or mutation has a significantly smaller effect on promoter strength. The difference between these two Inr elements was confirmed by our finding that the VP16 initiator element binds to the 65-kDa YY1 transcription factor, and the VP5 Inr element competes poorly for the binding between the VP16 element and infected cell proteins in comparative bandshift assays. While the VP16 Inr sequence is identical to that of several murine TATA-less promoters, the VP16 Inr requires a TATA box for measurable activity.
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Affiliation(s)
- P T Lieu
- Program in Animal Virology, University of California, Irvine, California 92697-3900, USA
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24
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Lieu PT, Pande NT, Rice MK, Wagner EK. The exchange of cognate TATA boxes results in a corresponding change in the strength of two HSV-1 early promoters. Virus Genes 2000; 20:5-10. [PMID: 10766301 DOI: 10.1023/a:1008108121028] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Previous analysis of two Herpes Simplex Virus Type-1 (HSV-1) promoters controlling expression of mRNA encoding early genes (U(L)37 and U(L)50) showed that the U(L)50 (dUTPase) promoter is at least 6-fold stronger both in its normal genomic location and in the non-essential gC locus. In the present report we demonstrate that the TATA element of either promoter is the major determinant of promoter strength. When the U(L)37 TATA element (CGTATAAC) was mutated with two base changes to the U(L)50 TATA sequence (CATAAAAC) in recombinant viruses, the activity of the U(L)37 promoter was increased to that of the U(L)50 promoter. Conversely, when the U(L)50 TATA element was changed to that of the U(L)37 promoter, U(L)50 promoter activity was reduced to the level of the U(L)37 promoter. In addition, we investigated the spacing of the TATA box with respect to upstream promoter elements. We found that re-positioning the U(L)37 TATA box to a location equivalent to that of the U(L)50 promoter relative to the transcript start site; i.e. three bases upstream of its cognate location, significantly diminished activity. Substitution of the U(L)50 TATA box at the new position could only partially restore promoter activity. Thus, we also conclude that the spacing of TATA elements vis-à-vis upstream promoter elements is also a critical determinant of promoter strength.
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Affiliation(s)
- P T Lieu
- Department of Molecular Biology and Biochemistry, University of California Irvine, 92697, USA
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25
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Abstract
We generated recombinant viruses in which the kinetics of expression of the leaky-late VP5 mRNA was altered. We then analyzed the effect of such alterations on viral replication in cultured cells. The VP5 promoter and leader sequences from positions -36 to +20, containing the TATA box and an initiator element, were deleted and replaced with a strong early (dUTPase), an equal-strength leaky-late (VP16), or a strict-late (U(L)38) promoter. We found that recombinant viruses containing the dUTPase promoter inserted in the VP5 locus expressed VP5-encoding mRNA with early kinetics, while virus with the U(L)38 promoter inserted expressed such mRNA with strict-late kinetics. Further, in spite of differences in its functional architecture, the VP16 promoter fully substituted for the VP5 promoter. Western blot analysis demonstrated that the amounts of VP5 capsid protein produced by the recombinant viruses differed somewhat; however, on complementing C32 and noncomplementing Vero cells, such viruses replicated to titers equivalent to those of the rescued wild-type virus controls. Multistep virus growth in mouse embryo fibroblasts, rabbit skin cells, and Vero cells also demonstrated equivalent replication efficiencies for both recombinant and wild-type viruses. Further, recombinant viruses did not show any impairment in their ability to replicate on serum-starved or quiescent human lung fibroblasts. We conclude that the kinetics of the essential VP5 mRNA expression is not critical for viral replication in cultured cells.
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Affiliation(s)
- P T Lieu
- Program in Animal Virology, Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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26
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Abstract
Previous studies using cell culture systems to evaluate LAT expression demonstrated that the LAT promoter expresses at much higher levels in neuroblastoma cell lines than fibroblast lines. The high level of LAT expression in neuronal-derived cell lines correlates with the high level of LAT accumulation observed in sensory ganglia neurons during a latent infection. We have found that using LAT promoters to express reporter genes from recombinant viruses in vivo produces high levels of LAT promoter activity in the epithelium of the mouse foot. An analysis of LAT promoter activity during an acute infection in the mouse clearly demonstrates that in contrast to studies performed with selected cell lines, the LAT promoter expresses similar levels of reporter gene product in peripheral cells and in neurons. In addition, the amount of reporter gene product is higher when the LAT promoter is located within the R(L) as compared to the U(L) region, and when expression is adjusted for copy number of the reporter construct, expression is roughly the same. These results suggest the activity of the LAT promoter varies greatly according to cell type and that high levels of expression is not limited solely to neurons, especially in the in vivo setting.
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MESH Headings
- Acute Disease
- Animals
- Cell Line
- DNA, Recombinant/genetics
- Epithelium/metabolism
- Epithelium/virology
- Female
- Foot/virology
- Ganglia, Spinal/metabolism
- Ganglia, Spinal/virology
- Gene Dosage
- Gene Expression Regulation, Viral
- Genes, Reporter/genetics
- Genes, Viral/genetics
- Herpes Simplex/virology
- Herpesvirus 1, Human/genetics
- Herpesvirus 1, Human/physiology
- Kinetics
- Mice
- Neurons/metabolism
- Neurons/virology
- Organ Specificity
- Promoter Regions, Genetic/genetics
- Pyrophosphatases/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Virus Latency/genetics
- Virus Replication/genetics
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Affiliation(s)
- R G Jarman
- Department of Microbiology, Arizona State University, Tempe, Arizona, 85287-2701, USA
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27
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Abstract
Several polysulfonate compounds have been shown to have the potential to inhibit the replication of herpesviruses by blocking binding and penetration of the host cell. We analyzed the actions of the polysulfonate compound suramin on the replication of herpes simplex virus type 1 (HSV-1) and compared them with the actions of heparin. We used the expression of a reporter gene (beta-galactosidase) recombined into the latency-associated transcript region of the 17syn+ strain of HSV-1 to quickly evaluate productive cycle activity and have shown that it can be directly correlated with virus replication under the conditions used. We find that suramin, like heparin, blocks the binding of HSV-1 to the cell membrane. Also, suramin efficiently blocks the cell-to-cell spread of the virus; this effect has not been previously reported. Our control experiments demonstrate that heparin also has some effect on intercellular spread of HSV-1 but to a significantly lesser degree than does suramin. We suggest that suramin and related polysulfonate compounds have potential for developing of antiherpes treatments.
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Affiliation(s)
- J S Aguilar
- Department of Molecular Biology and Biochemistry and Program in Animal Virology, University of California, Irvine, Irvine, California, 92697, USA
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28
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Petroski MD, Wagner EK. Purification and characterization of a cellular protein that binds to the downstream activation sequence of the strict late UL38 promoter of herpes simplex virus type 1. J Virol 1998; 72:8181-90. [PMID: 9733860 PMCID: PMC110164 DOI: 10.1128/jvi.72.10.8181-8190.1998] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/1998] [Accepted: 07/03/1998] [Indexed: 11/20/2022] Open
Abstract
Previous work on the strict late (gamma) UL38 promoter of herpes simplex virus type 1 identified three cis-acting elements required for wild-type levels of transcription: a TATA box at -31, a consensus mammalian initiator element at the transcription start site, and a downstream activation sequence (DAS) at +20 to +33. DAS is found in similar locations on several other late promoters, suggesting an important regulatory role in late gene expression. In this communication, we further characterize the interaction between DAS and a cellular protein which is found in both uninfected and infected nuclear extracts. This protein was purified from HeLa nuclear extracts and identified as the DNA binding component (Ku heterodimer) of DNA-dependent protein kinase (DNA-PK) by peptide mapping. Highly purified DNA-PK was able to stimulate UL38 transcription in vitro approximately 10-fold. DAS is similar in sequence to another element, nuclear regulatory element 1 (NRE1) of the glucocorticoid-responsive mouse mammary tumor virus long terminal repeat. NRE1 is known to specifically bind Ku in the absence of DNA ends. We demonstrated that NRE1 is able to substitute for DAS in the UL38 promoter to activate transcription as measured by in vitro transcription and in vivo during infection of tissue culture cells with recombinant virus. Also, we found that the binding of DNA-PK to DAS involves the bases demonstrated to be important in UL38 transcription and that the 70-kDa subunit of Ku binds to DAS.
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Affiliation(s)
- M D Petroski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, USA
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29
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Wagner EK, Petroski MD, Pande NT, Lieu PT, Rice M. Analysis of factors influencing kinetics of herpes simplex virus transcription utilizing recombinant virus. Methods 1998; 16:105-16. [PMID: 9774520 DOI: 10.1006/meth.1998.0648] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [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: 11/22/2022] Open
Abstract
The herpes simplex virus type 1 (HSV-1) transcription program is a regulated cascade in which early and late phases of gene expression are separated by viral DNA replication. While promoters controlling expression of transcripts encoding immediate-early proteins contain virus-specific cis-acting elements, these are in the context of cellular promoter elements, and the promoters controlling expression of other viral transcripts contain only cellular cis-acting elements. We had developed and continue to refine a general method for the production of recombinant viruses in which modified promoters can be inserted into nonessential loci within the viral genome through homologous recombination. This approach has been especially useful in defining the features of model promoters of the various kinetic classes. Our work suggests that class-specific differences in promoter architecture are critical factors in the ability of the cellular transcription machinery to form stable preinitiation complexes at various phases of infection and, thus, mediate kinetic class-specific transcription. Early (beta) promoters contain a TATA box and upstream activation elements while sequences downstream of the TATA homology are dispensible for transcription. Late transcripts can be catagorized as either leaky-late (beta gamma) or strict late (gamma) depending on whether they are readily detectable prior to viral DNA replication. Promoters controlling both types are clearly distinct from early ones in that sequences near the transcription start site which resemble consensus mammalian initiator elements are required along with the TATA box and activator elements. Strict late promoters do not contain elements upstream of the TATA box but include what appears to be a class specific element downstream of the transcription start site.
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Affiliation(s)
- E K Wagner
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, 92697-3900, USA.
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30
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Pande NT, Petroski MD, Wagner EK. Functional modules important for activated expression of early genes of herpes simplex virus type 1 are clustered upstream of the TATA box. Virology 1998; 246:145-57. [PMID: 9657002 DOI: 10.1006/viro.1998.9189] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [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: 11/22/2022]
Abstract
Functional analysis of two promoters controlling early herpes simplex virus type 1 (HSV-1) transcripts encoding the UL37 and UL50 (dUTPase) proteins are described in this report. Transcripts expressed under the control of these promoters were found to be expressed early regardless of the position of the transcription unit within the viral genome. Despite this, wt dUTPase mRNA was 6-10 times more abundant than the UL37 transcript both in wt and recombinant viruses. This same difference in transcript abundance was seen when a reporter gene (beta-galactosidase) was controlled by the two promoters in recombinant viruses in the heterologous glycoprotein C (gC) locus. Thus, both the kinetics and relative abundance of UL50 and UL37 transcripts are a direct function of their respective promoter regulatory elements. Characterization of mutated UL37 and UL50 promoters in recombinant viruses showed that the functional modules important for expression from these promoters are concentrated upstream of the transcription start site; however the extent and composition of these modules in terms of the cis-acting elements they contain was different for each. For the UL37 promoter, both a HiNF-P factor binding site (-53 to -58 bp) and the TATA homology (-22 to -27) were required for any detectable expression, while an Sp1 binding site at -123 augmented this but was not absolutely required. In contrast, the only functional elements crucial for expression from the UL50 promoter were the TATA box (-25 to -31) and an Sp1 binding site at -117 bp relative to the cap site. Despite differences in detail, when the functional architecture of these two early promoters were compared to the extensively characterized HSV-1 thymidine kinase (UL23) promoter, class-specific similarities are clearly apparent.
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Affiliation(s)
- N T Pande
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92697, USA
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31
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Devi-Rao GB, Aguilar JS, Rice MK, Garza HH, Bloom DC, Hill JM, Wagner EK. Herpes simplex virus genome replication and transcription during induced reactivation in the rabbit eye. J Virol 1997; 71:7039-47. [PMID: 9261434 PMCID: PMC191991 DOI: 10.1128/jvi.71.9.7039-7047.1997] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [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: 02/05/2023] Open
Abstract
PCR analysis of herpes simplex virus (HSV) genome replication and productive-cycle transcription was used to examine the role of the cornea in the latency-associated transcript (LAT)-mediated reactivation of HSV type 1 (HSV-1) in the rabbit eye model. The reduced relative reactivation frequency of 17 delta Pst (a LAT- virus) compared to those of wild-type and LAT+ rescuants correlated with reduced levels of viral DNA and transcription in the cornea following epinephrine induction. The timing of virus appearance in the cornea was most consistent with tissue peripheral to the cornea itself mediating a LAT-sensitive step in the reactivation process. Specific results include the following. (i) While viral DNA was found in the corneas of rabbits latently infected with either the LAT+ or LAT- virus prior to and during the first 16 to 24 h following induction, more was found in animals infected with the LAT+ virus. (ii) A significant increase in levels of viral DNA occurred 20 to 168 h following induction. (iii) The average relative amount of viral DNA was lower at all time points following reactivation of animals infected with the LAT- virus. (iv) Expression of productive-cycle transcripts could be detected in corneas of some rabbits latently infected with either the LAT+ or LAT- virus, and the amount recovered and the timing of appearance differed during the reactivation of rabbits latently infected with the LAT+ or LAT- virus. (v) Despite the reduced recoveries of LAT- virus DNA and productive-cycle transcripts in reactivating corneas in vivo compared to those of their LAT+ counterparts, such differences were not detected in cultured keratinocytes or in experiments in which relatively high titers of virus were superinfected into the eyes of latently infected rabbits. (vi) A number of LAT(+)-virus-infected rabbits expressed LAT in corneas isolated from uninduced rabbits. When seen, its amount was significantly higher than that of a productive-cycle (VP5) transcript.
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Affiliation(s)
- G B Devi-Rao
- Department of Molecular Biology and Biochemistry, University of California-Irvine 92697-3900, USA
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32
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Abstract
The clinical manifestations of herpes simplex virus infection generally involve a mild and localized primary infection followed by asymptomatic (latent) infection interrupted sporadically by periods of recrudescence (reactivation) where virus replication and associated cytopathologic findings are manifest at the site of initial infection. During the latent phase of infection, viral genomes, but not infectious virus itself, can be detected in sensory and autonomic neurons. The process of latent infection and reactivation has been subject to continuing investigation in animal models and, more recently, in cultured cells. The initiation and maintenance of latent infection in neurons are apparently passive phenomena in that no virus gene products need be expressed or are required. Despite this, a single latency-associated transcript (LAT) encoded by DNA encompassing about 6% of the viral genome is expressed during latent infection in a minority of neurons containing viral DNA. This transcript is spliced, and the intron derived from this splicing is stably maintained in the nucleus of neurons expressing it. Reactivation, which can be induced by stress and assayed in several animal models, is facilitated by the expression of LAT. Although the mechanism of action of LAT-mediated facilitation of reactivation is not clear, all available evidence argues against its involving the expression of a protein. Rather, the most consistent models of action involve LAT expression playing a cis-acting role in a very early stage of the reactivation process.
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Affiliation(s)
- E K Wagner
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, USA.
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33
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Bloom DC, Hill JM, Devi-Rao G, Wagner EK, Feldman LT, Stevens JG. A 348-base-pair region in the latency-associated transcript facilitates herpes simplex virus type 1 reactivation. J Virol 1996; 70:2449-59. [PMID: 8642650 PMCID: PMC190088 DOI: 10.1128/jvi.70.4.2449-2459.1996] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.1] [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: 02/01/2023] Open
Abstract
Latency-associated transcript (LAT) promoter deletion mutants of herpes simplex virus type 1 have a reduced capacity to reactivate following adrenergic induction in the rabbit eye model. We have mapped a reactivation phenotype within LAT and describe the construction of recombinants in which poly(A) addition sites have been placed at intervals within the LAT region to form truncated LAT transcripts. These mutants localize the induced reactivation phenotype to the 5' end of LAT. To further define this region, we constructed a recombinant containing a 348-bp deletion located 217 bp downstream of the transcription start site of the 8.5-kb LAT. This virus, 17delta348, expresses LAT but exhibits a significantly reduced ability to reactivate following epinephrine iontophoresis into the cornea. Quantitative DNA PCR analysis reveals that 17delta 348 establishes a latent infection within rabbit trigeminal ganglia with the same efficiency as does either the rescuant or wild-type virus. The region deleted in 17delta348 encodes three potential translational initiators (ATGs) which we have mutated and demonstrated to be dispensable for epinephrine-induced reactivation. In addition, three smaller deletions within this region have been constructed and were shown to reactivate at wild-type (parent) frequencies. These studies indicate that an undefined portion of the 348-bp region is required to facilitate induced reactivation. Sequence analysis of this 348-bp region revealed a CpG island which extends into the LAT promoter and which possesses homology to conserved elements within the mouse and human XIST transcript encoded on the X chromosome. Possible implications of these elements in the regulation of LAT expression are discussed.
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Affiliation(s)
- D C Bloom
- Department of Microbiology and Immunology, UCLA School of Medicine, Los Angeles, California 90095, USA
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34
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Huang CJ, Petroski MD, Pande NT, Rice MK, Wagner EK. The herpes simplex virus type 1 VP5 promoter contains a cis-acting element near the cap site which interacts with a cellular protein. J Virol 1996; 70:1898-904. [PMID: 8627715 PMCID: PMC190018 DOI: 10.1128/jvi.70.3.1898-1904.1996] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The promoter controlling the expression of the transcript encoding the major herpes simplex virus type 1 capsid protein (VP5, UL19) extends only 60 bases or so from a functional Sp1 site at --48 to include a cis-acting element 3' of the transcript start site. In the present communication, we report the generation of recombinant viruses bearing mutations between --6 and + 8 relative to the cap site in the VP5 promoter controlling expression of a reporter gene. Analysis of the effects of these mutations upon reporter gene expression along with the results of protein binding assays demonstrates that this cap transcription element functionally interacts with a cellular protein of a normal size of 40 kDa. Thus, like the strict late UL38 promoter characterized earlier, the late VP5 promoter has the essential properties of a cellular promoter.
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Affiliation(s)
- C J Huang
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717, USA
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35
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Singh J, Wagner EK. Herpes simplex virus recombination vectors designed to allow insertion of modified promoters into transcriptionally "neutral" segments of the viral genome. Virus Genes 1995; 10:127-36. [PMID: 8560772 DOI: 10.1007/bf01702593] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [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: 01/31/2023]
Abstract
The use of recombinant viruses has been essential in investigation of the biology of herpes simplex virus (HSV). In this communication we describe a number of viral recombination vectors that we have generated for use in promoter structure/function analysis within the context of the HSV-1 genome. We have utilized two regions of the HSV genome that contain genes nonessential for replication in cultured cells--the glycoprotein C (gC or UL44) locus in the UL of the genome and the area encompassing the promoter and 5' portion of the latency associated transcript (LAT) within the RL factual influence on promoters due to the site of insertion. Two different kinetic promoters were analyzed, those controlling expression of the gamma UL 38 and the beta dUTPase genes, in both loci. All constructs tested displayed reporter gene mRNA expression with expected kinetics, and we conclude that there are no neighboring cryptic promoter elements that could interfere with expression studies using the vectors described.
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Affiliation(s)
- J Singh
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717, USA
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36
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Bohenzky RA, Lagunoff M, Roizman B, Wagner EK, Silverstein S. Two overlapping transcription units which extend across the L-S junction of herpes simplex virus type 1. J Virol 1995; 69:2889-97. [PMID: 7707513 PMCID: PMC188986 DOI: 10.1128/jvi.69.5.2889-2897.1995] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [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] [Indexed: 01/26/2023] Open
Abstract
A region of the herpes simplex virus type 1 genome located upstream of the alpha 0 promoter contains a promoter which regulates transcription in the opposite orientation to that driven by alpha 0. Analyses of mutants from which this promoter, alpha X, was deleted and a mutant in which a fragment that serves as a transcription terminator and polyadenylation signal was inserted upstream of this promoter demonstrate that two distinct transcription units overlap this region of the genome and are transcribed in a direction antisense to the neurovirulence gene gamma (1)34.5. One unit, dependent on the alpha X promoter, is active when cells are infected in the presence of the protein synthesis inhibitor cycloheximide. The second unit, independent of alpha X, is active during the course of productive infection. This transcription unit originates from a promoter upstream of alpha X which is distinct from the latency-associated promoter (LAP). Two polyadenylated transcripts of 0.9 and 4.9 kb accumulate from this region of the genome during productive infection, but no mature transcripts accumulate in infected cells maintained in the presence of cycloheximide. Kinetic analyses demonstrate that the transcripts that accumulate during productive infection fall into the beta class of herpes simplex virus type 1 genes.
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Affiliation(s)
- R A Bohenzky
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
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37
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Wagner EK, Guzowski JF, Singh J. Transcription of the herpes simplex virus genome during productive and latent infection. Prog Nucleic Acid Res Mol Biol 1995; 51:123-65. [PMID: 7659774 DOI: 10.1016/s0079-6603(08)60878-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- E K Wagner
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717, USA
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Guzowski JF, Singh J, Wagner EK. Transcriptional activation of the herpes simplex virus type 1 UL38 promoter conferred by the cis-acting downstream activation sequence is mediated by a cellular transcription factor. J Virol 1994; 68:7774-89. [PMID: 7966567 PMCID: PMC237239 DOI: 10.1128/jvi.68.12.7774-7789.1994] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [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: 01/28/2023] Open
Abstract
The herpes simplex virus (HSV) type 1 strict late (gamma) UL38 promoter contains three cis-acting transcriptional elements: a TATA box, a specific initiator element, and the downstream activation sequence (DAS). DAS is located between positions +20 and +33 within the 5' untranslated leader region and strongly influences transcript levels during productive infection. In this communication, we further characterize DAS and investigate its mechanism of action. DAS function has a strict spacing requirement, and DAS contains an essential 6-bp core element. A similarly positioned element from the gamma gC gene (UL44) has partial DAS function within the UL38 promoter context, and the promoter controlling expression of the gamma US11 transcript contains an identically located element with functional and sequence similarity to UL38 DAS. These data suggest that downstream elements are a common feature of many HSV gamma promoters. Results with recombinant viruses containing modifications of the TATA box or initiator element of the UL38 promoter suggest that DAS functions to increase transcription initiation and not the efficiency of transcription elongation. In vitro transcription assays using uninfected HeLa nuclear extracts show that, as in productive infection with recombinant viruses, the deletion of DAS from the UL38 promoter dramatically decreases RNA expression. Finally, electrophoretic mobility shift assays and UV cross-linking experiments show that DAS DNA forms a specific, stable complex with a cellular protein (the DAS-binding factor) of approximately 35 kDa. These data strongly suggest that the interaction of cellular DAS-binding factor with DAS is required for efficient expression of UL38 and other HSV late genes.
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Affiliation(s)
- J F Guzowski
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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39
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Abstract
The herpes simplex virus type 1 (HSV-1) major capsid protein VP5 gene (UL19) is expressed with beta gamma (gamma 1 [leaky late]) kinetics. We have previously described the construction of recombinant HSV-1 in which the VP5 promoter was engineered to control the expression of the bacterial beta-galactosidase gene as a reporter (C.-J. Huang, S. A. Goodart, M. K. Rice, J. F. Guzowski, and E. K. Wagner, J. Virol. 67:5109-5116, 1993). Here we describe further mutational analysis in recombinant viruses. We have precisely defined the boundaries of the VP5 promoter and identified two regions important for both the level and the kinetics of expression. The 5' boundary was located at -48 relative to the initiation site of transcription by analyzing a series of nested deletions in the upstream sequence, and although a number of cis-acting sites influencing transient expression have been identified upstream of this point, these sites have no role in promoter activity during productive infection. Deletion of an Sp1-binding site located between -48 and the TATA box at -30 greatly reduced VP5 promoter activity late but not early after infection. A cis-acting element whose sequence resembles the human immunodeficiency virus type 1 initiator was located between -2 and +10 in the VP5 sequence by characterizing a series of deletions and site-directed block mutations downstream the TATA box. This element defines the 3' limit of the VP5 promoter, and like the upstream element, disruption of this element also inhibited promoter activity late in the productive cycle.
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Affiliation(s)
- C J Huang
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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Bloom DC, Devi-Rao GB, Hill JM, Stevens JG, Wagner EK. Molecular analysis of herpes simplex virus type 1 during epinephrine-induced reactivation of latently infected rabbits in vivo. J Virol 1994; 68:1283-92. [PMID: 8107194 PMCID: PMC236581 DOI: 10.1128/jvi.68.3.1283-1292.1994] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.4] [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: 01/28/2023] Open
Abstract
Infectious virus assays and PCR amplification of DNA and RNA were used to investigate herpes simplex virus (HSV) DNA replication and gene expression in the rabbit corneal model for virus reactivation in vivo. We used carefully defined latency-associated transcript-negative (LAT-) and LAT+ promoter mutants of the 17syn+ strain of HSV type 1. In agreement with earlier studies using a more extensive LAT- deletion mutant, the 17 delta Pst(LAT-) virus reactivated with extremely low frequency upon epinephrine induction. In contrast to our findings with murine latency models, amounts of viral DNA recovered from rabbit ganglia latently infected with either LAT+ or LAT- virus were equivalent. Also in contrast with the murine models, no net increase in viral DNA was seen in latently infected rabbit trigeminal ganglia induced to reactivate in vivo by iontophoresis of epinephrine. Despite this, transcription of lytic-phase genes could be detected within 4 h following induction of rabbits latently infected with either LAT+ or LAT- virus; this transcription diminished by 16 h following induction. These results are discussed in relation to models for the mechanism of action of HSV LAT.
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Affiliation(s)
- D C Bloom
- Department of Microbiology and Immunology, UCLA Medical School 90024
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41
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Huang CJ, Rice MK, Devi-Rao GB, Wagner EK. The activity of the pseudorabies virus latency-associated transcript promoter is dependent on its genomic location in herpes simplex virus recombinants as well as on the type of cell infected. J Virol 1994; 68:1972-6. [PMID: 8107257 PMCID: PMC236661 DOI: 10.1128/jvi.68.3.1972-1976.1994] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [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: 01/28/2023] Open
Abstract
As do many other alphaherpesviruses, pseudorabies virus (PRV) transcribes a limited portion of its viral genome in latently infected neurons during latency. The sequence of the PRV latency-associated transcript (LAT) is bounded on its 5' end by a putative promoter region which contains sequence elements similar to those characterized for the herpes simplex virus (HSV) LAT promoter. Using the bacterial beta-galactosidase gene as a reporter, we have assayed PRV LAT promoter activity in the genomic environment in recombinant HSVs. The PRV LAT promoter-beta-galactosidase reporter gene was recombined into the terminal and internal long repeat regions (RL regions), replacing the normal HSV LAT promoter, the cap site, and the first 60 bases of the primary transcript. When recombined into the RL region, appreciable reporter gene expression was observed following infection of two cell lines of neuronal origin; little or no activity was seen with these recombinants following infection of rabbit skin or mouse embryo fibroblasts. No significant expression was seen when the promoter was recombined into the gC locus in the long unique region in any of the cell types utilized. Such results suggest that the PRV latency promoter contains neuronal cell-specific elements and that the HSV RL region provides an appropriate genomic environment for the manifestation of that specificity.
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Affiliation(s)
- C J Huang
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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42
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Devi-Rao GB, Bloom DC, Stevens JG, Wagner EK. Herpes simplex virus type 1 DNA replication and gene expression during explant-induced reactivation of latently infected murine sensory ganglia. J Virol 1994; 68:1271-82. [PMID: 8107193 PMCID: PMC236580 DOI: 10.1128/jvi.68.3.1271-1282.1994] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.3] [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: 01/28/2023] Open
Abstract
Infectious virus assays and PCR amplification of DNA and RNA were used to investigate herpes simplex virus DNA replication and gene expression in two murine in vitro models for virus reactivation. We examined latent infections with wild-type (wt), precisely defined latency-associated transcript-negative (LAT-) mutants, and LAT+ rescuants of these mutants of the 17syn+ strain of virus in both murine trigeminal and lumbosacral ganglia and of the KOS(M) strain in the latter. In explants of ganglia latently infected with the LAT- mutant of strain 17syn+ virus, a reduction in number of cultures exhibiting cytopathic effects due to virus reactivation and measurable delays in virus recovery were observed compared with wt or the LAT+ rescuant. This LAT-specific effect was not seen in explants of lumbosacral ganglia latently infected with mutants derived from the KOS(M) strain of virus. Although there was appreciable variation between individual animals, no significant difference between LAT+ and LAT- virus in time of onset of viral DNA replication in explanted ganglia was seen with use of either virus strain. There was a slight decrease in the relative amount of viral DNA recovered compared with internal cellular controls in latently infected ganglia harboring the LAT- mutant of 17syn+ compared with the wt virus or the LAT+ rescuant. This reduced relative amount ranged from 0 to as much as 50% but averaged 20%. Such differences were not seen in infections with KOS(M)-derived mutants. In contrast, although expression of productive-cycle transcripts could be detected within 4 h following explant cultivation of latently infected ganglia, no differences between LAT+ and LAT- viruses could be seen. As discussed, these data place specific constraints on possible models for the role of LAT expression in in vitro reactivation systems.
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Affiliation(s)
- G B Devi-Rao
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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43
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Abstract
In this study we have used a combination of Northern blot, cDNA, and RNAse protection analysis to characterize transcription occurring at the junction of the long terminal repeat (TRL) and long unique segment (UL) of herpes simplex virus type 1 (HSV-1). Two low abundance 5' colinear transcripts mapped between the junction of the TRL/UL and the cap site of the primary latency associated transcripts (LAT). Analysis of the region containing the first four open translational reading frames (ORFs) of the UL segment of the virus revealed a complex pattern of overlapping transcripts and polyadenylation site utilization. Inefficient termination late, but not early in infection, at the polyadenylation site following the UL2 ORF leads to an unusual situation where the promoter controlling a beta gamma transcript encoding the UL1 ORF also controls a 5' colinear gamma transcript. Further, although the entire UL3 ORF is conserved between HSV-1 and HSV-2, the only abundant uniquely UL3 encoding transcript in both virus types was found to originate within the UL3 ORF and has the capacity to encode only a truncated UL3 protein product.
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Affiliation(s)
- J Singh
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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44
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Huang CJ, Goodart SA, Rice MK, Guzowski JF, Wagner EK. Mutational analysis of sequences downstream of the TATA box of the herpes simplex virus type 1 major capsid protein (VP5/UL19) promoter. J Virol 1993; 67:5109-16. [PMID: 8394439 PMCID: PMC237908 DOI: 10.1128/jvi.67.9.5109-5116.1993] [Citation(s) in RCA: 17] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Transient expression assays with the herpes simplex virus type 1 (HSV-1) promoter/leader controlling the beta gamma (leaky-late) VP5 (UL19) mRNA encoding the major capsid protein showed that no more than 36 to 72 bases of VP5 leader are required for full-level expression. Constructs lacking the viral leader and the transcription initiation site expressed the reporter gene at about 20% of the maximum level. We confirmed this observation by using recombinant viruses in which VP5 promoter/leader deletions controlling the bacterial beta-galactosidase gene were inserted into the nonessential glycoprotein C (UL44) locus of the genome. Sequences within +36 are required for full-level expression, and removal of all leader sequences including the cap site resulted in a 10-fold decrease in reporter mRNA accumulation. The removal of the leader sequence had a measurable effect upon the kinetics of reporter mRNA accumulation, but insertion of the entire VP5 leader and cap site into a construct in which the reporter gene was controlled by the kinetically early (beta) dUTPase (UL50) promoter did not result in any significant change in the kinetics of dUTPase promoter expression. These results suggest that DNA sequences both 5' and 3' of the TATA box are important determinants of the beta gamma kinetics and levels of VP5 mRNA accumulation in the infected cell.
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Affiliation(s)
- C J Huang
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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45
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Guzowski JF, Wagner EK. Mutational analysis of the herpes simplex virus type 1 strict late UL38 promoter/leader reveals two regions critical in transcriptional regulation. J Virol 1993; 67:5098-108. [PMID: 8394438 PMCID: PMC237907 DOI: 10.1128/jvi.67.9.5098-5108.1993] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.6] [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: 01/30/2023] Open
Abstract
The unusual TATA homology TTTAAA at -31 relative to the transcriptional start site of the herpes simplex virus type 1 (HSV-1) strict late (gamma) UL38 gene defines the 5' extent of this promoter in recombinant virus. We have further analyzed this promoter by generating recombinant viruses containing nested deletions 3' of the transcriptional start site and with recombinant viruses containing specific promoter/leader alterations. A recombinant virus containing the UL38 promoter/leader from -50 to +9 expressed reporter gene enzyme levels at approximately 10% of those from a recombinant containing the full viral promoter/leader (-50 to +99). The accumulation of reporter gene mRNA in infections with the -50 to +9 recombinant was still regulated with gamma kinetics. Further removal of UL38 leader sequences resulted in a nearly complete loss of expression. Analysis of promoter chimera recombinant viruses has shown that sequences downstream of the TATA box and spanning the transcriptional start site of the UL38 promoter are functionally distinct from those of either the beta UL37 gene or the beta gamma VP16 (UL48) gene; thus, we conclude that sequences from -31 to +9 of the UL38 gene constitute a core gamma promoter. Further deletional and substitutional analyses have also demonstrated the presence of a 14-bp element (the downstream activation sequence) located between +20 to +33 in the nontranslated leader region which is required for full levels of transcription.
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Affiliation(s)
- J F Guzowski
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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46
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Farrell MJ, Hill JM, Margolis TP, Stevens JG, Wagner EK, Feldman LT. The herpes simplex virus type 1 reactivation function lies outside the latency-associated transcript open reading frame ORF-2. J Virol 1993; 67:3653-5. [PMID: 8388517 PMCID: PMC237719 DOI: 10.1128/jvi.67.6.3653-3655.1993] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [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: 01/30/2023] Open
Abstract
The latency-associated transcription unit has been shown to be important for in vivo reactivation of herpes simplex virus from the latent state. A recombinant virus was constructed to alter the largest open reading frame in this region. This virus had a wild-type reactivation phenotype, suggesting that herpes simplex virus does not require a protein function from this reading frame for efficient reactivation from latency.
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Affiliation(s)
- M J Farrell
- Molecular Biology Institute, School of Medicine, University of California, Los Angeles 90024
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47
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Goodart SA, Guzowski JF, Rice MK, Wagner EK. Effect of genomic location on expression of beta-galactosidase mRNA controlled by the herpes simplex virus type 1 UL38 promoter. J Virol 1992; 66:2973-81. [PMID: 1313912 PMCID: PMC241056 DOI: 10.1128/jvi.66.5.2973-2981.1992] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [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: 12/26/2022] Open
Abstract
To examine the effect of genomic location on the details of expression of selected herpes simplex virus promoters, we have constructed recombination vectors for placing such promoters controlling the beta-galactosidase reporter gene into two regions of the viral genome lacking any nearby promoter or regulatory elements. The first vector generates the promoter-beta-galactosidase reporter gene inverted within the locus of the gC (UL44) translational reading frame; the second replaces the LAT promoter and the first 600 bases of the primary transcript in both copies of the RL region. These locations were chosen to obviate any possible influence of upstream but noncontiguous heterologous or homologous DNA sequence elements upon promoter activity. When the reporter gene controlled by the strict late (gamma) UL38 promoter was placed in the gC location, it was significantly less active than in its normal location; in contrast, promoter activity was comparable to wild-type values when the promoter was recombined into the RL region. The low level of activity in the gC location could be partially alleviated by the incorporation of additional DNA sequences upstream of the UL38 promoter. Despite the effect of genomic location upon the level of expression, the kinetics of expression in either location mirrors the wild-type UL38 strict late kinetics of expression. Finally, we used deletional analysis to demonstrate that no more than 29 bases of DNA sequence 5' of the mRNA cap site are required for promoter activity in either location; this result is consistent with earlier results of transient-expression assays and indicates that the UL38 promoter shares general features with other strict late (gamma) herpes simplex virus promoters.
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Affiliation(s)
- S A Goodart
- Department of Molecular Biology and Biochemistry, University of California Irvine 92717
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48
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Devi-Rao GB, Goodart SA, Hecht LM, Rochford R, Rice MK, Wagner EK. Relationship between polyadenylated and nonpolyadenylated herpes simplex virus type 1 latency-associated transcripts. J Virol 1991; 65:2179-90. [PMID: 1850005 PMCID: PMC240565 DOI: 10.1128/jvi.65.5.2179-2190.1991] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.8] [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] [Indexed: 12/29/2022] Open
Abstract
RNA from the region of the genome encoding herpes simplex virus type 1 latency-associated transcripts (LATs) expressed during lytic infection yields low abundances of both polyadenylated and nonpolyadenylated forms. As has been previously shown for latent infection (A. T. Dobson, F. Sedarati, G. Devi-Rao, W. M. Flanagan, M. J. Farrell, J. G. Stevens, E. K. Wagner, and L. T. Feldman. J. Virol. 63:3844-3851, 1989), all lytic-phase expression of such transcripts requires promoter elements situated approximately 600 bases 5' of the previously mapped 5' end of the poly(A)- forms of LAT. Transient expression experiments revealed no other clear promoter elements within this region, and relatively small amounts of latent-phase transcripts initiating at the same site as observed for lytic-phase LAT could be detected by RNase protection assays. In the lytic phase of infection, the most abundant forms of polyadenylated LAT extended 1,600 bases from the initiation site near the LAT promoter to a potential splice donor site. Poly(A)- LAT species were not recovered in significant amounts from lytically infected neuroblastoma cells, but such RNA from lytically infected rabbit skin cells comapped with poly(A)- LAT from latently infected sensory neurons. Both map between canonical 5' splice donor and 3' splice acceptor site 1,950 bases apart. Poly(A)- LAT cochromatographed with uncapped rRNA on m-aminophenyl boronate agarose under conditions in which capped mRNA was bound. All of these data confirm the previously presented scheme for the expression of poly(A)- LAT as a stable intron derived from the splicing of a large primary transcript; however, we were unable to detect the spliced polyadenylated product of this splicing reaction.
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Affiliation(s)
- G B Devi-Rao
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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49
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Flanagan WM, Papavassiliou AG, Rice M, Hecht LB, Silverstein S, Wagner EK. Analysis of the herpes simplex virus type 1 promoter controlling the expression of UL38, a true late gene involved in capsid assembly. J Virol 1991; 65:769-86. [PMID: 1846198 PMCID: PMC239817 DOI: 10.1128/jvi.65.2.769-786.1991] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [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: 12/29/2022] Open
Abstract
The cistrons encoding the herpes simplex virus type 1 (HSV-1) UL37 and UL38 genes are adjacent to one another but are transcribed from opposite strands of the viral DNA. The UL37 gene encodes a 1,123-amino-acid protein of unknown function, while the 465-amino-acid UL38 protein is involved in capsid assembly. Previous work from our laboratory indicated that the transcripts encoding these proteins are expressed with significantly different kinetics in productive infection. In the present communication we confirm the kinetic classes and precisely map the cap sites of the UL37 and UL38 mRNAs. A bifunctional reporter gene vector was used to demonstrate that divergent promoters control the expression of these reporter genes in trans-activation assays. The UL38 promoter is functionally separable from that controlling UL37 in a recombinant virus. We used deletion analysis to demonstrate that as few as 29 bases 5' of the mRNA cap site are adequate for full activity of the UL38 promoter in trans-activation assays. Finally, we analyzed the protein-binding properties of the UL38 promoter; several sites that form complexes containing ICP4, with clear homology to those identified in the HSV-1 gamma 42 promoter, are present. Thus, in general, the properties of this promoter are quite similar to those of other gamma promoters.
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Affiliation(s)
- W M Flanagan
- Department of Molecular Biology and Biochemistry, University of California-Irvine 92717
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50
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Abstract
Pseudorabies virus (PRV) is a porcine herpesvirus that establishes latent infections in trigeminal ganglia. To determine whether PRV expresses any transcripts that could play a role in latency, the trigeminal ganglia of 14 pigs previously inoculated through the nose and latently infected with PRV(Ka) were assayed by in situ nucleic acid hybridization for the presence of PRV-specific RNA. Hybridizations employing probes encompassing the entire viral genome revealed that an area extending from 0.64 to 0.82 map units was transcriptionally active. The DNA probe that most consistently detected transcripts was BamHI-8, a fragment which contains the gene for the immediate-early protein. With this probe, ganglia from 10 (71%) of 14 pigs scored positive for PRV RNA, although only 1 (8%) of 12 of the ganglia from the opposite side reactivated virus after explanation and culture of latently infected trigeminal ganglia. The RNA was transcribed from the strand opposite to that coding for the immediate-early protein; the signal was neuronally localized, with dense nuclear accumulation accompanied by variable numbers of grains over the cytoplasm. Northern RNA blot analysis showed that a discrete set of poly(A)- PRV transcripts were present in latently infected trigeminal ganglia. Additional in situ nucleic acid hybridization analysis revealed that the 3' limit of the transcriptionally active area was located in a 1.2-kilobase fragment upstream and adjacent to the 5' end of the immediate-early protein RNA, whereas the 5' limit was as much as 4.9 kilobases downstream from the 3' end of this RNA. PRV therefore expresses latent-phase transcripts that, although similar in many respects to latent-phase transcripts reported for other herpesviruses, have some unique properties.
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Affiliation(s)
- S A Priola
- Department of Microbiology and Immunology, University of California, Los Angeles School of Medicine 90024
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