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Massart A, Danger R, Olsen C, Emond MJ, Viklicky O, Jacquemin V, Soblet J, Duerinckx S, Croes D, Perazzolo C, Hruba P, Daneels D, Caljon B, Sever MS, Pascual J, Miglinas M, Pirson I, Ghisdal L, Smits G, Giral M, Abramowicz D, Abramowicz M, Brouard S. An exome-wide study of renal operational tolerance. Front Med (Lausanne) 2023; 9:976248. [PMID: 37265662 PMCID: PMC10230038 DOI: 10.3389/fmed.2022.976248] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/31/2022] [Indexed: 06/03/2023] Open
Abstract
Background Renal operational tolerance is a rare and beneficial state of prolonged renal allograft function in the absence of immunosuppression. The underlying mechanisms are unknown. We hypothesized that tolerance might be driven by inherited protein coding genetic variants with large effect, at least in some patients. Methods We set up a European survey of over 218,000 renal transplant recipients and collected DNAs from 40 transplant recipients who maintained good allograft function without immunosuppression for at least 1 year. We performed an exome-wide association study comparing the distribution of moderate to high impact variants in 36 tolerant patients, selected for genetic homogeneity using principal component analysis, and 192 controls, using an optimal sequence-kernel association test adjusted for small samples. Results We identified rare variants of HOMER2 (3/36, FDR 0.0387), IQCH (5/36, FDR 0.0362), and LCN2 (3/36, FDR 0.102) in 10 tolerant patients vs. 0 controls. One patient carried a variant in both HOMER2 and LCN2. Furthermore, the three genes showed an identical variant in two patients each. The three genes are expressed at the primary cilium, a key structure in immune responses. Conclusion Rare protein coding variants are associated with operational tolerance in a sizable portion of patients. Our findings have important implications for a better understanding of immune tolerance in transplantation and other fields of medicine.ClinicalTrials.gov, identifier: NCT05124444.
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Affiliation(s)
- Annick Massart
- Human Genetics Unit, Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles - Vrije Universiteit Brussel (ULB-VUB), Brussels, Belgium
- Department of Nephrology, Antwerp University Hospital and Laboratory of Experimental Medicine, University of Antwerp, Antwerp, Belgium
| | - Richard Danger
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, CR2TI, UMR 1064, ITUN, Nantes, France
| | - Catharina Olsen
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles - Vrije Universiteit Brussel (ULB-VUB), Brussels, Belgium
- Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), VUB-ULB, Brussels, Belgium
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Brussels, Belgium
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Ondrej Viklicky
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Valérie Jacquemin
- Human Genetics Unit, Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles - Vrije Universiteit Brussel (ULB-VUB), Brussels, Belgium
| | - Julie Soblet
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles - Vrije Universiteit Brussel (ULB-VUB), Brussels, Belgium
- Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Sarah Duerinckx
- Human Genetics Unit, Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles - Vrije Universiteit Brussel (ULB-VUB), Brussels, Belgium
| | - Didier Croes
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles - Vrije Universiteit Brussel (ULB-VUB), Brussels, Belgium
- Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), VUB-ULB, Brussels, Belgium
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Brussels, Belgium
- Center for Human Genetics, Clinique Universitaires Saint Luc, Brussels, Belgium
| | - Camille Perazzolo
- Human Genetics Unit, Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Petra Hruba
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Dorien Daneels
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles - Vrije Universiteit Brussel (ULB-VUB), Brussels, Belgium
- Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), VUB-ULB, Brussels, Belgium
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Brussels, Belgium
| | - Ben Caljon
- Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), VUB-ULB, Brussels, Belgium
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Brussels, Belgium
| | - Mehmet Sukru Sever
- Istanbul Tip Fakültesi, Istanbul School of Medicine, Internal Medicine, Nephrology, Istanbul, Türkiye
| | - Julio Pascual
- Department of Nephrology, Hospital del Mar, Institute Mar for Medical Research, Barcelona, Spain
- Department of Nephrology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Marius Miglinas
- Nephrology Center, Santaros Klinikos, Medical Faculty, Vilnius University, Vilnius, Lithuania
| | | | - Isabelle Pirson
- Human Genetics Unit, Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Lidia Ghisdal
- Department of Nephrology, Hospital Centre EpiCURA, Baudour, Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles - Vrije Universiteit Brussel (ULB-VUB), Brussels, Belgium
- Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Magali Giral
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, CR2TI, UMR 1064, ITUN, Nantes, France
- CHU Nantes, Centre d'Investigation Clinique en Biothérapie, Centre de Ressources Biologiques (CRB), Nantes, France
- LabEx IGO “Immunotherapy, Graft, Oncology”, Nantes, France
| | - Daniel Abramowicz
- Department of Nephrology, Antwerp University Hospital and Laboratory of Experimental Medicine, University of Antwerp, Antwerp, Belgium
| | - Marc Abramowicz
- Human Genetics Unit, Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles - Vrije Universiteit Brussel (ULB-VUB), Brussels, Belgium
- Department of Genetic Medicine and Development, Faculty of Medicine, Université de Geneve, Geneva, Switzerland
| | - Sophie Brouard
- CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, CR2TI, UMR 1064, ITUN, Nantes, France
- CHU Nantes, Centre d'Investigation Clinique en Biothérapie, Centre de Ressources Biologiques (CRB), Nantes, France
- LabEx IGO “Immunotherapy, Graft, Oncology”, Nantes, France
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2
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Zhai J, Emond MJ, Spangenberg A, Stern DA, Vasquez MM, Blue EE, Buckingham KJ, Sherrill DL, Halonen M, Gibson RL, Rosenfeld M, Sagel SD, Bamshad MJ, Morgan WJ, Guerra S. Club cell secretory protein and lung function in children with cystic fibrosis. J Cyst Fibros 2022; 21:811-820. [PMID: 35367162 PMCID: PMC9509401 DOI: 10.1016/j.jcf.2022.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/18/2022] [Accepted: 03/14/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Club cell secretory protein (CC16) exerts anti-inflammatory functions in lung disease. We sought to determine the relation of serum CC16 deficits and genetic variants that control serum CC16 to lung function among children with cystic fibrosis (CF). METHODS We used longitudinal data from CF children (EPIC Study) with no positive cultures for Pseudomonas aeruginosa prior to enrollment. Circulating levels of CC16 and an inflammatory score (generated from CRP, SAA, calprotectin, G-CSF) were compared between participants with the lowest and highest FEV1 levels in adolescence (LLF and HLF groups, respectively; N = 130-per-group). Single nucleotide variants (SNVs) in the SCGB1A1, EHF-APIP loci were tested for association with circulating CC16 and with decline of FEV1 and FEV1/FVC% predicted levels between ages 7-16 using mixed models. RESULTS Compared with the HLF group, the LLF group had lower levels of CC16 (geometric means: 8.2 vs 6.5 ng/ml, respectively; p = 0.0002) and higher levels of the normalized inflammatory score (-0.21 vs 0.21, p = 0.0007). Participants in the lowest CC16 and highest inflammation tertile had the highest odds for having LLF (p<0.0001 for comparison with participants in the highest CC16 and lowest inflammation tertile). Among seven SNVs associated with circulating CC16, the top SNV rs3741240 was associated with decline of FEV1/FVC and, marginally, FEV1 (p = 0.003 and 0.025, respectively; N = 611 participants, 20,801 lung function observations). CONCLUSIONS Serum CC16 deficits are strongly associated with severity of CF lung disease and their effects are additive with systemic inflammation. The rs3741240 A allele is associated with low circulating CC16 and, possibly, accelerated lung function decline in CF.
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Affiliation(s)
- Jing Zhai
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Mary J Emond
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Amber Spangenberg
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Debra A Stern
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Monica M Vasquez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States; Brotman-Baty Institute for Precision Medicine, Seattle, WA, United States
| | - Kati J Buckingham
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Duane L Sherrill
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Marilyn Halonen
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Ronald L Gibson
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
| | - Margaret Rosenfeld
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
| | - Scott D Sagel
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Michael J Bamshad
- Brotman-Baty Institute for Precision Medicine, Seattle, WA, United States; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, United States; Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Wayne J Morgan
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States; Department of Pediatrics, University of Arizona, Tucson, AZ, United States.
| | - Stefano Guerra
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States; Department of Medicine, University of Arizona, Tucson, AZ, United States.
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3
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Graustein AD, Berrington WR, Buckingham KJ, Nguyen FK, Joudeh LL, Rosenfeld M, Bamshad MJ, Gibson RL, Hawn TR, Emond MJ. Inflammasome Genetic Variants, Macrophage Function, and Clinical Outcomes in Cystic Fibrosis. Am J Respir Cell Mol Biol 2021; 65:157-166. [PMID: 33848452 DOI: 10.1165/rcmb.2020-0257oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cystic fibrosis (CF) is characterized by chronic airway infection, inflammation, and tissue damage that lead to progressive respiratory failure. NLRP3 and NLRC4 are cytoplasmic pattern recognition receptors that activate the inflammasome, initiating a caspase-1-mediated response. We hypothesized that gain-of-function inflammasome responses are associated with worse outcomes in children with CF. We genotyped nonsynonymous variants in NLRP3 and the NLRC4 pathway from individuals in the EPIC (Early Pseudomonas Infection Control) Observational Study cohort and tested for association with CF outcomes. We generated knockouts of NLRP3 and NLRC4 in human macrophage-like cells and rescued knockouts with wild-type or variant forms of NLRP3 and NLRC4. We identified a SNP in NLRP3, p.(Q705K), that was associated with a higher rate of P. aeruginosa colonization (N = 609; P = 0.01; hazard ratio, 2.3 [Cox model]) and worsened lung function over time as measured by forced expiratory volume in 1 second (N = 445; P = 0.001 [generalized estimating equation]). We identified a SNP in NLRC4, p.(A929S), that was associated with a lower rate of P. aeruginosa colonization as part of a composite of rare variants (N = 405; P = 0.045; hazard ratio, 0.68 [Cox model]) and that was individually associated with protection from lung function decline (P < 0.001 [generalized estimating equation]). Rescue of the NLRP3 knockout with the p.(Q705K) variant produced significantly more IL-1β in response to NLRP3 stimulation than rescue with the wild type (P = 0.020 [Student's t test]). We identified a subset of children with CF at higher risk of early lung disease progression. Knowledge of these genetic modifiers could guide therapies targeting inflammasome pathways.
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Affiliation(s)
| | | | | | | | | | - Margaret Rosenfeld
- Department of Pediatrics, School of Medicine.,Division of Pulmonary and Sleep Medicine and
| | - Michael J Bamshad
- Department of Pediatrics, School of Medicine.,Department of Genome Sciences, and.,Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Ronald L Gibson
- Department of Pediatrics, School of Medicine.,Division of Pulmonary and Sleep Medicine and
| | | | - Mary J Emond
- Department of Biostatistics, University of Washington, Seattle, Washington; and
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4
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Krimmel-Morrison JD, Lian S, Zhang Y, Fredrickson J, Nachmanson D, Baker KT, Radke MR, Hun E, Norquist B, Emond MJ, Swisher EM, Risques RA. Abstract B40: Characterization of TP53 mutations in Pap test DNA of women with and without serous ovarian cancer. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.ovca19-b40] [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
Objective: The development of Pap tests as a molecular diagnostic for serous ovarian cancer is a promising concept, but previous studies reported limited sensitivity. In addition, the presence of cancer-associated somatic mutations in normal tissue is increasingly recognized as a specificity challenge for mutational tests. We aimed to determine the diagnostic performance of Pap tests for ovarian cancer detection using ultra-accurate deep sequencing.
Methods: We used CRISPR-DS, a novel duplex sequencing method that employs CRISPR-based target enrichment to increase efficiency and reduce DNA input. We performed ultra-accurate deep sequencing (mean 2000x) of the TP53 gene in 30 Pap tests from 21 women without cancer and 9 women with serous ovarian cancer with known TP53 driver mutations. Mutations were annotated using the Seshat web service and compared to those in the UMD TP53 cancer database.
Results: The tumor-derived mutation was identified in 3 of 9 Pap tests from women with ovarian cancer (33% sensitivity). In addition, 221 low-frequency (≲0.001) mutations were identified in the coding region of TP53 in Pap tests from women with ovarian cancer (94 mutations) and without ovarian cancer (127 mutations). In both groups these mutations showed evidence of positive selection as indicated by clustering in exons 5 to 8, preferential location in hotspot codons and CpG dinucleotides, common presence in cancer database, impact on protein activity, and predicted pathogenicity. These “cancer-like” features were significantly more frequent in mutations identified in women with ovarian cancer than in women without cancer.
Conclusions: Pap tests have low sensitivity for ovarian cancer detection and carry abundant low-frequency TP53 mutations. These mutations are more frequently pathogenic in women with ovarian cancer and determining whether their presence is associated with an increased gynecologic cancer risk warrants further study.
Citation Format: Jeffrey D. Krimmel-Morrison, Shenyi Lian, Yuezheng Zhang, Jeanne Fredrickson, Daniela Nachmanson, Kathryn T. Baker, Marc R. Radke, Enna Hun, Barbara Norquist, Mary J. Emond, Elizabeth M. Swisher, Rosa Ana Risques. Characterization of TP53 mutations in Pap test DNA of women with and without serous ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B40.
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Affiliation(s)
| | | | | | | | | | | | | | - Enna Hun
- University of Washington, Seattle, WA
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5
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Krimmel-Morrison JD, Ghezelayagh TS, Lian S, Zhang Y, Fredrickson J, Nachmanson D, Baker KT, Radke MR, Hun E, Norquist BM, Emond MJ, Swisher EM, Risques RA. Characterization of TP53 mutations in Pap test DNA of women with and without serous ovarian carcinoma. Gynecol Oncol 2019; 156:407-414. [PMID: 31839337 DOI: 10.1016/j.ygyno.2019.11.124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Pap tests hold promise as a molecular diagnostic for serous ovarian cancer, but previous studies reported limited sensitivity. Furthermore, the presence of somatic mutations in normal tissue is increasingly recognized as a challenge to the specificity of mutation-based cancer diagnostics. We applied an ultra-deep sequencing method with the goal of improving sensitivity and characterizing the landscape of low-frequency somatic TP53 mutations in Pap tests. METHODS We used CRISPR-DS to deeply sequence (mean Duplex depth ~3000×) the TP53 gene in 30 Pap tests from 21 women without cancer and 9 women with serous ovarian carcinoma with known TP53 driver mutations. Mutations were annotated and compared to those in the TP53 cancer database. RESULTS The tumor-derived mutation was identified in 3 of 8 Pap tests from women with ovarian cancer and intact tubes. In addition, 221 low-frequency (≲0.001) exonic TP53 mutations were identified in Pap tests from women with ovarian cancer (94 mutations) and without ovarian cancer (127 mutations). Many of these mutations resembled TP53 mutations found in cancer: they impaired protein activity, were predicted to be pathogenic, and clustered in exons 5 to 8 and hotspot codons. Cancer-like mutations were identified in all women but at higher frequency in women with ovarian cancer. CONCLUSIONS Pap tests have low sensitivity for ovarian cancer detection and carry abundant low-frequency TP53 mutations. These mutations are more frequently pathogenic in women with ovarian cancer. Determining whether low-frequency TP53 mutations in normal gynecologic tissues are associated with an increased cancer risk warrants further study.
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Affiliation(s)
- Jeffrey D Krimmel-Morrison
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Talayeh S Ghezelayagh
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Shenyi Lian
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Yuezheng Zhang
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeanne Fredrickson
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Daniela Nachmanson
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Kathryn T Baker
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Marc R Radke
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Enna Hun
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Barbara M Norquist
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Mary J Emond
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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6
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Salk JJ, Loubet-Senear K, Maritschnegg E, Valentine CC, Williams LN, Higgins JE, Horvat R, Vanderstichele A, Nachmanson D, Baker KT, Emond MJ, Loter E, Tretiakova M, Soussi T, Loeb LA, Zeillinger R, Speiser P, Risques RA. Ultra-Sensitive TP53 Sequencing for Cancer Detection Reveals Progressive Clonal Selection in Normal Tissue over a Century of Human Lifespan. Cell Rep 2019; 28:132-144.e3. [PMID: 31269435 PMCID: PMC6639023 DOI: 10.1016/j.celrep.2019.05.109] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/06/2019] [Accepted: 05/29/2019] [Indexed: 01/08/2023] Open
Abstract
High-accuracy next-generation DNA sequencing promises a paradigm shift in early cancer detection by enabling the identification of mutant cancer molecules in minimally invasive body fluid samples. We demonstrate 80% sensitivity for ovarian cancer detection using ultra-accurate Duplex Sequencing to identify TP53 mutations in uterine lavage. However, in addition to tumor DNA, we also detect low-frequency TP53 mutations in nearly all lavages from women with and without cancer. These mutations increase with age and share the selection traits of clonal TP53 mutations commonly found in human tumors. We show that low-frequency TP53 mutations exist in multiple healthy tissues, from newborn to centenarian, and progressively increase in abundance and pathogenicity with older age across tissue types. Our results illustrate that subclonal cancer evolutionary processes are a ubiquitous part of normal human aging, and great care must be taken to distinguish tumor-derived from age-associated mutations in high-sensitivity clinical cancer diagnostics.
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Affiliation(s)
- Jesse J Salk
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, WA 98195, USA; TwinStrand Biosciences, Seattle, WA 98121, USA
| | | | - Elisabeth Maritschnegg
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center-Gynecologic Cancer Unit, Medical University of Vienna, Vienna, Austria
| | | | | | | | - Reinhard Horvat
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Adriaan Vanderstichele
- Department of Gynecologic Oncology, Leuven Cancer Institute, University Hospitals Leuven, Katholieke Universiteit, Leuven, Belgium
| | - Daniela Nachmanson
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Kathryn T Baker
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Mary J Emond
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Emily Loter
- Department of Pathology, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Maria Tretiakova
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Thierry Soussi
- Sorbonne Université, UPMC Université Paris 06, 75005 Paris, France; Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; INSERM, U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Lawrence A Loeb
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center-Gynecologic Cancer Unit, Medical University of Vienna, Vienna, Austria
| | - Paul Speiser
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center-Gynecologic Cancer Unit, Medical University of Vienna, Vienna, Austria
| | - Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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7
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Wright SW, Emond MJ, Lovelace-Macon L, Ducken D, Kashima J, Hantrakun V, Chierakul W, Teparrukkul P, Chantratita N, Limmathurotsakul D, West TE. Exonic sequencing identifies TLR1 genetic variation associated with mortality in Thais with melioidosis. Emerg Microbes Infect 2019; 8:282-290. [PMID: 30866782 PMCID: PMC6455179 DOI: 10.1080/22221751.2019.1575172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Melioidosis, an infectious disease caused by the bacterium Burkholderia pseudomallei, is a common cause of sepsis in Southeast Asia. We investigated whether novel TLR1 coding variants are associated with outcome in Thai patients with melioidosis. We performed exonic sequencing on a discovery set of patients with extreme phenotypes (mild vs. severe) of bacteremic melioidosis. We analysed the association of missense variants in TLR1 with severe melioidosis in a by-gene analysis. We then genotyped key variants and tested the association with death in two additional sets of melioidosis patients. Using a by-gene analysis, TLR1 was associated with severe bacteremic melioidosis (P = 0.016). One of the eight TLR1 variants identified, rs76600635, a common variant in East Asians, was associated with in-hospital mortality in a replication set of melioidosis patients (adjusted odds ratio 1.71, 95% CI 1.01–2.88, P = 0.04.) In a validation set of patients, the point estimate of effect of the association of rs76600635 with 28-day mortality was similar but not statistically significant (adjusted odds ratio 1.81, 95% CI 0.96–3.44, P = 0.07). Restricting the validation set analysis to patients recruited in a comparable fashion to the discovery and replication sets, rs76600635 was significantly associated with 28-day mortality (adjusted odds ratio 3.88, 95% CI 1.43–10.56, P = 0.01). Exonic sequencing identifies TLR1 as a gene associated with a severe phenotype of bacteremic melioidosis. The TLR1 variant rs76600635, common in East Asian populations, may be associated with poor outcomes from melioidosis. This variant has not been previously associated with outcomes in sepsis and requires further study.
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Affiliation(s)
- Shelton W Wright
- a Division of Pediatric Critical Care Medicine, Department of Pediatrics , University of Washington , Seattle , WA , USA
| | - Mary J Emond
- b Department of Biostatistics , University of Washington , Seattle , WA , USA
| | - Lara Lovelace-Macon
- c Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine , University of Washington , Seattle , WA , USA
| | - Deirdre Ducken
- c Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine , University of Washington , Seattle , WA , USA
| | - James Kashima
- c Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine , University of Washington , Seattle , WA , USA
| | - Viriya Hantrakun
- d Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine , Mahidol University , Bangkok , Thailand
| | - Wirongrong Chierakul
- d Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine , Mahidol University , Bangkok , Thailand.,e Department of Clinical Tropical Medicine, Faculty of Tropical Medicine , Mahidol University , Bangkok , Thailand
| | - Prapit Teparrukkul
- f Department of Internal Medicine , Sunpasitthiprasong Hospital , Ubon Ratchathani , Thailand
| | - Narisara Chantratita
- d Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine , Mahidol University , Bangkok , Thailand.,g Department of Microbiology and Immunology, Faculty of Tropical Medicine , Mahidol University , Bangkok , Thailand
| | - Direk Limmathurotsakul
- d Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine , Mahidol University , Bangkok , Thailand.,h Department of Tropical Hygiene, Faculty of Tropical Medicine , Mahidol University , Bangkok , Thailand
| | - T Eoin West
- c Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine , University of Washington , Seattle , WA , USA.,i International Respiratory and Severe Illness Center , University of Washington , Seattle , WA , USA
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8
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Mackelprang RD, Bamshad MJ, Chong JX, Hou X, Buckingham KJ, Shively K, deBruyn G, Mugo NR, Mullins JI, McElrath MJ, Baeten JM, Celum C, Emond MJ, Lingappa JR. Correction: Whole genome sequencing of extreme phenotypes identifies variants in CD101 and UBE2V1 associated with increased risk of sexually acquired HIV-1. PLoS Pathog 2019; 15:e1007588. [PMID: 30742678 PMCID: PMC6370236 DOI: 10.1371/journal.ppat.1007588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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9
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Baker KT, Nachmanson D, Kumar S, Emond MJ, Ussakli C, Brentnall TA, Kennedy SR, Risques RA. Mitochondrial DNA Mutations are Associated with Ulcerative Colitis Preneoplasia but Tend to be Negatively Selected in Cancer. Mol Cancer Res 2018; 17:488-498. [PMID: 30446624 DOI: 10.1158/1541-7786.mcr-18-0520] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/04/2018] [Accepted: 11/05/2018] [Indexed: 02/07/2023]
Abstract
The role of mitochondrial DNA (mtDNA) mutations in cancer remains controversial. Ulcerative colitis is an inflammatory bowel disease that increases the risk of colorectal cancer and involves mitochondrial dysfunction, making it an ideal model to study the role of mtDNA in tumorigenesis. Our goal was to comprehensively characterize mtDNA mutations in ulcerative colitis tumorigenesis using Duplex Sequencing, an ultra-accurate next-generation sequencing method. We analyzed 46 colon biopsies from non-ulcerative colitis control patients and ulcerative colitis patients with and without cancer, including biopsies at all stages of dysplastic progression. mtDNA was sequenced at a median depth of 1,364x. Mutations were classified by mutant allele frequency: clonal > 0.95, subclonal 0.01-0.95, and very low frequency (VLF) < 0.01. We identified 208 clonal and subclonal mutations and 56,764 VLF mutations. Mutations were randomly distributed across the mitochondrial genome. Clonal and subclonal mutations increased in number and pathogenicity in early dysplasia, but decreased in number and pathogenicity in cancer. Most clonal, subclonal, and VLF mutations were C>T transitions in the heavy strand of mtDNA, which likely arise from DNA replication errors. A subset of VLF mutations were C>A transversions, which are probably due to oxidative damage. VLF transitions and indels were less abundant in the non-D-loop region and decreased with progression. Our results indicate that mtDNA mutations are frequent in ulcerative colitis preneoplasia but negatively selected in cancers. IMPLICATIONS: While mtDNA mutations might contribute to early ulcerative colitis tumorigenesis, they appear to be selected against in cancer, suggesting that functional mitochondria might be required for malignant transformation in ulcerative colitis.
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Affiliation(s)
- Kathryn T Baker
- Department of Pathology, University of Washington, Seattle, Washington
| | | | - Shilpa Kumar
- Department of Pathology, University of Washington, Seattle, Washington
| | - Mary J Emond
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Cigdem Ussakli
- Department of Pathology, University of Washington, Seattle, Washington.,Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Teresa A Brentnall
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
| | - Scott R Kennedy
- Department of Pathology, University of Washington, Seattle, Washington
| | - Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, Washington.
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10
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Barton JC, McLaren CE, Chen WP, Ramm GA, Anderson GJ, Powell LW, Subramaniam VN, Adams PC, Phatak PD, Gurrin LC, Phillips JD, Parker CJ, Emond MJ, McLaren GD. Cirrhosis in Hemochromatosis: Independent Risk Factors in 368 HFE p.C282Y Homozygotes. Ann Hepatol 2018; 17:871-879. [PMID: 30145563 PMCID: PMC6368858 DOI: 10.5604/01.3001.0012.3169] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND AIM We sought to identify independent risk factors for cirrhosis in HFE p.C282Y homozygotes in a cross-sectional study. MATERIAL AND METHODS We evaluated 368 p.C282Y homozygotes who underwent liver biopsy and compared characteristics of those with and without cirrhosis. We performed multivariable logistic regression on cirrhosis with: age; sex; race/ethnicity; diabetes; blood pints/units donated voluntarily; erythrocyte pints/units received; iron supplement use; alcohol intake, g/d; body mass index, kg/m2; swollen/tender 2nd/3rd metacarpophalangeal joints; elevated alanine aminotransferase; elevated aspartate aminotransferase; steatosis/fatty liver; iron removed by phlebotomy, g; and GNPAT p.D519G positivity. RESULTS Mean age of 368 participants (73.6% men) was 47 ± 13 (standard deviation) y. Cirrhosis was diagnosed in 86 participants (23.4%). Participants with cirrhosis had significantly greater mean age, proportion of men, diabetes prevalence, mean daily alcohol intake, prevalence of swollen/ tender 2nd/3rd metacarpophalangeal joints, mean serum ferritin, elevated alanine aminotransferase, elevated aspartate aminotransferase, and mean iron removed; and significantly fewer mean blood pints/units donated. GNPAT p.D519G positivity was detected in 82 of 188 participants (43.6%). In a multivariable model for cirrhosis, there were four significant positive associations: age (10-y intervals) (odds ratio 2.2 [95% confidence interval 1.5, 3.3]); diabetes (3.3; [1.1, 9.7]); alcohol intake (14 g alcohol drinks/d) (1.5 [1.2, 1.8]); and iron removed, g (1.3 [1.2, 1.4]). There was no statistical evidence of two-way interactions between these variables. CONCLUSION In conclusion, cirrhosis in HFE p.C282Y homozygotes is significantly associated with age, diabetes, daily alcohol intake, and iron removed by phlebotomy, taking into account the effect of other variables.
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Affiliation(s)
- James C. Barton
- Southern Iron Disorders Center, Birmingham, AL, USA
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Wen-pin Chen
- Chao Family Comprehensive Cancer Center, lrvine, CA, USA
| | - Grant A. Ramm
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Gregory J. Anderson
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane St. Lucia, QLD, Australia
| | - Lawrie W Powell
- Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane St. Lucia, QLD, Australia
- Royal Brisbane & Women’s Hospital, Herston, QLD, Australia
| | - V. Nathan Subramaniam
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Paul C. Adams
- Department of Medicine, London Health Sciences Centre, London, ONT, Canada
| | | | - Lyle C. Gurrin
- Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - John D. Phillips
- Departments of Medicine and Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Charles J. Parker
- Division of Hematology and Hematologic Malignancies, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Gordon D. McLaren
- Department of Veterans Affairs Long Beach Healthcare System, Long Beach, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, CA, USA
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11
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Agrawal PB, Wang R, Li HL, Schmitz-Abe K, Simone-Roach C, Chen J, Shi J, Louie T, Sheng S, Towne MC, Brainson CF, Matthay MA, Kim CF, Bamshad M, Emond MJ, Gerard NP, Kleyman TR, Gerard C. The Epithelial Sodium Channel Is a Modifier of the Long-Term Nonprogressive Phenotype Associated with F508del CFTR Mutations. Am J Respir Cell Mol Biol 2017; 57:711-720. [PMID: 28708422 PMCID: PMC5765421 DOI: 10.1165/rcmb.2017-0166oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/05/2017] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) remains the most lethal genetic disease in the Caucasian population. However, there is great variability in clinical phenotypes and survival times, even among patients harboring the same genotype. We identified five patients with CF and a homozygous F508del mutation in the CFTR gene who were in their fifth or sixth decade of life and had shown minimal changes in lung function over a longitudinal period of more than 20 years. Because of the rarity of this long-term nonprogressive phenotype, we hypothesized these individuals may carry rare genetic variants in modifier genes that ameliorate disease severity. Individuals at the extremes of survival time and lung-function trajectory underwent whole-exome sequencing, and the sequencing data were filtered to include rare missense, stopgain, indel, and splicing variants present with a mean allele frequency of <0.2% in general population databases. Epithelial sodium channel (ENaC) mutants were generated via site-directed mutagenesis and expressed for Xenopus oocyte assays. Four of the five individuals carried extremely rare or never reported variants in the SCNN1D and SCNN1B genes of the ENaC. Separately, an independently enriched rare variant in SCNN1D was identified in the Exome Variant Server database associated with a milder pulmonary disease phenotype. Functional analysis using Xenopus oocytes revealed that two of the three variants in δ-ENaC encoded by SCNN1D exhibited hypomorphic channel activity. Our data suggest a potential role for δ-ENaC in controlling sodium reabsorption in the airways, and advance the plausibility of ENaC as a therapeutic target in CF.
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Affiliation(s)
- Pankaj B. Agrawal
- Divisions of Newborn Medicine
- Genetics and Genomics
- Gene Discovery Core, Manton Center for Orphan Disease Research
| | | | - Hongmei Lisa Li
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Department of Genetics, and
| | - Klaus Schmitz-Abe
- Genetics and Genomics
- Gene Discovery Core, Manton Center for Orphan Disease Research
| | | | | | - Jiahai Shi
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR
| | - Tin Louie
- Biostatistics and Center for Biomedical Statistics
| | | | - Meghan C. Towne
- Genetics and Genomics
- Gene Discovery Core, Manton Center for Orphan Disease Research
| | | | - Michael A. Matthay
- Departments of Medicine and
- Anesthesia, Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California
| | - Carla F. Kim
- Pulmonary and Respiratory Diseases, and
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Department of Genetics, and
| | - Michael Bamshad
- Pediatrics and Genome Sciences, University of Washington, Seattle, Washington
| | | | - Norma P. Gerard
- Pulmonary and Respiratory Diseases, and
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Thomas R. Kleyman
- Departments of Medicine
- Cell Biology, and Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
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12
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Mackelprang RD, Bamshad MJ, Chong JX, Hou X, Buckingham KJ, Shively K, deBruyn G, Mugo NR, Mullins JI, McElrath MJ, Baeten JM, Celum C, Emond MJ, Lingappa JR. Whole genome sequencing of extreme phenotypes identifies variants in CD101 and UBE2V1 associated with increased risk of sexually acquired HIV-1. PLoS Pathog 2017; 13:e1006703. [PMID: 29108000 PMCID: PMC5690691 DOI: 10.1371/journal.ppat.1006703] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 02/10/2017] [Revised: 11/16/2017] [Accepted: 10/19/2017] [Indexed: 12/27/2022] Open
Abstract
Host genetic variation modifying HIV-1 acquisition risk can inform development of HIV-1 prevention strategies. However, associations between rare or intermediate-frequency variants and HIV-1 acquisition are not well studied. We tested for the association between variation in genic regions and extreme HIV-1 acquisition phenotypes in 100 sub-Saharan Africans with whole genome sequencing data. Missense variants in immunoglobulin-like regions of CD101 and, among women, one missense/5' UTR variant in UBE2V1, were associated with increased HIV-1 acquisition risk (p = 1.9x10-4 and p = 3.7x10-3, respectively, for replication). Both of these genes are known to impact host inflammatory pathways. Effect sizes increased with exposure to HIV-1 after adjusting for the independent effect of increasing exposure on acquisition risk. TRIAL REGISTRATION ClinicalTrials.gov NCT00194519; NCT00557245.
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Affiliation(s)
- Romel D. Mackelprang
- Department of Global Health, University of Washington, Seattle, United States of America
| | - Michael J. Bamshad
- Department of Pediatrics, University of Washington, Seattle, United States of America
- Department of Genome Sciences, University of Washington, Seattle, United States of America
| | - Jessica X. Chong
- Department of Pediatrics, University of Washington, Seattle, United States of America
| | - Xuanlin Hou
- Department of Global Health, University of Washington, Seattle, United States of America
| | - Kati J. Buckingham
- Department of Pediatrics, University of Washington, Seattle, United States of America
| | - Kathryn Shively
- Department of Pediatrics, University of Washington, Seattle, United States of America
| | - Guy deBruyn
- Perinatal HIV Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Nelly R. Mugo
- Department of Global Health, University of Washington, Seattle, United States of America
- Partners in Health Research and Development, Kenya Medical Research Institute, Thika, Kenya
| | - James I. Mullins
- Department of Global Health, University of Washington, Seattle, United States of America
- Department of Microbiology, University of Washington, Seattle, United States of America
- Department of Medicine, University of Washington, Seattle, United States of America
| | - M. Juliana McElrath
- Department of Medicine, University of Washington, Seattle, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Jared M. Baeten
- Department of Global Health, University of Washington, Seattle, United States of America
- Department of Medicine, University of Washington, Seattle, United States of America
- Department of Epidemiology, University of Washington, Seattle, United States of America
| | - Connie Celum
- Department of Global Health, University of Washington, Seattle, United States of America
- Department of Medicine, University of Washington, Seattle, United States of America
- Department of Epidemiology, University of Washington, Seattle, United States of America
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, United States of America
| | - Jairam R. Lingappa
- Department of Global Health, University of Washington, Seattle, United States of America
- Department of Pediatrics, University of Washington, Seattle, United States of America
- Department of Epidemiology, University of Washington, Seattle, United States of America
- * E-mail:
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13
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Kamath-Loeb AS, Zavala-van Rankin DG, Flores-Morales J, Emond MJ, Sidorova JM, Carnevale A, Cárdenas-Cortés MDC, Norwood TH, Monnat RJ, Loeb LA, Mercado-Celis GE. Homozygosity for the WRN Helicase-Inactivating Variant, R834C, does not confer a Werner syndrome clinical phenotype. Sci Rep 2017; 7:44081. [PMID: 28276523 PMCID: PMC5343477 DOI: 10.1038/srep44081] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/02/2017] [Indexed: 11/08/2022] Open
Abstract
Loss-of-function mutations in the WRN helicase gene cause Werner syndrome- a progeroid syndrome with an elevated risk of cancer and other age-associated diseases. Large numbers of single nucleotide polymorphisms have been identified in WRN. We report here the organismal, cellular, and molecular phenotypes of variant rs3087425 (c. 2500C > T) that results in an arginine to cysteine substitution at residue 834 (R834C) and up to 90% reduction of WRN helicase activity. This variant is present at a high (5%) frequency in Mexico, where we identified 153 heterozygous and three homozygous individuals among 3,130 genotyped subjects. Family studies of probands identified ten additional TT homozygotes. Biochemical analysis of WRN protein purified from TT lymphoblast cell lines confirmed that the R834C substitution strongly and selectively reduces WRN helicase, but not exonuclease activity. Replication track analyses showed reduced replication fork progression in some homozygous cells following DNA replication stress. Among the thirteen TT homozygotes, we identified a previously unreported and statistically significant gender bias in favor of males (p = 0.0016), but none of the clinical findings associated with Werner syndrome. Our results indicate that WRN helicase activity alone is not rate-limiting for the development of clinical WS.
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Affiliation(s)
- Ashwini S. Kamath-Loeb
- Departments of Pathology, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
- Biochemistry, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Diego G. Zavala-van Rankin
- INMEGEN, National Institute of Genomic Medicine, Periferico Sur No.4809, Col. Arenal Tepepan, Del. Tlalpan Mèxico, D.F, C.P. 14610, Mexico
| | - Jeny Flores-Morales
- INMEGEN, National Institute of Genomic Medicine, Periferico Sur No.4809, Col. Arenal Tepepan, Del. Tlalpan Mèxico, D.F, C.P. 14610, Mexico
| | - Mary J. Emond
- Biostatistics, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Julia M. Sidorova
- Departments of Pathology, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Alessandra Carnevale
- INMEGEN, National Institute of Genomic Medicine, Periferico Sur No.4809, Col. Arenal Tepepan, Del. Tlalpan Mèxico, D.F, C.P. 14610, Mexico
| | - Maria del Carmen Cárdenas-Cortés
- National Institute of Medical Science and Nutrition Salvador Zubiran, Vasco de Quiroga 15, Colonia Sección XVI, Tlalpan C.P.14000, México D.F., Mexico
| | - Thomas H. Norwood
- Departments of Pathology, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Raymond J. Monnat
- Departments of Pathology, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
- Genome Sciences, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Lawrence A. Loeb
- Departments of Pathology, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
- Biochemistry, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Gabriela E. Mercado-Celis
- INMEGEN, National Institute of Genomic Medicine, Periferico Sur No.4809, Col. Arenal Tepepan, Del. Tlalpan Mèxico, D.F, C.P. 14610, Mexico
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14
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McLaren GD, Barton JC, Ramm GA, Emond MJ, Subramaniam VN, Phatak PD, Adams PC, Powell LW, Gurrin LC, Anderson GJ, McLaren CE. Reply. Hepatology 2017; 65:1072-1073. [PMID: 28010035 PMCID: PMC5319902 DOI: 10.1002/hep.29002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 12/07/2022]
Affiliation(s)
- Gordon D. McLaren
- Department of Veterans Affairs Long Beach Healthcare System, Long
Beach, CA, USA,Division of Hematology/Oncology, Department of Medicine, University
of California, Irvine, CA USA
| | | | - Grant A. Ramm
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of
Queensland, Brisbane, Australia
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, WA,
USA
| | - V. Nathan Subramaniam
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Institute of Health and Biomedical Innovation, School of Biomedical
Sciences, Queensland University of Technology, Brisbane, Australia
| | | | - Paul C. Adams
- Department of Medicine, London Health Sciences Centre, London, ON,
Canada
| | - Lawrie W. Powell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of
Queensland, Brisbane, Australia,Royal Brisbane & Women’s Hospital, Brisbane,
Australia
| | - Lyle C. Gurrin
- Centre for MEGA Epidemiology, The University of Melbourne,
Melbourne, Australia
| | - Gregory J. Anderson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,School of Medicine and School of Chemistry and Molecular
Bioscience, University of Queensland, Brisbane, Australia
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15
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Barton JC, Chen WP, Emond MJ, Phatak PD, Subramaniam VN, Adams PC, Gurrin LC, Anderson GJ, Ramm GA, Powell LW, Allen KJ, Phillips JD, Parker CJ, McLaren GD, McLaren CE. GNPAT p.D519G is independently associated with markedly increased iron stores in HFE p.C282Y homozygotes. Blood Cells Mol Dis 2016; 63:15-20. [PMID: 27936396 DOI: 10.1016/j.bcmd.2016.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND GNPAT p.D519G positivity is significantly increased in HFE p.C282Y homozygotes with markedly increased iron stores. We sought to determine associations of p.D519G and iron-related variables with iron stores in p.C282Y homozygotes. METHODS We defined markedly increased iron stores as serum ferritin >2247pmol/L (>1000μg/L) and either hepatic iron >236μmol/g dry weight or iron >10g by induction phlebotomy (men and women). We defined normal or mildly elevated iron stores as serum ferritin <674.1pmol/L (<300μg/L) or either age≥40y with iron ≤2.5g iron by induction phlebotomy or age≥50y with ≤3.0g iron by induction phlebotomy (men only). We compared participant subgroups using univariate methods. Using multivariable logistic regression, we evaluated associations of markedly increased iron stores with these variables: age; iron supplement use (dichotomous); whole blood units donated; erythrocyte units received as transfusion; daily alcohol consumption, g; and p.D519G positivity (heterozygosity or homozygosity). RESULTS The mean age of 56 participants (94.6% men) was 55±10 (SD) y; 41 had markedly increased iron stores. Prevalences of swollen/tender 2nd/3rd metacarpophalangeal joints and elevated aspartate or alanine aminotransferase were significantly greater in participants with markedly increased iron stores. Only participants with markedly increased iron stores had cirrhosis. In multivariable analyses, p.D519G positivity was the only exposure variable significantly associated with markedly increased iron stores (odds ratio 9.9, 95% CI [1.6, 60.3], p=0.0126). CONCLUSIONS GNPAT p.D519G is strongly associated with markedly increased iron stores in p.C282Y homozygotes after correction for age, iron-related variables, and alcohol consumption.
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Affiliation(s)
- James C Barton
- Southern Iron Disorders Center, Birmingham, AL, 35209, USA; Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Wen-Pin Chen
- Chao Family Comprehensive Cancer Center, Irvine, CA 92697, USA
| | - Mary J Emond
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | | | - V Nathan Subramaniam
- QIMR Berghofer Medical Research Institute, Brisbane City, QLD 4006, Australia; Faculty of Medicine and Biomedical Sciences, The University of Queensland, Herston, QLD, 4006, Australia
| | - Paul C Adams
- Department of Medicine, London Health Sciences Centre, London, Ontario, N6A 5W9, Canada
| | - Lyle C Gurrin
- Centre for MEGA Epidemiology, The University of Melbourne, Victoria 3010, Australia
| | - Gregory J Anderson
- QIMR Berghofer Medical Research Institute, Brisbane City, QLD 4006, Australia; School of Medicine and School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, QLD 4072, Australia
| | - Grant A Ramm
- QIMR Berghofer Medical Research Institute, Brisbane City, QLD 4006, Australia; Faculty of Medicine and Biomedical Sciences, The University of Queensland, Herston, QLD, 4006, Australia
| | - Lawrie W Powell
- QIMR Berghofer Medical Research Institute, Brisbane City, QLD 4006, Australia; Faculty of Medicine and Biomedical Sciences, The University of Queensland, Herston, QLD, 4006, Australia; Royal Brisbane & Women's Hospital, Herston, QLD, 4029, Australia
| | - Katrina J Allen
- Murdoch Childrens Research Institute, Parkville, Victoria 3052, Australia
| | - John D Phillips
- Departments of Medicine and Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Charles J Parker
- Division of Hematology and Hematologic Malignancies, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Gordon D McLaren
- Department of Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA; Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, CA 92868, USA
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16
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Chantratita N, Tandhavanant S, Seal S, Wikraiphat C, Wongsuvan G, Ariyaprasert P, Suntornsut P, Teerawattanasook N, Jutrakul Y, Srisurat N, Chaimanee P, Mahavanakul W, Srisamang P, Phiphitaporn S, Mokchai M, Anukunananchai J, Wongratanacheewin S, Chetchotisakd P, Emond MJ, Peacock SJ, West TE. TLR4 genetic variation is associated with inflammatory responses in Gram-positive sepsis. Clin Microbiol Infect 2016; 23:47.e1-47.e10. [PMID: 27615723 DOI: 10.1016/j.cmi.2016.08.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/06/2016] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVES To identify important pathogen recognition receptor (PRR) pathways regulating innate immune responses and outcome in Staphylococcus aureus sepsis. METHODS We analysed whether candidate PRR pathway genetic variants were associated with killed S. aureus-induced cytokine responses ex vivo and performed follow-up in vitro studies. We tested the association of our top-ranked variant with cytokine responses and clinical outcomes in a prospective multicentre cohort of patients with staphylococcal sepsis. RESULTS An intronic TLR4 polymorphism and expression quantitative trait locus, rs1927907, was highly associated with cytokine release induced by stimulation of blood from healthy Thai subjects with S. aureus ex vivo. S. aureus did not induce TLR4-dependent NF-κB activation in transfected HEK293 cells. In monocytes, tumor necrosis factor (TNF)-α release induced by S. aureus was not blunted by a TLR4/MD-2 neutralizing antibody, but in a monocyte cell line, TNF-α was reduced by knockdown of TLR4. In Thai patients with staphylococcal sepsis, rs1927907 was associated with higher interleukin (IL)-6 and IL-8 levels as well as with respiratory failure. S. aureus-induced responses in blood were most highly correlated with responses to Gram-negative stimulants whole blood. CONCLUSIONS A genetic variant in TLR4 is associated with cytokine responses to S. aureus ex vivo and plasma cytokine levels and respiratory failure in staphylococcal sepsis. While S. aureus does not express lipopolysaccharide or activate TLR4 directly, the innate immune response to S. aureus does appear to be modulated by TLR4 and shares significant commonality with that induced by Gram-negative pathogens and lipopolysaccharide.
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Affiliation(s)
- N Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - S Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - S Seal
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - C Wikraiphat
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - G Wongsuvan
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - P Ariyaprasert
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - P Suntornsut
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - N Teerawattanasook
- Department of Clinical Pathology, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Y Jutrakul
- Department of Clinical Pathology, Udon Thani Hospital, Udon Thani, Thailand
| | - N Srisurat
- Department of Clinical Pathology, Khon Kaen Hospital, Khon Kaen, Thailand
| | - P Chaimanee
- Srinagarind Hospital, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - W Mahavanakul
- Department of Medicine, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - P Srisamang
- Department of Pediatrics, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - S Phiphitaporn
- Department of Medicine, Udon Thani Hospital, Udon Thani, Thailand
| | - M Mokchai
- Department of Medicine, Khon Kaen Hospital, Khon Kaen, Thailand
| | | | - S Wongratanacheewin
- Department of Microbiology and Melioidosis Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - P Chetchotisakd
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - M J Emond
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - S J Peacock
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - T E West
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, WA, USA; International Respiratory and Severe Illness Center, University of Washington, Seattle, USA
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17
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Basisty N, Dai D, Gagnidze A, Gitari L, Fredrickson J, Maina Y, Beyer RP, Emond MJ, Hsieh EJ, MacCoss MJ, Martin GM, Rabinovitch PS. Mitochondrial-targeted catalase is good for the old mouse proteome, but not for the young: 'reverse' antagonistic pleiotropy? Aging Cell 2016; 15:634-45. [PMID: 27061426 PMCID: PMC4933659 DOI: 10.1111/acel.12472] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2016] [Indexed: 12/31/2022] Open
Abstract
Reactive oxygen species (ROS) are highly reactive oxygen‐containing molecules associated with aging and a broad spectrum of pathologies. We have previously shown that transgenic expression of the antioxidant enzyme catalase targeted to the mitochondria (mCAT) in mice reduces ROS, attenuates age‐related disease, and increases lifespan. However, it has been increasingly recognized that ROS also has beneficial roles in signaling, hormesis, stress response, and immunity. We therefore hypothesized that mCAT might be beneficial only when ROS approaches pathological levels in older age and might not be advantageous at a younger age when basal ROS is low. We analyzed abundance and turnover of the global proteome in hearts and livers of young (4 month) and old (20 month) mCAT and wild‐type (WT) mice. In old hearts and livers of WT mice, protein half‐lives were reduced compared to young, while in mCAT mice the reverse was observed; the longest half‐lives were seen in old mCAT mice and the shortest in young mCAT. Protein abundance of old mCAT hearts recapitulated a more youthful proteomic expression profile (P‐value < 0.01). However, young mCAT mice partially phenocopied the older wild‐type proteome (P‐value < 0.01). Age strongly interacts with mCAT, consistent with antagonistic pleiotropy in the reverse of the typical direction. These findings underscore the contrasting roles of ROS in young vs. old mice and indicate the need for better understanding of the interaction between dose and age in assessing the efficacy of therapeutic interventions in aging, including mitochondrial antioxidants.
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Affiliation(s)
- Nathan Basisty
- Department of Pathology University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Dao‐Fu Dai
- Department of Pathology University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Arni Gagnidze
- Department of Pathology University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Lemuel Gitari
- Department of Pathology University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Jeanne Fredrickson
- Department of Pathology University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Yvonne Maina
- Department of Pathology University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Richard P. Beyer
- Department of Environmental Health University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Mary J. Emond
- Department of Biostatistics University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Edward J. Hsieh
- Department of Genome Sciences University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Michael J. MacCoss
- Department of Genome Sciences University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - George M. Martin
- Department of Pathology University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
| | - Peter S. Rabinovitch
- Department of Pathology University of Washington 1959 NE Pacific Ave Seattle WA 98195 USA
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18
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McLaren CE, Barton JC, Phatak PD, Emond MJ, Subramaniam VN, Gurrin LC, Adams PC, Powell LW, Ramm GA, Anderson GJ, McLaren GD. Reply. Hepatology 2016; 63:2056-7. [PMID: 26417986 PMCID: PMC4811743 DOI: 10.1002/hep.28260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
| | | | | | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle,
WA
| | - V. Nathan Subramaniam
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of
Queensland, Brisbane, Australia
| | - Lyle C. Gurrin
- Centre for MEGA Epidemiology, The University of Melbourne,
Melbourne, Australia
| | - Paul C. Adams
- Department of Medicine, London Health Sciences Centre, London, ON,
Canada
| | - Lawrie W. Powell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of
Queensland, Brisbane, Australia,Royal Brisbane & Women's Hospital, Brisbane,
Australia
| | - Grant A. Ramm
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of
Queensland, Brisbane, Australia
| | - Gregory J. Anderson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,School of Medicine and School of Chemistry and Molecular
Bioscience, University of Queensland
| | - Gordon D. McLaren
- Department of Veterans Affairs Long Beach Healthcare System, Long
Beach, CA,Division of Hematology/Oncology, Department of Medicine, University
of California, Irvine, CA
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19
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McLaren CE, Barton JC, Subramaniam VN, Ramm GA, Phatak PD, Emond MJ, Gurrin LC, Adams PC, Powell LW, Anderson GJ, McLaren GD. Reply. Hepatology 2016; 63:2058-60. [PMID: 26845080 PMCID: PMC4874893 DOI: 10.1002/hep.28479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
| | | | - V. Nathan Subramaniam
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of
Queensland, Brisbane, Australia
| | - Grant A. Ramm
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of
Queensland, Brisbane, Australia
| | | | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle,
WA
| | - Lyle C. Gurrin
- Centre for MEGA Epidemiology, The University of Melbourne,
Melbourne, Australia
| | - Paul C. Adams
- Department of Medicine, London Health Sciences Centre, London, ON,
Canada
| | - Lawrie W. Powell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of
Queensland, Brisbane, Australia,Royal Brisbane & Women’s Hospital, Brisbane,
Australia
| | - Gregory J. Anderson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,School of Medicine and School of Chemistry and Molecular
Bioscience, University of Queensland
| | - Gordon D. McLaren
- Department of Veterans Affairs Long Beach Healthcare System, Long
Beach, CA,Division of Hematology/Oncology, Department of Medicine, University
of California, Irvine, CA
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20
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Krimmel JD, Schmitt MW, Harrell MI, Agnew KJ, Kennedy SR, Emond MJ, Loeb LA, Swisher EM, Risques RA. Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues. Proc Natl Acad Sci U S A 2016; 113:6005-10. [PMID: 27152024 PMCID: PMC4889384 DOI: 10.1073/pnas.1601311113] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Current sequencing methods are error-prone, which precludes the identification of low frequency mutations for early cancer detection. Duplex sequencing is a sequencing technology that decreases errors by scoring mutations present only in both strands of DNA. Our aim was to determine whether duplex sequencing could detect extremely rare cancer cells present in peritoneal fluid from women with high-grade serous ovarian carcinomas (HGSOCs). These aggressive cancers are typically diagnosed at a late stage and are characterized by TP53 mutations and peritoneal dissemination. We used duplex sequencing to analyze TP53 mutations in 17 peritoneal fluid samples from women with HGSOC and 20 from women without cancer. The tumor TP53 mutation was detected in 94% (16/17) of peritoneal fluid samples from women with HGSOC (frequency as low as 1 mutant per 24,736 normal genomes). Additionally, we detected extremely low frequency TP53 mutations (median mutant fraction 1/13,139) in peritoneal fluid from nearly all patients with and without cancer (35/37). These mutations were mostly deleterious, clustered in hotspots, increased with age, and were more abundant in women with cancer than in controls. The total burden of TP53 mutations in peritoneal fluid distinguished cancers from controls with 82% sensitivity (14/17) and 90% specificity (18/20). Age-associated, low frequency TP53 mutations were also found in 100% of peripheral blood samples from 15 women with and without ovarian cancer (none with hematologic disorder). Our results demonstrate the ability of duplex sequencing to detect rare cancer cells and provide evidence of widespread, low frequency, age-associated somatic TP53 mutation in noncancerous tissue.
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Affiliation(s)
- Jeffrey D Krimmel
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Michael W Schmitt
- Department of Pathology, University of Washington, Seattle, WA 98195; Divisions of Hematology and Medical Oncology, Department of Medicine, University of Washington, Seattle, WA 98195
| | - Maria I Harrell
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195
| | - Kathy J Agnew
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195
| | - Scott R Kennedy
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Mary J Emond
- Department of Statistics, University of Washington, Seattle, WA 98195
| | - Lawrence A Loeb
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195
| | - Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, WA 98195;
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21
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Pinto NR, Emond MJ, Spiekerman C, Naranjo A, Makar KW, Park JR, McCune JS. Pharmacogenetics of treatment response in patients with high-risk neuroblastoma: A Children’s Oncology Group study. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.10560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Mary J Emond
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA
| | - Charles Spiekerman
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA
| | - Arlene Naranjo
- Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, FL
| | | | - Julie R. Park
- Seattle Children's Hospital and University of Washington School of Medicine, Seattle, WA
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22
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Gao L, Emond MJ, Louie T, Cheadle C, Berger AE, Rafaels N, Vergara C, Kim Y, Taub MA, Ruczinski I, Mathai SC, Rich SS, Nickerson DA, Hummers LK, Bamshad MJ, Hassoun PM, Mathias RA, Barnes KC. Identification of Rare Variants in ATP8B4 as a Risk Factor for Systemic Sclerosis by Whole-Exome Sequencing. Arthritis Rheumatol 2016; 68:191-200. [PMID: 26473621 DOI: 10.1002/art.39449] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/24/2015] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To determine the contribution of rare variants as genetic modifiers of the expressivity, penetrance, and severity of systemic sclerosis (SSc). METHODS We performed whole-exome sequencing of 78 European American patients with SSc, including 35 patients without pulmonary arterial hypertension (PAH) and 43 patients with PAH. Association testing of case-control probability for rare variants was performed using the unified sequence kernel association test with optimal kernel weighting and small sample adjustment by comparing all SSc patients with a reference population of 3,179 controls from the Exome Sequencing Project 5,500 exome data set. Replication genotyping was performed in an independent sample of 3,263 patients (415 patients with SSc and 2,848 controls). We conducted expression profiling of messenger RNA from 61 SSc patients (19 without PAH and 42 with PAH) and 41 corresponding controls. RESULTS The ATP8B4 gene was associated with a significant increase in the risk of SSc (P = 2.77 × 10(-7)). Among the 64 ATP8B4 variants tested, a single missense variant, c.1308C>G (F436L, rs55687265), provided the most compelling evidence of association (P = 9.35 × 10(-10), odds ratio [OR] 6.11), which was confirmed in the replication cohort (P = 0.012, OR 1.86) and meta-analysis (P = 1.92 × 10(-7), OR 2.5). Genes involved in E3 ubiquitin-protein ligase complex (ASB10) and cyclic nucleotide gated channelopathies (CNGB3) as well as HLA-DRB5 and HSPB2 (heat-shock protein 27) provided additional evidence of association (P < 10(-5)). Differential ATP8B4 expression was observed among the SSc patients compared to the controls (P = 0.0005). CONCLUSION ATP8B4 may represent a putative genetic risk factor for SSc and pulmonary vascular complications.
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Affiliation(s)
- Li Gao
- Johns Hopkins University, Baltimore, Maryland
| | | | | | | | | | | | | | - Yoonhee Kim
- National Human Genome Research Institute, NIH, Baltimore, Maryland
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23
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Chang TC, Tang W, Koh WJH, Rettie AJE, Emond MJ, Monnat RJ, Folch A. Microwell arrays reveal cellular heterogeneity during the clonal expansion of transformed human cells. Technology (Singap World Sci) 2015; 3:163-171. [PMID: 27158641 PMCID: PMC4854201 DOI: 10.1142/s2339547815200046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We developed micromolded microwell arrays to study the proliferation and senescence of single cells. Microwell arrays were designed to be compatible with conventional cell culture protocols to simplify cell loading, cell culture, and imaging. We demonstrated the utility of these arrays by measuring the proliferation and senescence of isogenic cells which expressed or had been depleted of the human Werner syndrome protein. Our results allowed us to reveal cell-to-cell heterogeneity in proliferation in WRN+ and WRN-depleted fibroblasts during clonal growth.
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Affiliation(s)
- Tim C Chang
- Departments of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Weiliang Tang
- Departments of Pathology, University of Washington, Seattle, WA 98195, USA
| | - William Jen Hoe Koh
- Departments of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | | | - Mary J Emond
- Departments of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Raymond J Monnat
- Departments of Pathology, University of Washington, Seattle, WA 98195, USA; Departments of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Albert Folch
- Departments of Bioengineering, University of Washington, Seattle, WA 98195, USA
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24
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McLaren CE, Emond MJ, Subramaniam VN, Phatak PD, Barton JC, Adams PC, Powell LW, Gurrin LC, Ramm GA, Anderson GJ, McLaren GD. Reply: To PMID 25605615. Hepatology 2015; 62:1918-9. [PMID: 25914125 DOI: 10.1002/hep.27851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Mary J Emond
- Department of Biostatistics, University of Washington, Seattle, WA
| | - V Nathan Subramaniam
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine and Biomedical Sciences, The University of Queensland Brisbane, Australia
| | | | | | - Paul C Adams
- Department of Medicine, London Health Sciences Center, London, Ontario, Canada
| | - Lawrie W Powell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine and Biomedical Sciences, The University of Queensland Brisbane, Australia.,Royal Brisbane & Women's Hospital, Brisbane, Australia
| | - Lyle C Gurrin
- Center for MEGA Epidemiology, The University of Melbourne, Melbourne, Australia
| | - Grant A Ramm
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine and Biomedical Sciences, The University of Queensland Brisbane, Australia
| | - Gregory J Anderson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Medicine and School of Chemistry and Molecular Bioscience, University of Queensland, St. Lucia, Australia
| | - Gordon D McLaren
- Department of Veterans Affairs Long Beach Healthcare System, Long Beach, CA.,Division of Hematology/Oncology, Department of Medicine, University of California Irvine, CA
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25
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Emond MJ, Louie T, Emerson J, Chong JX, Mathias RA, Knowles MR, Rieder MJ, Tabor HK, Nickerson DA, Barnes KC, Go L, Gibson RL, Bamshad MJ. Correction: Exome Sequencing of Phenotypic Extremes Identifies CAV2 and TMC6 as Interacting Modifiers of Chronic Pseudomonas aeruginosa Infection in Cystic Fibrosis. PLoS Genet 2015; 11:e1005424. [PMID: 26284524 PMCID: PMC4540584 DOI: 10.1371/journal.pgen.1005424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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McLaren CE, Emond MJ, Subramaniam VN, Phatak PD, Barton JC, Adams PC, Goh JB, McDonald CJ, Powell LW, Gurrin LC, Allen KJ, Nickerson DA, Louie T, Ramm GA, Anderson GJ, McLaren GD. Exome sequencing in HFE C282Y homozygous men with extreme phenotypes identifies a GNPAT variant associated with severe iron overload. Hepatology 2015; 62:429-39. [PMID: 25605615 PMCID: PMC4508230 DOI: 10.1002/hep.27711] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [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: 10/07/2014] [Accepted: 01/13/2015] [Indexed: 12/12/2022]
Abstract
UNLABELLED To identify polymorphisms associated with variability of iron overload severity in HFE-associated hemochromatosis, we performed exome sequencing of DNA from 35 male HFE C282Y homozygotes with either markedly increased iron stores (n = 22; cases) or with normal or mildly increased iron stores (n = 13; controls). The 35 participants, residents of the United States, Canada, and Australia, reported no or light alcohol consumption. Sequencing data included 82,068 single-nucleotide variants, and 10,337 genes were tested for a difference between cases and controls. A variant in the GNPAT gene showed the most significant association with severe iron overload (P = 3 × 10(-6) ; P = 0.033 by the likelihood ratio test after correction for multiple comparisons). Sixteen of twenty-two participants with severe iron overload had glyceronephosphate O-acyltransferase (GNPAT) polymorphism p.D519G (rs11558492; 15 heterozygotes, one homozygote). No control participant had this polymorphism. To examine functional consequences of GNPAT deficiency, we performed small interfering RNA-based knockdown of GNPAT in the human liver-derived cell line, HepG2/C3A. This knockdown resulted in a >17-fold decrease in expression of the messenger RNA encoding the iron-regulatory hormone, hepcidin. CONCLUSION GNPAT p.D519G is associated with a high-iron phenotype in HFE C282Y homozygotes and may participate in hepcidin regulation.
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Affiliation(s)
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, WA
| | - V. Nathan Subramaniam
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | | | | | - Paul C. Adams
- Department of Medicine, London Health Sciences Centre, London, ON, Canada
| | - Justin B. Goh
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | | | - Lawrie W. Powell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, Australia,Royal Brisbane & Women’s Hospital, Brisbane, Australia
| | - Lyle C. Gurrin
- Centre for MEGA Epidemiology, The University of Melbourne, Melbourne, Australia
| | | | | | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Grant A. Ramm
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Gregory J. Anderson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,School of Medicine and School of Chemistry and Molecular Bioscience, University of Queensland
| | - Gordon D. McLaren
- Department of Veterans Affairs Long Beach Healthcare System, Long Beach, CA,Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, CA
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27
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Karunadharma PP, Basisty N, Chiao YA, Dai DF, Drake R, Levy N, Koh WJ, Emond MJ, Kruse S, Marcinek D, Maccoss MJ, Rabinovitch PS. Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments. FASEB J 2015; 29:3582-92. [PMID: 25977255 DOI: 10.1096/fj.15-272666] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/04/2015] [Indexed: 11/11/2022]
Abstract
The mitochondrial respiratory chain (RC) produces most of the cellular ATP and requires strict quality-control mechanisms. To examine RC subunit proteostasis in vivo, we measured RC protein half-lives (HLs) in mice by liquid chromatography-tandem mass spectrometry with metabolic [(2)H3]-leucine heavy isotope labeling under divergent conditions. We studied 7 tissues/fractions of young and old mice on control diet or one of 2 diet regimens (caloric restriction or rapamycin) that altered protein turnover (42 conditions in total). We observed a 6.5-fold difference in mean HL across tissues and an 11.5-fold difference across all conditions. Normalization to the mean HL of each condition showed that relative HLs were conserved across conditions (Spearman's ρ = 0.57; P < 10(-4)), but were highly heterogeneous between subunits, with a 7.3-fold mean range overall, and a 2.2- to 4.6-fold range within each complex. To identify factors regulating this conserved distribution, we performed statistical analyses to study the correlation of HLs to the properties of the subunits. HLs significantly correlated with localization within the mitochondria, evolutionary origin, location of protein-encoding, and ubiquitination levels. These findings challenge the notion that all subunits in a complex turnover at comparable rates and suggest that there are common rules governing the differential proteolysis of RC protein subunits under divergent cellular conditions.
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Affiliation(s)
- Pabalu P Karunadharma
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Nathan Basisty
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Ying Ann Chiao
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Dao-Fu Dai
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Rachel Drake
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Nick Levy
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - William J Koh
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Mary J Emond
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Shane Kruse
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - David Marcinek
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Michael J Maccoss
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Peter S Rabinovitch
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
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Mackelprang RD, Birsie K, Emond MJ, Burgener A, Ball B, Baeten J, Celum C, Cohen CR, Mugo NR, Lingappa JR. Genital Proteome Correlates of Highly HIV-1 Exposed Uninfected African Women. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5151.abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Mary J. Emond
- University of Washington, Seattle, WA, United States
| | | | - Blake Ball
- University of Manitoba, Winnipeg, MB, Canada
| | - Jared Baeten
- University of Washington, Seattle, WA, United States
| | - Connie Celum
- University of Washington, Seattle, WA, United States
| | - Craig R. Cohen
- University of California at San Francisco, San Francisco, CA, United States
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29
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Shiovitz S, Bertagnolli MM, Renfro LA, Nam E, Foster NR, Dzieciatkowski S, Luo Y, Lao VV, Monnat RJ, Emond MJ, Maizels N, Niedzwiecki D, Goldberg RM, Saltz LB, Venook A, Warren RS, Grady WM. CpG island methylator phenotype is associated with response to adjuvant irinotecan-based therapy for stage III colon cancer. Gastroenterology 2014; 147:637-45. [PMID: 24859205 PMCID: PMC4143495 DOI: 10.1053/j.gastro.2014.05.009] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [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: 02/28/2014] [Revised: 04/30/2014] [Accepted: 05/16/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS The CpG island methylator phenotype (CIMP), defined by a high frequency of aberrantly methylated genes, is a characteristic of a subclass of colon tumors with distinct clinical and molecular features. Cohort studies have produced conflicting results on responses of CIMP-positive tumors to chemotherapy. We assessed the association between tumor CIMP status and survival of patients receiving adjuvant fluorouracil and leucovorin alone or with irinotecan (IFL). METHODS We analyzed data from patients with stage III colon adenocarcinoma randomly assigned to groups given fluorouracil and leucovorin or IFL after surgery, from April 1999 through April 2001. The primary end point of the trial was overall survival and the secondary end point was disease-free survival. DNA isolated from available tumor samples (n = 615) was used to determine CIMP status based on methylation patterns at the CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1 loci. The effects of CIMP on survival were modeled using Kaplan-Meier and Cox proportional hazards; interactions with treatment and BRAF, KRAS, and mismatch repair (MMR) status were also investigated. RESULTS Of the tumor samples characterized for CIMP status, 145 were CIMP positive (23%). Patients with CIMP-positive tumors had shorter overall survival times than patients with CIMP-negative tumors (hazard ratio = 1.36; 95% confidence interval: 1.01-1.84). Treatment with IFL showed a trend toward increased overall survival for patients with CIMP-positive tumors, compared with treatment with fluorouracil and leucovorin (hazard ratio = 0.62; 95% CI: 0.37-1.05; P = .07), but not for patients with CIMP-negative tumors (hazard ratio = 1.38; 95% CI: 1.00-1.89; P = .049). In a 3-way interaction analysis, patients with CIMP-positive, MMR-intact tumors benefited most from the addition of irinotecan to fluorouracil and leucovorin therapy (for the interaction, P = .01). CIMP was more strongly associated with response to IFL than MMR status. Results for disease-free survival times were comparable among all analyses. CONCLUSIONS Patients with stage III, CIMP-positive, MMR-intact colon tumors have longer survival times when irinotecan is added to combination therapy with fluorouracil and leucovorin.
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Affiliation(s)
- Stacey Shiovitz
- Department of Medicine, University of Washington (UW),Clinical Research Division, Fred Hutchinson Cancer Research Center
| | | | | | - Eunmi Nam
- Division of Hematology/Oncology, Ewha Womans University School of Medicine, South Korea
| | | | | | - Yanxin Luo
- Clinical Research Division, Fred Hutchinson Cancer Research Center,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, P.R. China
| | - Victoria Valinluck Lao
- Clinical Research Division, Fred Hutchinson Cancer Research Center,Department of Surgery, UW Medical School
| | | | | | | | | | | | | | - Alan Venook
- University of California-San Francisco and the Helen Diller Family Comprehensive Cancer Center
| | - Robert S. Warren
- University of California-San Francisco and the Helen Diller Family Comprehensive Cancer Center
| | - William M. Grady
- Department of Medicine, University of Washington (UW),Clinical Research Division, Fred Hutchinson Cancer Research Center
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30
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Kamath-Loeb AS, Balakrishna S, Whittington D, Shen JC, Emond MJ, Okabe T, Masutani C, Hanaoka F, Nishimura S, Loeb LA. Sphingosine, a modulator of human translesion DNA polymerase activity. J Biol Chem 2014; 289:21663-72. [PMID: 24928506 DOI: 10.1074/jbc.m114.570242] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Translesion (TLS) DNA polymerases are specialized, error-prone enzymes that synthesize DNA across bulky, replication-stalling DNA adducts. In so doing, they facilitate the progression of DNA synthesis and promote cell proliferation. To potentiate the effect of cancer chemotherapeutic regimens, we sought to identify inhibitors of TLS DNA polymerases. We screened five libraries of ∼ 3000 small molecules, including one comprising ∼ 600 nucleoside analogs, for their effect on primer extension activity of DNA polymerase η (Pol η). We serendipitously identified sphingosine, a lipid-signaling molecule that robustly stimulates the activity of Pol η by ∼ 100-fold at low micromolar concentrations but inhibits it at higher concentrations. This effect is specific to the Y-family DNA polymerases, Pols η, κ, and ι. The addition of a single phosphate group on sphingosine completely abrogates this effect. Likewise, the inclusion of other sphingolipids, including ceramide and sphingomyelin to extension reactions does not elicit this response. Sphingosine increases the rate of correct and incorrect nucleotide incorporation while having no effect on polymerase processivity. Endogenous Pol η activity is modulated similarly as the recombinant enzyme. Importantly, sphingosine-treated cells exhibit increased lesion bypass activity, and sphingosine tethered to membrane lipids mimics the effects of free sphingosine. Our studies have uncovered sphingosine as a modulator of TLS DNA polymerase activity; this property of sphingosine may be associated with its known role as a signaling molecule in regulating cell proliferation in response to cellular stress.
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Affiliation(s)
- Ashwini S Kamath-Loeb
- From the Departments of Pathology and Biochemistry, The Gottstein Memorial Cancer Research Laboratory, University of Washington, Seattle, Washington 98195
| | - Sharath Balakrishna
- From the Departments of Pathology and Biochemistry, The Gottstein Memorial Cancer Research Laboratory, University of Washington, Seattle, Washington 98195
| | - Dale Whittington
- the Department of Medicinal Chemistry, Mass Spectrometry Center, University of Washington, Seattle, Washington 98195
| | - Jiang-Cheng Shen
- From the Departments of Pathology and Biochemistry, The Gottstein Memorial Cancer Research Laboratory, University of Washington, Seattle, Washington 98195
| | - Mary J Emond
- Biostatistics and Center for Biomedical Statistics, University of Washington, Seattle, Washington 98195
| | - Takayoshi Okabe
- the Open Innovation Center for Drug Discovery, University of Tokyo, Tokyo 113-0033, Japan
| | - Chikahide Masutani
- the Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Fumio Hanaoka
- the Institute for Biomolecular Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan, and
| | - Susumu Nishimura
- the Laboratory Animal Resource Center, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Lawrence A Loeb
- From the Departments of Pathology and Biochemistry, The Gottstein Memorial Cancer Research Laboratory, University of Washington, Seattle, Washington 98195,
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31
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Chantratita N, Tandhavanant S, Myers ND, Seal S, Arayawichanont A, Kliangsa-ad A, Hittle LE, Ernst RK, Emond MJ, Wurfel MM, Day NPJ, Peacock SJ, West TE. Survey of innate immune responses to Burkholderia pseudomallei in human blood identifies a central role for lipopolysaccharide. PLoS One 2013; 8:e81617. [PMID: 24303060 PMCID: PMC3841221 DOI: 10.1371/journal.pone.0081617] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 10/25/2013] [Indexed: 12/28/2022] Open
Abstract
B. pseudomallei is a gram-negative bacterium that causes the tropical infection melioidosis. In northeast Thailand, mortality from melioidosis approaches 40%. As exemplified by the lipopolysaccharide-Toll-like receptor 4 interaction, innate immune responses to invading bacteria are precipitated by activation of host pathogen recognition receptors by pathogen associated molecular patterns. Human melioidosis is characterized by up-regulation of pathogen recognition receptors and pro-inflammatory cytokine release. In contrast to many gram-negative pathogens, however, the lipopolysaccharide of B. pseudomallei is considered only weakly inflammatory. We conducted a study in 300 healthy Thai subjects to investigate the ex vivo human blood response to various bacterial pathogen associated molecular patterns, including lipopolysaccharide from several bacteria, and to two heat-killed B. pseudomallei isolates. We measured cytokine levels after stimulation of fresh whole blood with a panel of stimuli. We found that age, sex, and white blood cell count modulate the innate immune response to B. pseudomallei. We further observed that, in comparison to other stimuli, the innate immune response to B. pseudomallei is most highly correlated with the response to lipopolysaccharide. The magnitude of cytokine responses induced by B. pseudomallei lipopolysaccharide was significantly greater than those induced by lipopolysaccharide from Escherichia coli and comparable to many responses induced by lipopolysaccharide from Salmonella minnesota despite lower amounts of lipid A in the B. pseudomallei lipopolysaccharide preparation. In human monocytes stimulated with B. pseudomallei, addition of polymyxin B or a TLR4/MD-2 neutralizing antibody inhibited the majority of TNF-α production. Challenging existing views, our data indicate that the innate immune response to B. pseudomallei in human blood is largely driven by lipopolysaccharide, and that the response to B. pseudomallei lipopolysaccharide in blood is greater than the response to other lipopolysaccharide expressing isolates. Our findings suggest that B. pseudomallei lipopolysaccharide may play a central role in stimulating the host response in melioidosis.
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Affiliation(s)
- Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicolle D. Myers
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Sudeshna Seal
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | | | - Aroonsri Kliangsa-ad
- Department of Clinical Pathology, Sappasithiprasong Hospital, Ubon Ratchathani, Thailand
| | - Lauren E. Hittle
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Maryland, United States of America
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Maryland, United States of America
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Mark M. Wurfel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Nicholas P. J. Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Center for Clinical Vaccinology and Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Sharon J. Peacock
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - T. Eoin West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- International Respiratory and Severe Illness Center, University of Washington, Seattle, Washington, United States of America
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Ussakli CH, Ebaee A, Binkley J, Brentnall TA, Emond MJ, Rabinovitch PS, Risques RA. Mitochondria and tumor progression in ulcerative colitis. J Natl Cancer Inst 2013; 105:1239-48. [PMID: 23852949 DOI: 10.1093/jnci/djt167] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The role of mitochondria in cancer is poorly understood. Ulcerative colitis (UC) is an inflammatory bowel disease that predisposes to colorectal cancer and is an excellent model to study tumor progression. Our goal was to characterize mitochondrial alterations in UC tumorigenesis. METHODS Nondysplastic colon biopsies from UC patients with high-grade dysplasia or cancer (progressors; n = 9) and UC patients dysplasia free (nonprogressors; n = 9) were immunostained for cytochrome C oxidase (COX), a component of the electron transport chain, and were quantified by multispectral imaging. For six additional progressors, nondysplastic and dysplastic biopsies were stained for COX and additional mitochondrial proteins including PGC1α, the master regulator of mitochondrial biogenesis. Mitochondrial DNA (mtDNA) copy number was determined by quantitative polymerase chain reaction. Generalized estimating equations with two-sided tests were used to account for correlation of measurements within individuals. RESULTS Nondysplastic biopsies of UC progressors showed statistically significant COX loss compared with UC nonprogressors by generalized estimating equation (-18.5 units, 95% confidence interval = -12.1 to -24.9; P < .001). COX intensity progressively decreased with proximity to dysplasia and was the lowest in adjacent to dysplasia and dysplastic epithelium. Surprisingly, COX intensity was statistically significantly increased in cancers. This bimodal pattern was observed for other mitochondrial proteins, including PGC1α, and was confirmed by mtDNA copy number. CONCLUSIONS Mitochondrial loss precedes the development of dysplasia, and it could be used to detect and potentially predict cancer. Cancer cells restore mitochondria, suggesting that mitochondria are needed for further proliferation. This bimodal pattern might be driven by transcriptional regulation of mitochondrial biogenesis by PGC1α.
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West TE, Chantratita N, Chierakul W, Limmathurotsakul D, Wuthiekanun V, Myers ND, Emond MJ, Wurfel MM, Hawn TR, Peacock SJ, Skerrett SJ. Impaired TLR5 functionality is associated with survival in melioidosis. J Immunol 2013; 190:3373-9. [PMID: 23447684 DOI: 10.4049/jimmunol.1202974] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Melioidosis is infection caused by the flagellated saprophyte Burkholderia pseudomallei. TLR5 is a pathogen recognition receptor activated by bacterial flagellin. We studied a genetic variant that encodes a defective TLR5 protein, TLR5(1174C)>T, to elucidate the role of TLR5 in melioidosis. We measured NF-κB activation induced by B. pseudomallei in human embryonic kidney-293 cells transfected with TLR5 and found that B. pseudomallei induced TLR5(1174C)- but not TLR5(1174T)-dependent activation of NF-κB. We tested the association of TLR5(1174C)>T with outcome in 600 Thai subjects with melioidosis. In a dominant model, TLR5(1174C)>T was associated with protection against in-hospital death (adjusted odds ratio: 0.20; 95% confidence interval: 0.08-0.50; p = 0.001) and organ failure (adjusted odds ratio: 0.37; 95% confidence interval: 0.19-0.71; p = 0.003). We analyzed blood cytokine production induced by flagellin or heat-killed B. pseudomallei by TLR5(1174C)>T genotype in healthy subjects. Flagellin induced lower monocyte-normalized levels of IL-6, IL-8, TNF-α, IL-10, MCP-1, IL-1ra, G-CSF, and IL-1β in carriers of TLR5(1174T) compared with carriers of TLR5(1174C). B. pseudomallei induced lower monocyte-normalized levels of IL-10 in carriers of TLR5(1174T). We conclude that the hypofunctional genetic variant TLR5(1174C)>T is associated with reduced organ failure and improved survival in melioidosis. This conclusion suggests a deleterious immunoregulatory effect of TLR5 that may be mediated by IL-10 and identifies this receptor as a potential therapeutic target in melioidosis.
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Affiliation(s)
- T Eoin West
- International Respiratory and Severe Illness Center, University of Washington, Seattle, WA 98104, USA.
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Lee S, Emond MJ, Bamshad MJ, Barnes KC, Rieder MJ, Nickerson DA, Christiani D, Wurfel M, Lin X, Lin X. Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am J Hum Genet 2012; 91:224-37. [PMID: 22863193 DOI: 10.1016/j.ajhg.2012.06.007] [Citation(s) in RCA: 697] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/22/2012] [Accepted: 06/12/2012] [Indexed: 12/23/2022] Open
Abstract
We propose in this paper a unified approach for testing the association between rare variants and phenotypes in sequencing association studies. This approach maximizes power by adaptively using the data to optimally combine the burden test and the nonburden sequence kernel association test (SKAT). Burden tests are more powerful when most variants in a region are causal and the effects are in the same direction, whereas SKAT is more powerful when a large fraction of the variants in a region are noncausal or the effects of causal variants are in different directions. The proposed unified test maintains the power in both scenarios. We show that the unified test corresponds to the optimal test in an extended family of SKAT tests, which we refer to as SKAT-O. The second goal of this paper is to develop a small-sample adjustment procedure for the proposed methods for the correction of conservative type I error rates of SKAT family tests when the trait of interest is dichotomous and the sample size is small. Both small-sample-adjusted SKAT and the optimal unified test (SKAT-O) are computationally efficient and can easily be applied to genome-wide sequencing association studies. We evaluate the finite sample performance of the proposed methods using extensive simulation studies and illustrate their application using the acute-lung-injury exome-sequencing data of the National Heart, Lung, and Blood Institute Exome Sequencing Project.
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35
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Emond MJ, Louie T, Emerson J, Zhao W, Mathias RA, Knowles MR, Wright FA, Rieder MJ, Tabor HK, Nickerson DA, Barnes KC, Gibson RL, Bamshad MJ. Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Nat Genet 2012; 44:886-9. [PMID: 22772370 PMCID: PMC3702264 DOI: 10.1038/ng.2344] [Citation(s) in RCA: 168] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/08/2012] [Indexed: 12/17/2022]
Abstract
Exome sequencing has become a powerful and effective strategy for discovery of genes underlying Mendelian disorders1. However, use of exome sequencing to identify variants associated with complex traits has been more challenging, partly because the samples sizes needed for adequate power may be very large2. One strategy to increase efficiency is to sequence individuals who are at both ends of a phenotype distribution (i.e., extreme phenotypes). Because the frequency of alleles that contribute to the trait are enriched in one or both extremes of phenotype, a modest sample size can potentially identify novel candidate genes/alleles3. As part of the National Heart, Lung, and Blood Institute Exome Sequencing Project (ESP), we used an extreme phenotype design to discover that variants in DCTN4, encoding a dynactin protein, are associated with time to first Pseudomonas aeruginosa (P. aeruginosa) airway infection, chronic P. aeruginosa infection and mucoid P. aeruginosa among individuals with cystic fibrosis (MIM219700).
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Affiliation(s)
- Mary J Emond
- Department of Biostatistics, University of Washington, Seattle, Washington, USA.
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Sangle NA, Emond MJ, Taylor SL, Bronner MP. High Prevalence of Overdiagnosis of High-Grade Dysplasia in Barrett Esophagus: A Multicenter International Phase 3 Trial in 485 Patients. Am J Clin Pathol 2012. [DOI: 10.1093/ajcp/138.suppl1.330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Bigham AW, Buckingham KJ, Husain S, Emond MJ, Bofferding KM, Gildersleeve H, Rutherford A, Astakhova NM, Perelygin AA, Busch MP, Murray KO, Sejvar JJ, Green S, Kriesel J, Brinton MA, Bamshad M. Host genetic risk factors for West Nile virus infection and disease progression. PLoS One 2011; 6:e24745. [PMID: 21935451 PMCID: PMC3174177 DOI: 10.1371/journal.pone.0024745] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [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: 05/25/2011] [Accepted: 08/16/2011] [Indexed: 11/19/2022] Open
Abstract
West Nile virus (WNV), a category B pathogen endemic in parts of Africa, Asia and Europe, emerged in North America in 1999, and spread rapidly across the continental U.S. Outcomes of infection with WNV range from asymptomatic to severe neuroinvasive disease manifested as encephalitis, paralysis, and/or death. Neuroinvasive WNV disease occurs in less than one percent of cases, and although host genetic factors are thought to influence risk for symptomatic disease, the identity of these factors remains largely unknown. We tested 360 common haplotype tagging and/or functional SNPs in 86 genes that encode key regulators of immune function in 753 individuals infected with WNV including: 422 symptomatic WNV cases and 331 cases with asymptomatic infections. After applying a Bonferroni correction for multiple tests and controlling for population stratification, SNPs in IRF3 (OR 0.54, p = 0.035) and MX1, (OR 0.19, p = 0.014) were associated with symptomatic WNV infection and a single SNP in OAS1 (OR 9.79, p = 0.003) was associated with increased risk for West Nile encephalitis and paralysis (WNE/P). Together, these results suggest that genetic variation in the interferon response pathway is associated with both risk for symptomatic WNV infection and WNV disease progression.
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Affiliation(s)
- Abigail W. Bigham
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
- * E-mail: (AWB); (MB)
| | - Kati J. Buckingham
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Sofia Husain
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Kathryn M. Bofferding
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Heidi Gildersleeve
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Ann Rutherford
- Department of Internal Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, Utah, United States of America
| | - Natalia M. Astakhova
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Andrey A. Perelygin
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Michael P. Busch
- Blood Systems, San Francisco, California, United States of America
| | - Kristy O. Murray
- School of Public Health, University of Texas Health Sciences Center at Houston, Houston, Texas, United States of America
| | - James J. Sejvar
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Sharone Green
- Department of Medicine, Center for Infectious Disease and Vaccine Research, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - John Kriesel
- Department of Internal Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, Utah, United States of America
| | - Margo A. Brinton
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
- * E-mail: (AWB); (MB)
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Bronner MP, Skacel M, Crispin DA, Hoff PD, Emond MJ, Lai LA, Tubbs RR, Rabinovitch PS, Brentnall TA, Brentnall TA. Array-based comparative genomic hybridization in ulcerative colitis neoplasia: single non-dysplastic biopsies distinguish progressors from non-progressors. Mod Pathol 2010; 23:1624-33. [PMID: 20802465 PMCID: PMC2932629 DOI: 10.1038/modpathol.2010.161] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Approximately 10% of ulcerative colitis patients develop colorectal neoplasia. At present, identification of this subset is markedly limited and necessitates lifelong colonoscopic surveillance for the entire ulcerative colitis population. Better risk markers are needed to focus surveillance onto the patients who are most likely to benefit. Using array-based comparative genomic hybridization, we analyzed single, non-dysplastic biopsies from three patient groups: ulcerative colitis progressors (n=9) with cancer or high-grade dysplasia at a mean distance of 18 cm from the analyzed site; ulcerative colitis non-progressors (n=8) without dysplasia during long-term surveillance; and non-ulcerative colitis normal controls (n=2). Genomic DNA from fresh colonic epithelium purified from stroma was hybridized to 287 (low-density) and 4342 (higher-density) feature bacterial artificial chromosome arrays. Sample-to-reference fluorescence ratios were calculated for individual chromosomal targets and globally across the genome. The low-density arrays yielded pronounced genomic gains and losses in 3 of 9 (33%) ulcerative colitis progressors but in none of the 10 control patients. Identical DNA samples analyzed on the higher-density arrays, using a combination of global and individual high variance assessments, distinguished all nine progressors from all 10 controls. These data confirm that genomic alterations in ulcerative colitis progressors are widespread, even involving single non-dysplastic biopsies that are far distant from neoplasia. They therefore show promise toward eliminating full colonoscopic surveillance with extensive biopsy sampling in the majority of ulcerative colitis patients.
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Affiliation(s)
- Mary P. Bronner
- Division of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Marek Skacel
- Dahl-Chase Pathology Associates, Bangor, Maine, USA
| | - David A. Crispin
- Department of Medicine in the Division of Gastroenterology; University of Washington, Seattle, Washington, USA
| | - Peter D. Hoff
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Lisa A. Lai
- Department of Medicine in the Division of Gastroenterology; University of Washington, Seattle, Washington, USA
| | - Raymond R. Tubbs
- Division of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Teresa A. Brentnall
- Department of Medicine in the Division of Gastroenterology; University of Washington, Seattle, Washington, USA
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Enns LC, Bible KL, Emond MJ, Ladiges WC. Mice lacking the Cβ subunit of PKA are resistant to angiotensin II-induced cardiac hypertrophy and dysfunction. BMC Res Notes 2010; 3:307. [PMID: 21080942 PMCID: PMC2993729 DOI: 10.1186/1756-0500-3-307] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [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: 05/07/2010] [Accepted: 11/16/2010] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND PKA is a ubiquitous, multi-subunit cellular kinase that regulates a number of different physiological responses in response to cAMP, including metabolism, cell division, and cardiac function. Numerous studies have implicated altered PKA signaling in cardiac dysfunction. Recently, it has been shown that mice lacking the catalytic β subunit of PKA (PKA Cβ) are protected from age-related problems such as weight gain and enlarged livers, and we hypothesized that these mice might also be resistant to cardiomyopathy. FINDINGS Angiotensin II (ang II) induced hypertension in both PKA Cβ null mice and their WT littermates. However, PKA Cβ null mice were resistant to a number of ang II-induced, cardiopathological effects observed in the WT mice, including hypertrophy, decreased diastolic performance, and enlarged left atria. CONCLUSION The Cβ subunit of PKA plays an important role in angiotensin-induced cardiac dysfunction. The Cβ null mouse highlights the potential of the PKA Cβ subunit as a pharmaceutical target for hypertrophic cardiac disease.
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Affiliation(s)
- Linda C Enns
- Departments of Comparative Medicine, Physiology and Biophysics, and Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Kenneth L Bible
- Departments of Comparative Medicine, Physiology and Biophysics, and Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Mary J Emond
- Departments of Comparative Medicine, Physiology and Biophysics, and Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Warren C Ladiges
- Departments of Comparative Medicine, Physiology and Biophysics, and Biostatistics, University of Washington, Seattle, WA, 98195, USA
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Dai DF, Chen T, Wanagat J, Laflamme M, Marcinek DJ, Emond MJ, Ngo CP, Prolla TA, Rabinovitch PS. Age-dependent cardiomyopathy in mitochondrial mutator mice is attenuated by overexpression of catalase targeted to mitochondria. Aging Cell 2010; 9:536-44. [PMID: 20456298 DOI: 10.1111/j.1474-9726.2010.00581.x] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [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: 11/28/2022] Open
Abstract
Mitochondrial defects have been found in aging and several age-related diseases. Mice with a homozygous mutation in the exonuclease encoding domain of mitochondrial DNA polymerase gamma (Polg(m/m)) are prone to age-dependent accumulation of mitochondrial DNA mutations and have shown a broad spectrum of aging-like phenotypes. However, the mechanism of cardiac phenotypes in relation to the role of mitochondrial DNA mutations and oxidative stress in this mouse model has not been fully addressed. We demonstrate age-dependent cardiomyopathy in Polg(m/m) mice, which by 13-14 months of age displays marked cardiac hypertrophy and dilatation, impairment of systolic and diastolic function, and increased cardiac fibrosis. This age-dependent cardiomyopathy is associated with increases in mitochondrial DNA (mtDNA) deletions and protein oxidative damage, increased expression of apoptotic and senescence markers, as well as a decline in signaling for mitochondrial biogenesis. The relationship of these changes to mitochondrial reactive oxygen species (ROS) was tested by crossing Polg(m/m) mice with mice that overexpress mitochondrial targeted catalase (mCAT). All of the above phenotypes were partially rescued in Polg(m/m)/mCAT mice. These data indicate that accumulation of mitochondrial DNA damage with age can lead to cardiomyopathy and that this phenotype is partly mediated by mitochondrial oxidative stress.
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Affiliation(s)
- Dao-Fu Dai
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
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Mao FJ, Sidorova JM, Lauper JM, Emond MJ, Monnat RJ. The human WRN and BLM RecQ helicases differentially regulate cell proliferation and survival after chemotherapeutic DNA damage. Cancer Res 2010; 70:6548-55. [PMID: 20663905 DOI: 10.1158/0008-5472.can-10-0475] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [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
Loss-of-function mutations in the human RecQ helicase genes WRN and BLM respectively cause the genetic instability/cancer predisposition syndromes Werner syndrome and Bloom syndrome. To identify common and unique functions of WRN and BLM, we systematically analyzed cell proliferation, cell survival, and genomic damage in isogenic cell lines depleted of WRN, BLM, or both proteins. Cell proliferation and survival were assessed before and after treatment with camptothecin, cis-diamminedichloroplatinum(II), hydroxyurea, or 5-fluorouracil. Genomic damage was assessed, before and after replication arrest, by gamma-H2AX staining, which was quantified at the single-cell level by flow cytometry. Cell proliferation was affected strongly by the extent of WRN and/or BLM depletion, and more strongly by BLM than by WRN depletion (P = 0.005). The proliferation of WRN/BLM-codepleted cells, in contrast, did not differ from BLM-depleted cells (P = 0.34). BLM-depleted and WRN/BLM-codepleted cells had comparably impaired survival after DNA damage, whereas WRN-depleted cells displayed a distinct pattern of sensitivity to DNA damage. BLM-depleted and WRN/BLM-codepleted cells had similar, significantly higher gamma-H2AX induction levels than did WRN-depleted cells. Our results provide new information on the role of WRN and BLM in determining cell proliferation, cell survival, and genomic damage after chemotherapeutic DNA damage or replication arrest. We also provide new information on functional redundancy between WRN and BLM. These results provide a strong rationale for further developing WRN and BLM as biomarkers of tumor chemotherapeutic responsiveness.
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Affiliation(s)
- Frances J Mao
- Department of Pathology, University of Washington, Seattle, Washington 98195-7705, USA
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Abstract
BACKGROUND In order to establish a valid surrogate outcome measure, it must be shown that the outcome measure (chest HRCT scores in cystic fibrosis [CF] patients) demonstrates strong statistical association with established endpoints of disease, such as Pseudomonas aeruginosa (Pa) airway acquisition, acute exacerbations, or mortality. METHODS We estimated and tested the association between Pa infection status (Pa+ vs. Pa-) and baseline chest HRCT scores in 25 children with mild-to-moderate CF lung disease. For comparison, we estimated the association between Pa status and pulmonary function tests (PFTs), chest X-rays (CXR) scores, and BMI. Pa acquisition was determined from respiratory culture results and systematic review of clinic notes. RESULTS All subjects had respiratory cultures performed prior to or at baseline with a median of 19 months of retrospective culture observation (SD = 15.7 months, range: 0-52.5 months). The difference between age-adjusted mean total HRCT score for Pa+ versus Pa- was highly significant (P < 0.00001) with a near-perfect separation between scores in Pa+ versus Pa- patients. Similar results were found for several HRCT sub-scores. Among PFTs, only residual volume-to-total lung capacity (RV/TLC) had a significant difference between group means (P = 0.03), but the overlap between groups in RV/TLC measurements was large. CONCLUSIONS CF HRCT scores correlate highly with Pa acquisition, a clinically meaningful measure of progressing CF lung disease. HRCT scores are highly sensitive at predicting Pa acquisition status, while most PFT measures, chest radiograph (CXR) scores, and body mass index are not. These results provide further evidence that HRCT is appropriate for use in patient care and as an outcome measure in clinical trials.
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Affiliation(s)
- Terry E Robinson
- Center of Excellence for Pediatric Cystic Fibrosis and Pulmonary Diseases, Stanford University Medical Center, Palo Alto, California 94305-5715, USA.
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Robinson TE, Long FR, Raman P, Saha P, Emond MJ, Reinhardt JM, Raman R, Brody AS. An airway phantom to standardize CT acquisition in multicenter clinical trials. Acad Radiol 2009; 16:1134-41. [PMID: 19467609 DOI: 10.1016/j.acra.2009.02.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 02/26/2009] [Accepted: 02/27/2009] [Indexed: 11/19/2022]
Abstract
RATIONALE AND OBJECTIVES The purpose of this study was to demonstrate the use of a phantom to standardize low-dose chest computed tomographic (CT) protocols in children with cystic fibrosis. MATERIALS AND METHODS Spiral chest CT scans of a Plexiglas phantom simulating airway sizes (internal diameter, 1.1-16.4 mm; wall thickness, 0.4-4.6 mm) in children with cystic fibrosis were obtained using two multidetector CT (MDCT) scanners (GE VCT and Siemens Sensation 64). Quantitative airway measurements from both scanners were compared with micro-CT airway measurements over a range of doses (0.2-1.8 mSv) to evaluate bias and variance of measurements. The effective doses for CT protocols were estimated using the ImPACT CT Patient Dosimetry Calculator. RESULTS Both MDCT scanners were able to accurately measure airway sizes down to 3 mm internal diameter and 1.3 mm airway wall thickness, with errors of <3.5%. ImPACT estimates of effective dose were different for the MDCT scanners for a given peak tube voltage and product of tube current and exposure time. Accuracy and precision were not found to be associated with dose parameters for either machine. Bias in all measurements was strongly associated with airway diameter (P values < .00001), but the magnitude of bias was small (mean, 0.07 mm; maximum, 0.21 mm). Differences between machines in error components were on the order of a few micrometers. CONCLUSIONS The use of a standard airway phantom confirms that different MDCT scanners have similar results within dose ranges planned for potential future clinical trials. Standardized protocols can be developed that adjust for differences in radiation exposure for different MDCT scanners.
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Affiliation(s)
- Terry E Robinson
- Center of Excellence for Pulmonary Biology, Division of Pediatric Pulmonary, Stanford University Medical Center, 770 Welch Road, Suite 350, Palo Alto, CA 94305-5715, USA.
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Enns LC, Morton JF, Treuting PR, Emond MJ, Wolf NS, McKnight GS, Rabinovitch PS, Ladiges WC. Disruption of protein kinase A in mice enhances healthy aging. PLoS One 2009; 4:e5963. [PMID: 19536287 PMCID: PMC2693670 DOI: 10.1371/journal.pone.0005963] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [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: 09/16/2008] [Accepted: 05/21/2009] [Indexed: 11/19/2022] Open
Abstract
Mutations that cause a reduction in protein kinase A (PKA) activity have been shown to extend lifespan in yeast. Loss of function of mammalian RIIbeta, a regulatory subunit of PKA expressed in brain and adipose tissue, results in mice that are lean and insulin sensitive. It was therefore hypothesized that RIIB null (RIIbeta(-/-)) mice would express anti-aging phenotypes. We conducted lifespan studies using 40 mutant and 40 wild type (WT) littermates of equal gender numbers and found that both the median and maximum lifespans were significantly increased in mutant males compared to WT littermates. The median lifespan was increased from 884 days to 1005 days (p = 0.006 as determined by the log rank test) and the 80% lifespan (defined here as 80% deaths) was increased from 941 days to 1073 days (p = 0.004 as determined by the Wang-Allison test). There was no difference in either median or 80% lifespan in female genotypes. WT mice of both genders became increasingly obese with age, while mutant mice maintained their lean phenotype into old age. Adiposity was found to correlate with lifespan for males only. 50% of male mice between 30 and 35 g, corresponding to about 5% body fat, for either genotype lived over 1000 days. No male mouse outside of this weight range achieved this lifespan. During their last month of life, WT mice began losing weight (a total of 8% and 15% of body weight was lost for males and females, respectively), but RIIbeta(-/-) male mice maintained their lean body mass to end of life. This attenuation of decline was not seen in female mutant mice. Old male mutant mice were insulin sensitive throughout their life. Both genders showed modestly lower blood glucose levels in old mutants compared to WT. Male mutants were also resistant to age-induced fatty liver. Pathological assessment of tissues from end of life male mutant mice showed a decrease in tumor incidence, decreased severity of renal lesions, and a trend towards a decrease in age-related cardiac pathology. These findings help establish the highly conserved nature of PKA and suggest that disruption of PKA affects physiological mechanisms known to be associated with healthy aging.
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Affiliation(s)
- Linda C. Enns
- Departments of Comparative Medicine, Biostatistics, Pharmacology, and Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - John F. Morton
- Departments of Comparative Medicine, Biostatistics, Pharmacology, and Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Piper R. Treuting
- Departments of Comparative Medicine, Biostatistics, Pharmacology, and Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Mary J. Emond
- Departments of Comparative Medicine, Biostatistics, Pharmacology, and Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Norman S. Wolf
- Departments of Comparative Medicine, Biostatistics, Pharmacology, and Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - G. S. McKnight
- Departments of Comparative Medicine, Biostatistics, Pharmacology, and Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Peter S. Rabinovitch
- Departments of Comparative Medicine, Biostatistics, Pharmacology, and Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Warren C. Ladiges
- Departments of Comparative Medicine, Biostatistics, Pharmacology, and Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Dai DF, Santana LF, Vermulst M, Tomazela DM, Emond MJ, MacCoss MJ, Gollahon K, Martin GM, Loeb LA, Ladiges WC, Rabinovitch PS. Overexpression of catalase targeted to mitochondria attenuates murine cardiac aging. Circulation 2009; 119:2789-97. [PMID: 19451351 DOI: 10.1161/circulationaha.108.822403] [Citation(s) in RCA: 359] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Age is a major risk for cardiovascular diseases. Although mitochondrial reactive oxygen species have been proposed as one of the causes of aging, their role in cardiac aging remains unclear. We have previously shown that overexpression of catalase targeted to mitochondria (mCAT) prolongs murine median lifespan by 17% to 21%. METHODS AND RESULTS We used echocardiography to study cardiac function in aging cohorts of wild-type and mCAT mice. Changes found in wild-type mice recapitulate human aging: age-dependent increases in left ventricular mass index and left atrial dimension, worsening of the myocardial performance index, and a decline in diastolic function. Cardiac aging in mice is accompanied by accumulation of mitochondrial protein oxidation, increased mitochondrial DNA mutations and deletions and mitochondrial biogenesis, increased ventricular fibrosis, enlarged myocardial fiber size, decreased cardiac SERCA2 protein, and activation of the calcineurin-nuclear factor of activated T-cell pathway. All of these age-related changes were significantly attenuated in mCAT mice. Analysis of survival of 130 mice demonstrated that echocardiographic cardiac aging risk scores were significant predictors of mortality. The estimated attributable risk to mortality for these 2 parameters was 55%. CONCLUSIONS This study shows that cardiac aging in the mouse closely recapitulates human aging and demonstrates the critical role of mitochondrial reactive oxygen species in cardiac aging and the impact of cardiac aging on survival. These findings also support the potential application of mitochondrial antioxidants in reactive oxygen species-related cardiovascular diseases.
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Affiliation(s)
- Dao-Fu Dai
- Department of Pathology, University of Washington, Seattle, 98195, USA
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Bronner MP, O'Sullivan JN, Rabinovitch PS, Crispin DA, Chen L, Emond MJ, Rubin CE, Brentnall TA. Genomic biomarkers to improve ulcerative colitis neoplasia surveillance. Am J Pathol 2008; 173:1853-60. [PMID: 18988798 DOI: 10.2353/ajpath.2008.080250] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
No adequate means exist to identify the minority of ulcerative colitis (UC) patients destined to undergo neoplastic progression. Recognition of this subset would advance UC cancer surveillance by focusing the available management options onto the highest risk patients. Three different assays of genomic alterations in nondysplastic UC biopsies show promise for distinguishing patients with neoplasia (UC progressors) from those without (UC nonprogressors), including assays of telomere length, anaphase bridges, and chromosomal fluorescence in situ hybridization. Expanding the number of patients and testing of assays simultaneously in the same biopsy further validated their utility. A panel approach also improved testing outcome. A total of 14 UC progressors was readily separable from 15 UC nonprogressors and 6 normal controls. Chromosomal entropy (ie, the extent of alteration diversity) proved to be the most useful test. By receiver-operating characteristic analysis, mean chromosomal entropy in 28 patients over all four chromosomes yielded 100% sensitivity and 92% specificity for distinguishing progressors from nonprogressors with optimum choice of threshold. Moreover, separation was achieved using only nondysplastic and predominantly rectal (82.8%) biopsies that were remote from neoplasia, suggesting that full colonoscopy with extensive biopsies might be avoided for the majority of UC patients, the nonprogressors. These data further strengthen the concept that genomic biomarkers can distinguish UC progressors from nonprogressors and improve cancer surveillance in UC.
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Affiliation(s)
- Mary P Bronner
- The Cleveland Clinic, Department of Anatomic Pathology, Cleveland, OH 44195, USA.
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Treuting PM, Linford NJ, Knoblaugh SE, Emond MJ, Morton JF, Martin GM, Rabinovitch PS, Ladiges WC. Reduction of age-associated pathology in old mice by overexpression of catalase in mitochondria. J Gerontol A Biol Sci Med Sci 2008; 63:813-22. [PMID: 18772469 DOI: 10.1093/gerona/63.8.813] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe the effects of mitochondrially targeted catalase (MCAT) expression on end-of-life pathology in mice using detailed semiquantitative histopathological evaluation. We previously reported that the median and maximum life spans of MCAT mice were extended relative to those of wild-type littermates. We now report that MCAT expression is associated with reduced malignant nonhematopoietic tumor burden, reduced cardiac lesions, and a trend toward reduced systemic inflammation, with no effect on hematopoietic neoplasia or glomerulonephropathy. Combined disease burden and comorbidity are also reduced, and MCAT expression is not associated with any detrimental clinical effects. The results suggest that oxidative damage is involved in aging of C57BL/6J mice via modulation of a subset of age-associated lesions. Antioxidant interventions targeting mitochondria may therefore be a viable strategy for prevention or postponement of some age-associated diseases. The variability of the MCAT effect across tissues, however, illustrates the importance of developing semiquantitative histopathology for assessment of comorbidity in life-span studies.
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Affiliation(s)
- Piper M Treuting
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195-7190, USA.
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Davis SD, Brody AS, Emond MJ, Brumback LC, Rosenfeld M. Endpoints for clinical trials in young children with cystic fibrosis. Proc Am Thorac Soc 2007; 4:418-30. [PMID: 17652509 PMCID: PMC2647606 DOI: 10.1513/pats.200703-041br] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 05/03/2007] [Indexed: 11/20/2022]
Abstract
The availability of sensitive, reproducible, and feasible outcome measures for quantifying lung disease in children with cystic fibrosis (CF) younger than 6 years is critical to the conduct of clinical trials in this important population. Historically, identifying and quantifying the presence of lung disease in very young children with CF was hampered by a lack of reproducible measures of lung function or lung pathology. Over the past 10 years, significant progress has led to physiologic, anatomic, and bronchoscopic measures that may serve as endpoints for future intervention trials. These endpoints include infant and preschool lung function testing, computed tomography of the chest, and bronchoalveolar lavage markers of inflammation and infection. Much progress has occurred in standardizing lung function testing, which is essential for multicenter collaboration. Pulmonary exacerbation has the potential to serve as a clinical endpoint; however, there is currently no standardized definition in children with CF younger than 6 years. Further development of these outcomes measures will enable clinical trials in the youngest CF population with the objective of improving long-term prognosis.
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Affiliation(s)
- Stephanie D Davis
- Division of Pulmonology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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Nguyen D, Emond MJ, Mayer-Hamblett N, Saiman L, Marshall BC, Burns JL. Clinical response to azithromycin in cystic fibrosis correlates with in vitro effects on Pseudomonas aeruginosa phenotypes. Pediatr Pulmonol 2007; 42:533-41. [PMID: 17469154 DOI: 10.1002/ppul.20620] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A 6-month clinical trial of azithromycin (AZM) in American cystic fibrosis (CF) patients with chronic Pseudomonas aeruginosa infection showed clinical improvement without significant reduction in bacterial density. Sub-inhibitory AZM has been hypothesized to affect P. aeruginosa virulence, partly contributing to the mechanism of action of AZM. To correlate bacterial phenotypes of P. aeruginosa isolates with clinical response to AZM in CF patients. Pre-treatment P. aeruginosa isolates from subjects randomized to AZM in the US trial were characterized for bacterial phenotypes: AZM minimal inhibitory concentration (MIC), mucoidy, and baseline and AZM effects on twitching and swimming motility, and production of pyocyanin, protease and phospholipase C (PLC). Initial analyses of a subset of subjects identified phenotypes most strongly associated with FEV(1) response and pulmonary exacerbation. These phenotypes were subsequently characterized and tested in isolates from subjects of the complete AZM cohort. Exploratory analyses of the initial subset suggested that the MIC and in vitro change in PLC and swimming motility with AZM were the strongest candidates among the bacterial phenotypes. When tested, only the change in PLC was significantly correlated with the change in FEV(1) (P=0.05), and occurrence and time to pulmonary exacerbation (both P=0.02). In the complete cohort, change in PLC continued to show significant correlation with FEV(1) response (P=0.006), but not exacerbation. The in vitro effect of AZM on PLC correlates with FEV(1) response to AZM. This suggests that AZM anti-virulence effects may be predictive of clinical response and play a role in the mechanism of action of AZM in CF patients.
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Affiliation(s)
- Dao Nguyen
- Children's Hospital and Regional Medical Center, Seattle, Washington, USA
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50
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Steele RJ, Raftery AE, Emond MJ. Computing Normalizing Constants for Finite Mixture Models via Incremental Mixture Importance Sampling (IMIS). J Comput Graph Stat 2006. [DOI: 10.1198/106186006x132358] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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