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Donato CM, Handley A, Byars SG, Bogdanovic-Sakran N, Lyons EA, Watts E, Ong DS, Pavlic D, At Thobari J, Satria CD, Nirwati H, Soenarto Y, Bines JE. Vaccine Take of RV3-BB Rotavirus Vaccine Observed in Indonesian Infants Regardless of HBGA Status. J Infect Dis 2024; 229:1010-1018. [PMID: 37592804 PMCID: PMC11011179 DOI: 10.1093/infdis/jiad351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Histo-blood group antigen (HBGA) status may affect vaccine efficacy due to rotavirus strains binding to HBGAs in a P genotype-dependent manner. This study aimed to determine if HBGA status affected vaccine take of the G3P[6] neonatal vaccine RV3-BB. METHODS DNA was extracted from stool samples collected in a subset (n = 164) of the RV3-BB phase IIb trial in Indonesian infants. FUT2 and FUT3 genes were amplified and sequenced, with any single-nucleotide polymorphisms analyzed to infer Lewis and secretor status. Measures of positive cumulative vaccine take were defined as serum immune response (immunoglobulin A or serum-neutralizing antibody) and/or stool excretion of RV3-BB virus. Participants were stratified by HBGA status and measures of vaccine take. RESULTS In 147 of 164 participants, Lewis and secretor phenotype were determined. Positive vaccine take was recorded for 144 (97.9%) of 147 participants with the combined phenotype determined. Cumulative vaccine take was not significantly associated with secretor status (relative risk, 1.00 [95% CI, .94-1.06]; P = .97) or Lewis phenotype (relative risk, 1.03 [95% CI, .94-1.14]; P = .33), nor was a difference observed when analyzed by each component of vaccine take. CONCLUSIONS The RV3-BB vaccine produced positive cumulative vaccine take, irrespective of HBGA status in Indonesian infants.
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Affiliation(s)
- Celeste M Donato
- Enteric Diseases Group, Murdoch Children's Research Institute
- Department of Paediatrics, The University of Melbourne, Parkville
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne
| | - Amanda Handley
- Enteric Diseases Group, Murdoch Children's Research Institute
- Medicines Development for Global Health, Southbank
| | - Sean G Byars
- Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | | | - Eleanor A Lyons
- Enteric Diseases Group, Murdoch Children's Research Institute
| | - Emma Watts
- Enteric Diseases Group, Murdoch Children's Research Institute
| | - Darren S Ong
- Enteric Diseases Group, Murdoch Children's Research Institute
| | - Daniel Pavlic
- Enteric Diseases Group, Murdoch Children's Research Institute
| | | | | | - Hera Nirwati
- Center for Child Health
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada
| | - Yati Soenarto
- Center for Child Health
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr Sardjito Hospital, Yogyakarta, Indonesia
| | - Julie E Bines
- Enteric Diseases Group, Murdoch Children's Research Institute
- Department of Paediatrics, The University of Melbourne, Parkville
- Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville, Australia
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2
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Byars SG, Prestes P, Suphapimol V, Takeuchi F, De Vries N, Maier MC, Melo M, Balding D, Samani N, Allen AM, Kato N, Wilkinson-Berka JL, Charchar F, Harrap SB. Four-week inhibition of the renin-angiotensin system in spontaneously hypertensive rats results in persistently lower blood pressure with reduced kidney renin and changes in expression of relevant gene networks. Cardiovasc Res 2024:cvae053. [PMID: 38501595 DOI: 10.1093/cvr/cvae053] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/06/2023] [Accepted: 12/18/2023] [Indexed: 03/20/2024] Open
Abstract
AIMS Prevention of human hypertension is an important challenge and has been achieved in experimental models. Brief treatment with renin-angiotensin system (RAS) inhibitors permanently reduces the genetic hypertension of the spontaneously hypertensive rat (SHR). The kidney is involved in this fascinating phenomenon, but relevant changes in gene expression are unknown. METHODS In SHR, we studied the effect of treatment between 10 and 14 weeks of age with the angiotensin receptor blocker, losartan, or the angiotensin-converting enzyme (ACE) inhibitor, perindopril (with controls for non-specific effects of lowering BP) on differential RNA expression, DNA methylation and renin immunolabelling in the kidney at 20 weeks of age. RESULTS RNA sequencing revealed a 6-fold increase in renin gene (Ren) expression during losartan treatment (P < 0.0001). Six weeks after losartan, arterial pressure remained lower (P = 0.006), yet kidney Ren showed reduced expression by 23% after losartan (P = 0.03) and by 43% after perindopril (P = 1.4 x 10-6) associated with increased DNA methylation (P = 0.04). Immunolabelling confirmed reduced cortical renin after earlier RAS blockade (P = 0.002). RNA sequencing identified differential expression of mRNAs, miRNAs and lncRNAs with evidence of networking and co-regulation. These included 13 candidate genes (Grhl1, Ammecr1l, Hs6st1, Nfil3, Fam221a, Lmo4, Adamts1, Cish, Hif3a, Bcl6, Rad54l2, Adap1, Dok4), the miRNA miR-145-3p and the lncRNA AC115371. Gene ontogeny analyses revealed that these networks were enriched with genes relevant to BP, RAS and the kidneys. CONCLUSIONS Early RAS inhibition in SHR resets genetic pathways and networks resulting in a legacy of reduced Ren expression and BP persisting for a minimum of 6 weeks.
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Affiliation(s)
- Sean G Byars
- The Florey Institute of Neuroscience & Mental Health, Parkville, Victoria, Australia
| | - Priscilla Prestes
- Health Innovation and Transformation Centre, Federation University, Ballarat, Victoria, Australia
| | - Vara Suphapimol
- Department of Anatomy & Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nathan De Vries
- Health Innovation and Transformation Centre, Federation University, Ballarat, Victoria, Australia
| | - Michelle C Maier
- Health Innovation and Transformation Centre, Federation University, Ballarat, Victoria, Australia
| | - Mariana Melo
- Department of Anatomy & Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia
| | - David Balding
- Melbourne Integrative Genomic and School of Mathematics & Statistics, University of Melbourne, Victoria, Australia
| | - Nilesh Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Andrew M Allen
- The Florey Institute of Neuroscience & Mental Health, Parkville, Victoria, Australia
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jennifer L Wilkinson-Berka
- Department of Anatomy & Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia
| | - Fadi Charchar
- Health Innovation and Transformation Centre, Federation University, Ballarat, Victoria, Australia
| | - Stephen B Harrap
- Department of Anatomy & Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia
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3
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Pereira-Fantini PM, Pang B, Byars SG, Oakley RB, Perkins EJ, Dargaville PA, Davis PG, Nie S, Williamson NA, Ignjatovic V, Tingay DG. Preterm Lung Exhibits Distinct Spatiotemporal Proteome Expression at Initiation of Lung Injury. Am J Respir Cell Mol Biol 2020; 61:631-642. [PMID: 30995072 DOI: 10.1165/rcmb.2019-0084oc] [Citation(s) in RCA: 13] [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] [Indexed: 12/27/2022] Open
Abstract
The development of regional lung injury in the preterm lung is not well understood. This study aimed to characterize time-dependent and regionally specific injury patterns associated with early ventilation of the preterm lung using a mass spectrometry-based proteomic approach. Preterm lambs delivered at 124-127 days gestation received 15 or 90 minutes of mechanical ventilation (positive end-expiratory pressure = 8 cm H2O, Vt = 6-8 ml/kg) and were compared with unventilated control lambs. At study completion, lung tissue was taken from standardized nondependent and dependent regions, and assessed for lung injury via histology, quantitative PCR, and proteomic analysis using Orbitrap-mass spectrometry. Ingenuity pathway analysis software was used to identify temporal and region-specific enrichments in pathways and functions. Apoptotic cell numbers were ninefold higher in nondependent lung at 15 and 90 minutes compared with controls, whereas proliferative cells were increased fourfold in the dependent lung at 90 minutes. The relative gene expression of lung injury markers was increased at 90 minutes in nondependent lung and unchanged in gravity-dependent lung. Within the proteome, the number of differentially expressed proteins was fourfold higher in the nondependent lung than the dependent lung. The number of differential proteins increased over time in both lung regions. A total of 95% of enriched canonical pathways and 94% of enriched cellular and molecular functions were identified only in nondependent lung tissue from the 90-minute ventilation group. In conclusion, complex injury pathways are initiated within the preterm lung after 15 minutes of ventilation and amplified by continuing ventilation. Injury development is region specific, with greater alterations within the proteome of nondependent lung.
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Affiliation(s)
| | | | - Sean G Byars
- Department of Clinical Pathology.,Melbourne Integrative Genomics
| | | | | | - Peter A Dargaville
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Peter G Davis
- Neonatal Research, and.,Department of Obstetrics and Gynaecology, and.,The Royal Women's Hospital, Parkville, Victoria, Australia; and
| | - Shuai Nie
- Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | | | - Vera Ignjatovic
- Haematology Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics
| | - David G Tingay
- Neonatal Research, and.,Department of Paediatrics.,Department of Neonatology, Royal Children's Hospital, Parkville, Victoria, Australia
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4
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Boniface K, Byars SG, Cowley D, Kirkwood CD, Bines JE. Human Neonatal Rotavirus Vaccine (RV3-BB) Produces Vaccine Take Irrespective of Histo-Blood Group Antigen Status. J Infect Dis 2020; 221:1070-1078. [PMID: 31763671 PMCID: PMC7075413 DOI: 10.1093/infdis/jiz333] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/03/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND VP4 [P] genotype binding specificities of rotaviruses and differential expression of histo-blood group antigens (HBGAs) between populations may contribute to reduced efficacy against severe rotavirus disease. P[6]-based rotavirus vaccines could broaden protection in such settings, particularly in Africa, where the Lewis-negative phenotype and P[6] rotavirus strains are common. METHODS The association between HBGA status and G3P[6] rotavirus vaccine (RV3-BB) take was investigated in a phase 2A study of RV3-BB vaccine involving 46 individuals in Dunedin, New Zealand, during 2012-2014. FUT2 and FUT3 genotypes were determined from DNA extracted from stool specimens, and frequencies of positive cumulative vaccine take, defined as an RV3-BB serum immune response (either immunoglobulin A or serum neutralizing antibody) and/or stool excretion of the vaccine strain, stratified by HBGA status were determined. RESULTS RV3-BB produced positive cumulative vaccine take in 29 of 32 individuals (91%) who expressed a functional FUT2 enzyme (the secretor group), 13 of 13 (100%) who were FUT2 null (the nonsecretor group), and 1 of 1 with reduced FUT2 activity (i.e., a weak secretor); in 37 of 40 individuals (93%) who expressed a functional FUT3 enzyme (the Lewis-positive group) and 3 of 3 who were FUT3 null (the Lewis-negative group); and in 25 of 28 Lewis-positive secretors (89%), 12 of 12 Lewis-positive nonsecretors (100%), 2 of 2 Lewis-negative secretors, and 1 of 1 Lewis-negative weak secretor. CONCLUSIONS RV3-BB produced positive cumulative vaccine take irrespective of HBGA status. RV3-BB has the potential to provide an improved level of protection in settings where P[6] rotavirus disease is endemic, irrespective of the HBGA profile of the population.
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Affiliation(s)
- Karen Boniface
- Enteric Diseases Group, Murdoch Children’s Research Institute, Seattle, Washington
| | - Sean G Byars
- Melbourne School of Population and Global Health, Seattle, Washington
| | - Daniel Cowley
- Enteric Diseases Group, Murdoch Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Melbourne, Seattle, Washington
| | - Carl D Kirkwood
- Enteric Diseases Group, Murdoch Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Melbourne, Seattle, Washington
- Bill and Melinda Gates Foundation, Seattle, Washington
| | - Julie E Bines
- Enteric Diseases Group, Murdoch Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Melbourne, Seattle, Washington
- Department of Gastroenterology and Clinical Nutrition, Royal Children’s Hospital, Parkville, Australia
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5
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Byars SG, Stearns SC, Boomsma JJ. Association of Long-Term Risk of Respiratory, Allergic, and Infectious Diseases With Removal of Adenoids and Tonsils in Childhood. JAMA Otolaryngol Head Neck Surg 2019; 144:594-603. [PMID: 29879264 DOI: 10.1001/jamaoto.2018.0614] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Importance Surgical removal of adenoids and tonsils to treat obstructed breathing or recurrent middle-ear infections remain common pediatric procedures; however, little is known about their long-term health consequences despite the fact that these lymphatic organs play important roles in the development and function of the immune system. Objective To estimate long-term disease risks associated with adenoidectomy, tonsillectomy, and adenotonsillectomy in childhood. Design, Setting, and Participants A population-based cohort study of up to 1 189 061 children born in Denmark between 1979 and 1999 and evaluated in linked national registers up to 2009, covering at least the first 10 and up to 30 years of their life, was carried out. Participants in the case and control groups were selected such that their health did not differ significantly prior to surgery. Exposures Participants were classified as exposed if adenoids or tonsils were removed within the first 9 years of life. Main Outcomes and Measures The incidence of disease (defined by International Classification of Diseases, Eighth Revision [ICD-8] and Tenth Revision [ICD-10] diagnoses) up to age 30 years was examined using stratified Cox proportional hazard regressions that adjusted for 18 covariates, including parental disease history, pregnancy complications, birth weight, Apgar score, sex, socioeconomic markers, and region of Denmark born. Results A total of up to 1 189 061 children were included in this study (48% female); 17 460 underwent adenoidectomy, 11 830 tonsillectomy, and 31 377 adenotonsillectomy; 1 157 684 were in the control group. Adenoidectomy and tonsillectomy were associated with a 2- to 3-fold increase in diseases of the upper respiratory tract (relative risk [RR], 1.99; 95% CI, 1.51-2.63 and RR, 2.72; 95% CI, 1.54-4.80; respectively). Smaller increases in risks for infectious and allergic diseases were also found: adenotonsillectomy was associated with a 17% increased risk of infectious diseases (RR, 1.17; 95% CI, 1.10-1.25) corresponding to an absolute risk increase of 2.14% because these diseases are relatively common (12%) in the population. In contrast, the long-term risks for conditions that these surgeries aim to treat often did not differ significantly and were sometimes lower or higher. Conclusions and Relevance In this study of almost 1.2 million children, of whom 17 460 had adenoidectomy, 11 830 tonsillectomy, and 31 377 adenotonsillectomy, surgeries were associated with increased long-term risks of respiratory, infectious, and allergic diseases. Although rigorous controls for confounding were used where such data were available, it is possible these effects could not be fully accounted for. Our results suggest it is important to consider long-term risks when making decisions to perform tonsillectomy or adenoidectomy.
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Affiliation(s)
- Sean G Byars
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia.,Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Stephen C Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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6
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Byars SG, Voskarides K. Genes that improved fitness also cost modern humans: evidence for genes with antagonistic effects on longevity and disease. Evol Med Public Health 2019; 2019:4-6. [PMID: 30799869 PMCID: PMC6379702 DOI: 10.1093/emph/eoz002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/14/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Sean G Byars
- Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
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7
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Byars SG, Stearns SC, Boomsma JJ. Limitations to the Association of Risk of Airway Disease With Removal of Adenoids and Tonsils in Children—Reply. JAMA Otolaryngol Head Neck Surg 2018; 144:1188-1189. [DOI: 10.1001/jamaoto.2018.2437] [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: 11/14/2022]
Affiliation(s)
- Sean G. Byars
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Stephen C. Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Jacobus J. Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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8
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Pereira-Fantini PM, Byars SG, McCall KE, Perkins EJ, Oakley RB, Dellacà RL, Dargaville PA, Davis PG, Ignjatovic V, Tingay DG. Plasma proteomics reveals gestational age-specific responses to mechanical ventilation and identifies the mechanistic pathways that initiate preterm lung injury. Sci Rep 2018; 8:12616. [PMID: 30135517 PMCID: PMC6105628 DOI: 10.1038/s41598-018-30868-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 02/14/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022] Open
Abstract
The preterm lung is particularly vulnerable to ventilator-induced lung injury (VILI) as a result of mechanical ventilation. However the developmental and pathological cellular mechanisms influencing the changing patterns of VILI have not been comprehensively delineated, preventing the advancement of targeted lung protective therapies. This study aimed to use SWATH-MS to comprehensively map the plasma proteome alterations associated with the initiation of VILI following 60 minutes of standardized mechanical ventilation from birth in three distinctly different developmental lung states; the extremely preterm, preterm and term lung using the ventilated lamb model. Across these gestations, 34 proteins were differentially altered in matched plasma samples taken at birth and 60 minutes. Multivariate analysis of the plasma proteomes confirmed a gestation-specific response to mechanical ventilation with 79% of differentially-expressed proteins altered in a single gestation group only. Six cellular and molecular functions and two physiological functions were uniquely enriched in either the extremely preterm or preterm group. Correlation analysis supported gestation-specific protein-function associations within each group. In identifying the gestation-specific proteome and functional responses to ventilation we provide the founding evidence required for the potential development of individualized respiratory support approaches tailored to both the developmental and pathological state of the lung.
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Affiliation(s)
- Prue M Pereira-Fantini
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, Australia.
| | - Sean G Byars
- Department of Pathology, University of Melbourne, Parkville, Australia.,Centre for Systems Genomics, University of Melbourne, Parkville, Australia
| | - Karen E McCall
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia.,University College Dublin, Dublin, Ireland
| | - Elizabeth J Perkins
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia
| | - Regina B Oakley
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia
| | - R L Dellacà
- Laboratorio di Tecnologie Biomediche, Dipartimento di Elettronica, Informazione e Ingegneria Biomedica-DEIB, Politecnico di Milano University, Milano, Italy
| | - Peter A Dargaville
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Peter G Davis
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia.,The Royal Women's Hospital, Parkville, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Australia
| | - Vera Ignjatovic
- Department of Paediatrics, University of Melbourne, Parkville, Australia.,Haematology Research, Murdoch Childrens Research Institute, Parkville, Australia
| | - David G Tingay
- Neonatal Research, Murdoch Childrens Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Department of Neonatology, Royal Children's Hospital, Parkville, Australia
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9
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Nath AP, Ritchie SC, Byars SG, Fearnley LG, Havulinna AS, Joensuu A, Kangas AJ, Soininen P, Wennerström A, Milani L, Metspalu A, Männistö S, Würtz P, Kettunen J, Raitoharju E, Kähönen M, Juonala M, Palotie A, Ala-Korpela M, Ripatti S, Lehtimäki T, Abraham G, Raitakari O, Salomaa V, Perola M, Inouye M. An interaction map of circulating metabolites, immune gene networks, and their genetic regulation. Genome Biol 2017; 18:146. [PMID: 28764798 PMCID: PMC5540552 DOI: 10.1186/s13059-017-1279-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 01/05/2017] [Accepted: 07/14/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic control is still lacking. Here, we integrate blood transcriptomic, metabolomic, and genomic profiles from two population-based cohorts (total N = 2168), including a subset of individuals with matched multi-omic data at 7-year follow-up. RESULTS We identify topologically replicable gene networks enriched for diverse immune functions including cytotoxicity, viral response, B cell, platelet, neutrophil, and mast cell/basophil activity. These immune gene modules show complex patterns of association with 158 circulating metabolites, including lipoprotein subclasses, lipids, fatty acids, amino acids, small molecules, and CRP. Genome-wide scans for module expression quantitative trait loci (mQTLs) reveal five modules with mQTLs that have both cis and trans effects. The strongest mQTL is in ARHGEF3 (rs1354034) and affects a module enriched for platelet function, independent of platelet counts. Modules of mast cell/basophil and neutrophil function show temporally stable metabolite associations over 7-year follow-up, providing evidence that these modules and their constituent gene products may play central roles in metabolic inflammation. Furthermore, the strongest mQTL in ARHGEF3 also displays clear temporal stability, supporting widespread trans effects at this locus. CONCLUSIONS This study provides a detailed map of natural variation at the blood immunometabolic interface and its genetic basis, and may facilitate subsequent studies to explain inter-individual variation in cardiometabolic disease.
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Affiliation(s)
- Artika P Nath
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, 3010, Victoria, Australia.,Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Scott C Ritchie
- Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Sean G Byars
- Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia.,School of BioSciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Liam G Fearnley
- Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia.,School of BioSciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Aki S Havulinna
- National Institute for Health and Welfare, Helsinki, 00271, Finland.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, 00014, Finland
| | - Anni Joensuu
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Antti J Kangas
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland
| | - Pasi Soininen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, 70211, Finland
| | | | - Lili Milani
- University of Tartu, Estonian Genome Center, Tartu, 51010, Estonia
| | - Andres Metspalu
- University of Tartu, Estonian Genome Center, Tartu, 51010, Estonia
| | - Satu Männistö
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Peter Würtz
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland.,Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
| | - Johannes Kettunen
- National Institute for Health and Welfare, Helsinki, 00271, Finland.,Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, 70211, Finland.,Biocenter Oulu, University of Oulu, Oulu, 90014, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, 33014, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, FI-33521, Tampere, Finland
| | - Markus Juonala
- Department of Medicine, University of Turku and Division of Medicine, Turku University Hospital, FI-20520, Turku, Finland.,Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, 00014, Finland.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, 70211, Finland.,Biocenter Oulu, University of Oulu, Oulu, 90014, Finland.,Computational Medicine, School of Social and Community Medicine, University of Bristol, Bristol, BS8 1TH, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, 00014, Finland.,Department of Public Health, University of Helsinki, Helsinki, 00014, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, 33014, Tampere, Finland
| | - Gad Abraham
- Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia.,School of BioSciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Olli Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20520, Finland.,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, 20520, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, 00271, Finland
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, 00271, Finland.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, 00014, Finland.,University of Tartu, Estonian Genome Center, Tartu, 51010, Estonia
| | - Michael Inouye
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, 3010, Victoria, Australia. .,Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia. .,Department of Pathology, The University of Melbourne, Parkville, 3010, Victoria, Australia. .,School of BioSciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
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10
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Marques FZ, Prestes PR, Byars SG, Ritchie SC, Würtz P, Patel SK, Booth SA, Rana I, Minoda Y, Berzins SP, Curl CL, Bell JR, Wai B, Srivastava PM, Kangas AJ, Soininen P, Ruohonen S, Kähönen M, Lehtimäki T, Raitoharju E, Havulinna A, Perola M, Raitakari O, Salomaa V, Ala-Korpela M, Kettunen J, McGlynn M, Kelly J, Wlodek ME, Lewandowski PA, Delbridge LM, Burrell LM, Inouye M, Harrap SB, Charchar FJ. Experimental and Human Evidence for Lipocalin-2 (Neutrophil Gelatinase-Associated Lipocalin [NGAL]) in the Development of Cardiac Hypertrophy and heart failure. J Am Heart Assoc 2017; 6:e005971. [PMID: 28615213 PMCID: PMC5669193 DOI: 10.1161/jaha.117.005971] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/02/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Cardiac hypertrophy increases the risk of developing heart failure and cardiovascular death. The neutrophil inflammatory protein, lipocalin-2 (LCN2/NGAL), is elevated in certain forms of cardiac hypertrophy and acute heart failure. However, a specific role for LCN2 in predisposition and etiology of hypertrophy and the relevant genetic determinants are unclear. Here, we defined the role of LCN2 in concentric cardiac hypertrophy in terms of pathophysiology, inflammatory expression networks, and genomic determinants. METHODS AND RESULTS We used 3 experimental models: a polygenic model of cardiac hypertrophy and heart failure, a model of intrauterine growth restriction and Lcn2-knockout mouse; cultured cardiomyocytes; and 2 human cohorts: 114 type 2 diabetes mellitus patients and 2064 healthy subjects of the YFS (Young Finns Study). In hypertrophic heart rats, cardiac and circulating Lcn2 was significantly overexpressed before, during, and after development of cardiac hypertrophy and heart failure. Lcn2 expression was increased in hypertrophic hearts in a model of intrauterine growth restriction, whereas Lcn2-knockout mice had smaller hearts. In cultured cardiomyocytes, Lcn2 activated molecular hypertrophic pathways and increased cell size, but reduced proliferation and cell numbers. Increased LCN2 was associated with cardiac hypertrophy and diastolic dysfunction in diabetes mellitus. In the YFS, LCN2 expression was associated with body mass index and cardiac mass and with levels of inflammatory markers. The single-nucleotide polymorphism, rs13297295, located near LCN2 defined a significant cis-eQTL for LCN2 expression. CONCLUSIONS Direct effects of LCN2 on cardiomyocyte size and number and the consistent associations in experimental and human analyses reveal a central role for LCN2 in the ontogeny of cardiac hypertrophy and heart failure.
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Affiliation(s)
- Francine Z Marques
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
- Heart Failure Research Group, Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia
| | - Priscilla R Prestes
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Sean G Byars
- Centre for Systems Genomics, The University of Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Victoria, Australia
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Scott C Ritchie
- Centre for Systems Genomics, The University of Melbourne, Victoria, Australia
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Peter Würtz
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
| | - Sheila K Patel
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
| | - Scott A Booth
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Indrajeetsinh Rana
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Yosuke Minoda
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Stuart P Berzins
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute, The University of Melbourne, Victoria, Australia
| | - Claire L Curl
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - James R Bell
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Bryan Wai
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
- Department of Cardiology, Austin Health, Heidelberg, Victoria, Australia
| | - Piyush M Srivastava
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
- Department of Cardiology, Austin Health, Heidelberg, Victoria, Australia
| | - Antti J Kangas
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
| | - Pasi Soininen
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Saku Ruohonen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Terho Lehtimäki
- Fimlab Laboratories, Department of Clinical Chemistry, Pirkanmaa Hospital District, School of Medicine, University of Tampere, Finland
| | - Emma Raitoharju
- Fimlab Laboratories, Department of Clinical Chemistry, Pirkanmaa Hospital District, School of Medicine, University of Tampere, Finland
| | - Aki Havulinna
- National Institute for Health and Welfare, Helsinki, Finland
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, United Kingdom
| | - Johannes Kettunen
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Maree McGlynn
- School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia
| | - Jason Kelly
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Mary E Wlodek
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
| | | | - Lea M Delbridge
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Louise M Burrell
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
- Department of Cardiology, Austin Health, Heidelberg, Victoria, Australia
| | - Michael Inouye
- Heart Failure Research Group, Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia
- Centre for Systems Genomics, The University of Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Victoria, Australia
- Department of Pathology, The University of Melbourne, Victoria, Australia
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Stephen B Harrap
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Fadi J Charchar
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
- Department of Physiology, The University of Melbourne, Victoria, Australia
- Department of Cardiovascular Sciences, University of Leicester, United Kingdom
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11
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Pereira-Fantini PM, Byars SG, Pitt J, Lapthorne S, Fouhy F, Cotter PD, Bines JE. Unravelling the metabolic impact of SBS-associated microbial dysbiosis: Insights from the piglet short bowel syndrome model. Sci Rep 2017; 7:43326. [PMID: 28230078 PMCID: PMC5322370 DOI: 10.1038/srep43326] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/11/2017] [Indexed: 12/16/2022] Open
Abstract
Liver disease is a major source of morbidity and mortality in children with short bowel syndrome (SBS). SBS-associated microbial dysbiosis has recently been implicated in the development of SBS-associated liver disease (SBS-ALD), however the pathological implications of this association have not been explored. In this study high-throughput sequencing of colonic content from the well-validated piglet SBS-ALD model was examined to determine alterations in microbial communities, and concurrent metabolic alterations identified in urine samples via targeted mass spectrometry approaches (GC-MS, LC-MS, FIA-MS) further uncovered impacts of microbial disturbance on metabolic outcomes in SBS-ALD. Multi-variate analyses were performed to elucidate contributing SBS-ALD microbe and metabolite panels and to identify microbe-metabolite interactions. A unique SBS-ALD microbe panel was clearest at the genus level, with discriminating bacteria predominantly from the Firmicutes and Bacteroidetes phyla. The SBS-ALD metabolome included important alterations in the microbial metabolism of amino acids and the mitochondrial metabolism of branched chain amino acids. Correlation analysis defined microbe-metabolite clustering patterns unique to SBS-ALD and identified a metabolite panel that correlates with dysbiosis of the gut microbiome in SBS.
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Affiliation(s)
- Prue M Pereira-Fantini
- Intestinal Failure and Clinical Nutrition Group, Murdoch Childrens Research Institute, Parkville, Australia
| | - Sean G Byars
- Centre for Systems Genomics, School of Biosciences, The University of Melbourne, Parkville, Australia.,Department of Pathology, The University of Melbourne, Parkville, Australia
| | - James Pitt
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Susan Lapthorne
- Intestinal Failure and Clinical Nutrition Group, Murdoch Childrens Research Institute, Parkville, Australia
| | - Fiona Fouhy
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland.,APC Microbiome Institute, Cork, Ireland
| | - Julie E Bines
- Intestinal Failure and Clinical Nutrition Group, Murdoch Childrens Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville, Australia
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12
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Abraham G, Havulinna AS, Bhalala OG, Byars SG, De Livera AM, Yetukuri L, Tikkanen E, Perola M, Schunkert H, Sijbrands EJ, Palotie A, Samani NJ, Salomaa V, Ripatti S, Inouye M. Genomic prediction of coronary heart disease. Eur Heart J 2016; 37:3267-3278. [PMID: 27655226 PMCID: PMC5146693 DOI: 10.1093/eurheartj/ehw450] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/06/2016] [Accepted: 08/26/2016] [Indexed: 11/14/2022] Open
Abstract
AIMS Genetics plays an important role in coronary heart disease (CHD) but the clinical utility of genomic risk scores (GRSs) relative to clinical risk scores, such as the Framingham Risk Score (FRS), is unclear. Our aim was to construct and externally validate a CHD GRS, in terms of lifetime CHD risk and relative to traditional clinical risk scores. METHODS AND RESULTS We generated a GRS of 49 310 SNPs based on a CARDIoGRAMplusC4D Consortium meta-analysis of CHD, then independently tested it using five prospective population cohorts (three FINRISK cohorts, combined n = 12 676, 757 incident CHD events; two Framingham Heart Study cohorts (FHS), combined n = 3406, 587 incident CHD events). The GRS was associated with incident CHD (FINRISK HR = 1.74, 95% confidence interval (CI) 1.61-1.86 per S.D. of GRS; Framingham HR = 1.28, 95% CI 1.18-1.38), and was largely unchanged by adjustment for known risk factors, including family history. Integration of the GRS with the FRS or ACC/AHA13 scores improved the 10 years risk prediction (meta-analysis C-index: +1.5-1.6%, P < 0.001), particularly for individuals ≥60 years old (meta-analysis C-index: +4.6-5.1%, P < 0.001). Importantly, the GRS captured substantially different trajectories of absolute risk, with men in the top 20% of attaining 10% cumulative CHD risk 12-18 y earlier than those in the bottom 20%. High genomic risk was partially compensated for by low systolic blood pressure, low cholesterol level, and non-smoking. CONCLUSIONS A GRS based on a large number of SNPs improves CHD risk prediction and encodes different trajectories of lifetime risk not captured by traditional clinical risk scores.
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Affiliation(s)
- Gad Abraham
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aki S Havulinna
- National Institute for Health and Welfare, Helsinki FI-00271, Finland
| | - Oneil G Bhalala
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sean G Byars
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alysha M De Livera
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria 3010, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Laxman Yetukuri
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
| | - Emmi Tikkanen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki FI-00271, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
| | - Heribert Schunkert
- Deutsches Herzzentrum München, and Technische Universität München, Munich 80636, Germany.,Deutsches Zentrum für Herz- und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Munich 81377, Germany
| | - Eric J Sijbrands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, CA 3000, The Netherlands
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Psychiatry, Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Groby Rd, Leicester, LE3 9QP, United Kingdom .,National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, United Kingdom
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki FI-00271, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland .,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.,Department of Public Health, University of Helsinki, Helsinki FI-00014, Finland
| | - Michael Inouye
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia .,Department of Pathology, The University of Melbourne, Parkville, Victoria 3010, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria 3010, Australia
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13
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Byars SG, Boomsma JJ. Opposite differential risks for autism and schizophrenia based on maternal age, paternal age, and parental age differences. Evol Med Public Health 2016; 2016:286-98. [PMID: 27637201 PMCID: PMC5026125 DOI: 10.1093/emph/eow023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 07/26/2016] [Indexed: 01/06/2023]
Abstract
Background and objectives: Effects of maternal and paternal age on offspring autism and schizophrenia risks have been studied for over three decades, but inconsistent risks have often been found, precluding well-informed speculation on why these age-related risks might exist. Methodology: To help clarify this situation we analysed a massive single population sample from Denmark including the full spectrum of autistic and schizophrenic disorders (eliminating between-study confounding), used up to 30 follow-up years, controlled for over 20 potentially confounding factors and interpret the ultimate causation of the observed risk patterns using generally accepted principles of parent-offspring conflict and life-history theory. Results: We evaluated the effects of paternal age, maternal age and parental age difference on offspring mental disorders and found consistently similar risk patterns for related disorders and markedly different patterns between autistic and schizophrenic disorders. Older fathers and mothers both conferred increased risk for autistic but not schizophrenic disorders, but autism risk was reduced in younger parents and offspring of younger mothers had increased risk for many schizophrenic disorders. Risk for most disorders also increased when parents were more dissimilarly aged. Monotonically increasing autism risk is consistent with mutation accumulation as fathers’ age, but this explanation is invalid for schizophrenic disorders, which were not related to paternal age and were negatively correlated with maternal age. Conclusions and implications: We propose that the observed maternally induced risk patterns ultimately reflect a shifting ancestral life-history trade-off between current and future reproduction, mediated by an initially high but subsequently decreasing tendency to constrain foetal provisioning as women proceed from first to final pregnancy.
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Affiliation(s)
- Sean G Byars
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark Department of Pathology, The University of Melbourne, Parkville, VIC 3010, Australia Present address: Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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14
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Byars SG, Stearns SC, Boomsma JJ. Opposite risk patterns for autism and schizophrenia are associated with normal variation in birth size: phenotypic support for hypothesized diametric gene-dosage effects. Proc Biol Sci 2015; 281:20140604. [PMID: 25232142 DOI: 10.1098/rspb.2014.0604] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Opposite phenotypic and behavioural traits associated with copy number variation and disruptions to imprinted genes with parent-of-origin effects have led to the hypothesis that autism and schizophrenia share molecular risk factors and pathogenic mechanisms, but a direct phenotypic comparison of how their risks covary has not been attempted. Here, we use health registry data collected on Denmark's roughly 5 million residents between 1978 and 2009 to detect opposing risks of autism and schizophrenia depending on normal variation (mean ± 1 s.d.) in adjusted birth size, which we use as a proxy for diametric gene-dosage variation in utero. Above-average-sized babies (weight, 3691-4090 g; length, 52.8-54.3 cm) had significantly higher risk for autism spectrum (AS) and significantly lower risk for schizophrenia spectrum (SS) disorders. By contrast, below-average-sized babies (2891-3290 g; 49.7-51.2 cm) had significantly lower risk for AS and significantly higher risk for SS disorders. This is the first study directly comparing autism and schizophrenia risks in the same population, and provides the first large-scale empirical support for the hypothesis that diametric gene-dosage effects contribute to these disorders. Only the kinship theory of genomic imprinting predicts the opposing risk patterns that we discovered, suggesting that molecular research on mental disease risk would benefit from considering evolutionary theory.
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Affiliation(s)
- Sean G Byars
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Stephen C Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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15
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Hollegaard B, Byars SG, Lykke J, Boomsma JJ. Parent-offspring conflict and the persistence of pregnancy-induced hypertension in modern humans. PLoS One 2013; 8:e56821. [PMID: 23451092 PMCID: PMC3581540 DOI: 10.1371/journal.pone.0056821] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 01/14/2013] [Indexed: 11/18/2022] Open
Abstract
Preeclampsia is a major cause of perinatal mortality and disease affecting 5–10% of all pregnancies worldwide, but its etiology remains poorly understood despite considerable research effort. Parent-offspring conflict theory suggests that such hypertensive disorders of pregnancy may have evolved through the ability of fetal genes to increase maternal blood pressure as this enhances general nutrient supply. However, such mechanisms for inducing hypertension in pregnancy would need to incur sufficient offspring health benefits to compensate for the obvious risks for maternal and fetal health towards the end of pregnancy in order to explain why these disorders have not been removed by natural selection in our hunter-gatherer ancestors. We analyzed >750,000 live births in the Danish National Patient Registry and all registered medical diagnoses for up to 30 years after birth. We show that offspring exposed to pregnancy-induced hypertension (PIH) in trimester 1 had significantly reduced overall later-life disease risks, but increased risks when PIH exposure started or developed as preeclampsia in later trimesters. Similar patterns were found for first-year mortality. These results suggest that early PIH leading to improved postpartum survival and health represents a balanced compromise between the reproductive interests of parents and offspring, whereas later onset of PIH may reflect an unbalanced parent-offspring conflict at the detriment of maternal and offspring health.
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Affiliation(s)
- Birgitte Hollegaard
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sean G. Byars
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Lykke
- Department of Obstetrics and Gynaecology, Roskilde Hospital, Roskilde, Denmark
| | - Jacobus J. Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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16
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Affiliation(s)
- Sean G Byars
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
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17
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Wang X, Byars SG, Stearns SC. Genetic links between post-reproductive lifespan and family size in Framingham. Evol Med Public Health 2013; 2013:241-53. [PMID: 24481203 PMCID: PMC3868361 DOI: 10.1093/emph/eot013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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] [Received: 12/07/2012] [Accepted: 06/17/2013] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Is there a trade-off between children ever born (CEB) and post-reproductive lifespan in humans? Here, we report a comprehensive analysis of reproductive trade-offs in the Framingham Heart Study (FHS) dataset using phenotypic and genotypic correlations and a genome-wide association study (GWAS) to look for single-nucleotide polymorphisms (SNPs) that are related to the association between CEB and lifespan. METHODOLOGY We calculated the phenotypic and genetic correlations of lifespan with CEB for men and women in the Framingham dataset, and then performed a GWAS to search for SNPs that might affect the relationship between post-reproductive lifespan and CEB. RESULTS We found significant negative phenotypic correlations between CEB and lifespan in both women (rP = -0.133, P < 0.001) and men (rP = -0. 079, P = 0.036). The genetic correlation was large, highly significant and strongly negative in women (rG = -0.877, P = 0.009) in a model without covariates, but not in men (P = 0.777). The GWAS identified five SNPs associated with the relationship between CEB and post-reproductive lifespan in women; some are near genes that have been linked to cancer. None were identified in men. CONCLUSIONS AND IMPLICATIONS We identified several SNPs for which the relationship between CEB and post-reproductive lifespan differs by genotype in women in the FHS who were born between 1889 and 1958. That result was not robust to changes in the sample. Further studies on larger samples are needed to validate the antagonistic pleiotropy of these genes.
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Affiliation(s)
- Xiaofei Wang
- Department of Statistics, Yale University, New Haven, CT 06520-8102, USA, Department of Biology, Copenhagen University, Universitetsparken 15, 2100 Copenhagen, Denmark and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8102, USA
| | - Sean G. Byars
- Department of Statistics, Yale University, New Haven, CT 06520-8102, USA, Department of Biology, Copenhagen University, Universitetsparken 15, 2100 Copenhagen, Denmark and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8102, USA
| | - Stephen C. Stearns
- Department of Statistics, Yale University, New Haven, CT 06520-8102, USA, Department of Biology, Copenhagen University, Universitetsparken 15, 2100 Copenhagen, Denmark and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8102, USA
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18
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Abstract
Because autosomal genes in sexually reproducing organisms spend on average half their time in each sex, and because the traits that they influence encounter different selection pressures in males and females, the evolutionary responses of one sex are constrained by processes occurring in the other sex. Although intralocus sexual conflict can restrict sexes from reaching their phenotypic optima, no direct evidence currently supports its operation in humans. Here, we show that the pattern of multivariate selection acting on human height, weight, blood pressure and glucose, total cholesterol, and age at first birth differs significantly between males and females, and that the angles between male and female linear (77.8 ± 20.5°) and nonlinear (99.1 ± 25.9°) selection gradients were closer to orthogonal than zero, confirming the presence of sexually antagonistic selection. We also found evidence for intralocus sexual conflict demonstrated by significant changes in the predicted male and female responses to selection of individual traits when cross-sex genetic covariances were included and a significant reduction in the angle between male- and female-predicted responses when cross-sex covariances were included (16.9 ± 15.7°), compared with when they were excluded (87.9 ± 31.6°). We conclude that intralocus sexual conflict constrains the joint evolutionary responses of the two sexes in a contemporary human population.
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Affiliation(s)
- Stephen C Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8102, USA.
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19
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Stearns SC, Byars SG, Govindaraju DR, Ewbank D. Erratum: Measuring selection in contemporary human populations. Nat Rev Genet 2010. [DOI: 10.1038/nrg2930] [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: 11/09/2022]
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20
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Abstract
Are humans currently evolving? This question can be answered using data on lifetime reproductive success, multiple traits and genetic variation and covariation in those traits. Such data are available in existing long-term, multigeneration studies - both clinical and epidemiological - but they have not yet been widely used to address contemporary human evolution. Here we review methods to predict evolutionary change and attempts to measure selection and inheritance in humans. We also assemble examples of long-term studies in which additional measurements of evolution could be made. The evidence strongly suggests that we are evolving and that our nature is dynamic, not static.
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Affiliation(s)
- Stephen C Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8102, USA.
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21
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Byars SG, Parsons Y, Hoffmann AA. Effect of altitude on the genetic structure of an Alpine grass, Poa hiemata. Ann Bot 2009; 103:885-99. [PMID: 19208670 PMCID: PMC2707893 DOI: 10.1093/aob/mcp018] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 10/08/2008] [Accepted: 01/05/2009] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The persistence of plants inhabiting restricted alpine areas under climate change will depend upon many factors including levels of genetic variation in adaptive traits, population structure, and breeding system. METHODS Using microsatellite markers, the genetic structure of populations of a relatively common alpine grass, Poa hiemata, is examined across three altitudinal gradients within the restricted Australian alpine zone where this species has previously been shown to exhibit local adaptation across a narrow altitudinal gradient. KEY RESULTS Genetic variation across six microsatellite markers revealed genetic structuring along altitudinal transects, and a reduction in genetic variation at high and low altitude extremes relative to sites central within transects. There was less genetic variation among transect sites compared with altitudinal gradients within transects, even though distances among transects were relatively larger. Central sites within transects were less differentiated than those at extremes. CONCLUSIONS These patterns suggest higher rates of gene flow among sites at similar altitudes than along transects, a process that could assist altitudinal adaptation. Patterns of spatial autocorrelation and isolation by distance changed with altitude and may reflect altered patterns of dispersal via pollen and/or seed. There was evidence for selfing and clonality in neighbouring plants. Levels of gene flow along transects were insufficient to prevent adaptive changes in morphological traits, given previously measured levels of selection.
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Affiliation(s)
- Sean G Byars
- Centre for Environmental Stress and Adaptation Research, Department of Genetics, Melbourne University, Parkville, Australia.
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Abstract
Alpine environments are particularly susceptible to environmental changes associated with global warming but there is potential for alpine plants to adapt to warming if local adaptation occurs and gene flow allows genotypes adapted to low altitudes to colonize higher altitude sites. Here we examine the adaptive potential of a common alpine grass, Poa hiemata, within the restricted alpine habitat of Australian mountains, across a narrow altitudinal gradient replicated in three areas. Grasses at high altitude sites had shorter leaf lengths and larger circumferences than those at lower sites. Transplant experiments with clonal material and plants grown from seed indicated that these differences were partly genetic, with environmental and genetic factors both contributing to the differences between altitudes. Differences in altitudinal forms were also evident in a common garden experiment. Plants showed a home-site advantage in terms of survival. A fitness analysis indicated that at high altitude sites, selection favored plants with short leaves and larger circumferences, whereas these traits were selected in the opposite direction at the low altitude sites. These findings indicate cogradient selection and potential for both plastic and genotypic shifts in response to climate change in P. hiemata.
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Affiliation(s)
- Sean G Byars
- Department of Genetics, Melbourne University, Parkville, Australia.
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Worland MR, Wharton DA, Byars SG. Intracellular freezing and survival in the freeze tolerant alpine cockroach Celatoblatta quinquemaculata. J Insect Physiol 2004; 50:225-232. [PMID: 15019525 DOI: 10.1016/j.jinsphys.2003.12.001] [Citation(s) in RCA: 18] [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] [Subscribe] [Scholar Register] [Received: 09/08/2003] [Revised: 11/28/2003] [Accepted: 12/01/2003] [Indexed: 05/24/2023]
Abstract
The alpine cockroach Celatoblatta quinquemaculata is common at altitudes of around 1500 m on the Rock and Pillar range of Central Otago, New Zealand where it experiences freezing conditions in the winter. The cockroach is freeze tolerant, but only to c. -9 degrees C. The cause of death at temperatures below this is unknown but likely to be due to osmotic damage to cells (shrinkage). This study compared the effect of different ice nucleation temperatures (-2 and -4 degrees C) on the viability of three types of cockroach tissue (midgut, Malpighian tubules and fat body cells) and cooling to three different temperatures (-5, -8, -12 degrees C). Two types of observations were made (i) cryomicroscope observations of ice formation and cell shrinkage (ii) cell integrity (viability) using vital stains. Cell viability decreased with lower treatment temperatures but ice nucleation temperature had no significant effect. Cryomicroscope observations showed that ice spread through tissue faster at -4 than -2 degrees C and that intracellular freezing only occurred when nucleated at -4 degrees C. From temperature records during cooling, it was observed that when freezing occurred, latent heat immediately increased the insect's body temperature close to its melting point (c. -0.3 degrees C). This "rebound" temperature was independent of nucleation temperature. Some tissues were more vulnerable to damage than others. As the gut is thought to be the site of freezing, it is significant that this tissue was the most robust. The ecological importance of the effect of nucleation temperature on survival of whole animals under field conditions is discussed.
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Affiliation(s)
- M R Worland
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
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