1
|
Chen SY, Gloria LS, Pedrosa VB, Doucette J, Boerman JP, Brito LF. Unraveling the genomic background of resilience based on variability in milk yield and milk production levels in North American Holstein cattle through genome-wide association study and Mendelian randomization analyses. J Dairy Sci 2024; 107:1035-1053. [PMID: 37776995 DOI: 10.3168/jds.2023-23650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/04/2023] [Indexed: 10/02/2023]
Abstract
Breeding more resilient animals will benefit the dairy cattle industry in the long term, especially as global climate changes become more severe. Previous studies have reported genetic parameters for various milk yield-based resilience indicators, but the underlying genomic background of these traits remain unknown. In this study, we conducted GWAS of 62,029 SNPs with 4 milk yield-based resilience indicators, including the weighted occurrence frequency (wfPert) and accumulated milk losses (dPert) of milk yield perturbations, and log-transformed variance (LnVar) and lag-1 autocorrelation (rauto) of daily yield residuals. These variables were previously derived from 5.6 million daily milk yield records from 21,350 lactations (parities 1-3) of 11,787 North American Holstein cows. The average daily milk yield (ADMY) throughout lactation was also included to compare the shared genetic background of resilience indicators with milk yield. The differential genetic background of these indicators was first revealed by the significant genomic regions identified and significantly enriched biological pathways of positional candidate genes, which confirmed the genetic difference among resilience indicators. Interestingly, the functional analyses of candidate genes suggested that the regulation of intestinal homeostasis is most likely affecting resilience derived based on variability in milk yield. Based on Mendelian randomization analyses of multiple instrumental SNPs, we further found an unfavorable causal association of ADMY with LnVar. In conclusion, the resilience indicators evaluated are genetically different traits, and there are causal associations of milk yield with some of the resilience indicators evaluated. In addition to providing biological insights into the molecular regulation mechanisms of resilience derived based on variability in milk yield, this study also indicates the need for developing selection indexes combining multiple indicator traits and taking into account their genetic relationship for breeding more resilient dairy cattle.
Collapse
Affiliation(s)
- Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Leonardo S Gloria
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Jarrod Doucette
- Agriculture Information Technology (AgIT), Purdue University, West Lafayette, IN 47907
| | | | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
| |
Collapse
|
2
|
Han P, Wang C, Zhang W, Wu Y, Wang D, Zhao S, Zhu M. Pleiotropic architectures of porcine immune and growth trait pairs revealed by a self-product-based transcriptome method. Anim Genet 2023; 54:123-131. [PMID: 36478569 DOI: 10.1111/age.13282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/18/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
Abstract
Pleiotropy is an important biological phenomenon with complicated genetic architectures for multiple traits. To date, pleiotropy has been mainly identified by multi-trait genome-wide association studies, but this method has its disadvantages, and new developments for pleiotropy detection methods are needed. Here we define a novel metric, self-product, to measure individual-level co-variation of two traits, and develop a novel self-product-based transcriptome method to detect pleiotropic genes (PGs). Our method was tested using four immune-growth trait pairs and four immune-immune trait pairs in pigs. Comparative transcriptome analyses identified hundreds of candidate PGs related to eight trait pairs from two tails of self-product distribution. Gene Ontology enrichment analysis indicated that most of identified PGs were involved in immune- or growth-related biological processes. We established PG interaction networks to exhibit core genes shared by eight trait pairs, of which CCL5 and IL-10 genes were the hub genes. Genetic association analyses showed that SmaI-polymorphisms of CCL5 and IL-10 genes had significant associations with phenotypic co-variations of multiple trait pairs, indicating that the variants in pleiotropic genes were also pleiotropic variants. Taken together, the validity of our proposed method was preliminarily verified, and our findings provide new insights into the genetic basis of pleiotropic architectures of immune and growth trait pairs in pigs.
Collapse
Affiliation(s)
- Pingping Han
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Chao Wang
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhang
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yalan Wu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Daoyuan Wang
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Mengjin Zhu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
3
|
Sarvari-Kalouti H, Maghsoudi A, Rokouei M, Faraji-Arough H, Bagherzadeh-Kasmani F. Direct and maternal genetic effects for preinflection point growth traits and humoral immunity in quail. Poult Sci 2022; 102:102340. [PMID: 36470033 PMCID: PMC9719865 DOI: 10.1016/j.psj.2022.102340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
Early growth traits in quails are considered as the growth performances before the inflection point which are genetically different from body weights (BW) at later stages. Moreover, in addition to growth performance, humoral immunity is moderately heritable and is considered in some breeding programs. However, estimating the direct genetic, particularly the maternal genetic correlations between growth and immunity in quail, are not studied sufficiently, which were the aims of the present study. The quails' BW were recorded at hatch (BW0) to 25 d of age with a 5-d interval and body weight gains (BWG) were measured as average growth performance of the birds in a 5-d period. Antibody titer against Newcastle disease virus (IgN) was measured through the hemagglutination inhibition (HI) test. For titration of anti-SRBC antibodies (IgY and IgM), a hemagglutination microtiter assay was used. In general, growth records in 4,181 birds and humoral immune responses in 1,023 birds were assigned to the study. The genetic parameters were estimated by single-trait analysis via Gibb's sampling. After finding the best model for each trait, multi-trait analysis was done to estimate the direct and maternal genetic correlations. Direct heritabilities (h2) were estimated to be moderate for BW (0.481-0.551) and BWG (0.524-0.557), while h2 for immune responses were low (0.035-0.079). Maternal environmental effect (c2) was only significant for BW0, BW5, and BWG0-5. Maternal heritabilities (m2) for BW and BWG were all lower than corresponding h2, ranging from 0.072 (BW25) to 0.098 (BW0). The m2 for IgN (0.098) was more than 2.5 times greater than h2 (0.040) for this trait. Direct (ra) and maternal (rm) genetic correlations between IgN-BW, IgY-BW, and IgY-BWG were negative, while ra and rm for IgM-BW, IgN-BWG, and IgM-BWG were positive. The ra between humoral immune responses were low to moderate and rm was significant only for IgY-IgM (0.339). Given positive genetic correlations in BWG-IgN and BWG-IgM as well as positive genetic correlations between both IgN and IgM with IgY, it is suggested that including the BWG in the breeding programs would directly result in the improvement of the birds' growth performance. It would also contribute indirectly to the improvement of the birds' humoral immune responses.
Collapse
Affiliation(s)
- Hojjat Sarvari-Kalouti
- Department of Animal Science, Faculty of Agriculture, University of Zabol, P.O. Box 98661-5538, Zabol, Iran
| | - Ali Maghsoudi
- Department of Animal Science, Faculty of Agriculture, University of Zabol, P.O. Box 98661-5538, Zabol, Iran,Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115–336, Tehran, Iran.,Corresponding author:
| | - Mohammad Rokouei
- Department of Animal Science, Faculty of Agriculture, University of Zabol, P.O. Box 98661-5538, Zabol, Iran
| | - Hadi Faraji-Arough
- Department of Ostrich, Special Domestic Animals Institute, Research Institute of Zabol, P.O. Box 98661-5538, Zabol, Iran
| | - Farzad Bagherzadeh-Kasmani
- Department of Animal Science, Faculty of Agriculture, University of Zabol, P.O. Box 98661-5538, Zabol, Iran
| |
Collapse
|
4
|
Wielscher M, Amaral AFS, van der Plaat D, Wain LV, Sebert S, Mosen-Ansorena D, Auvinen J, Herzig KH, Dehghan A, Jarvis DL, Jarvelin MR. Genetic correlation and causal relationships between cardio-metabolic traits and lung function impairment. Genome Med 2021; 13:104. [PMID: 34154662 PMCID: PMC8215837 DOI: 10.1186/s13073-021-00914-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Associations of low lung function with features of poor cardio-metabolic health have been reported. It is, however, unclear whether these co-morbidities reflect causal associations, shared genetic heritability or are confounded by environmental factors. METHODS We performed three analyses: (1) cardio-metabolic health to lung function association tests in Northern Finland Birth cohort 1966, (2) cross-trait linkage disequilibrium score regression (LDSC) to compare genetic backgrounds and (3) Mendelian randomisation (MR) analysis to assess the causal effect of cardio-metabolic traits and disease on lung function, and vice versa (bidirectional MR). Genetic associations were obtained from the UK Biobank data or published large-scale genome-wide association studies (N > 82,000). RESULTS We observed a negative genetic correlation between lung function and cardio-metabolic traits and diseases. In Mendelian Randomisation analysis (MR), we found associations between type 2 diabetes (T2D) instruments and forced vital capacity (FVC) as well as FEV1/FVC. Body mass index (BMI) instruments were associated to all lung function traits and C-reactive protein (CRP) instruments to FVC. These genetic associations provide evidence for a causal effect of cardio-metabolic traits on lung function. Multivariable MR suggested independence of these causal effects from other tested cardio-metabolic traits and diseases. Analysis of lung function specific SNPs revealed a potential causal effect of FEV1/FVC on blood pressure. CONCLUSIONS The present study overcomes many limitations of observational studies by using Mendelian Randomisation. We provide evidence for an independent causal effect of T2D, CRP and BMI on lung function with some of the T2D effect on lung function being attributed to inflammatory mechanisms. Furthermore, this analysis suggests a potential causal effect of FEV1/FVC on blood pressure. Our detailed analysis of the interplay between cardio-metabolic traits and impaired lung function provides the opportunity to improve the quality of existing intervention strategies.
Collapse
Affiliation(s)
- Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Andre F S Amaral
- National Heart and Lung Institute (NHLI), Imperial College London, Emmanuel Kaye Building, London, SW3 6LR, UK
| | - Diana van der Plaat
- National Heart and Lung Institute (NHLI), Imperial College London, Emmanuel Kaye Building, London, SW3 6LR, UK
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, George Davies Centre, University of Leicester, University Rd, Leicester, LE1 7RH, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, University Rd, Leicester, LE1 7RH, UK
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, P.O.Box 8000, FI-90014, Oulu, Finland
- Biocenter of Oulu, University of Oulu, Aapistie 5, FI-90014, Oulu, Finland
| | - David Mosen-Ansorena
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Juha Auvinen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, P.O.Box 8000, FI-90014, Oulu, Finland
- Biocenter of Oulu, University of Oulu, Aapistie 5, FI-90014, Oulu, Finland
| | - Karl-Heinz Herzig
- Biocenter of Oulu, University of Oulu, Aapistie 5, FI-90014, Oulu, Finland
- Research Unit of Biomedicine, Medical Research Center (MRC), University of Oulu, University Hospital, P.O. Box 8000, Oulu, Finland
- Department of Gastroenterology and Metabolism, Poznan University of Medical Sciences, 41 Jackowskiego St, 60-512, Poznan, Poland
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Debbie L Jarvis
- National Heart and Lung Institute (NHLI), Imperial College London, Emmanuel Kaye Building, London, SW3 6LR, UK.
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK.
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, P.O.Box 8000, FI-90014, Oulu, Finland.
- Biocenter of Oulu, University of Oulu, Aapistie 5, FI-90014, Oulu, Finland.
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Kingston Lane, London, UB8 3PH, UK.
| |
Collapse
|
5
|
Saraiva LC, Cappi C, Simpson HB, Stein DJ, Viswanath B, van den Heuvel OA, Reddy YCJ, Miguel EC, Shavitt RG. Cutting-edge genetics in obsessive-compulsive disorder. Fac Rev 2020; 9:30. [PMID: 33659962 PMCID: PMC7886082 DOI: 10.12703/r/9-30] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This article reviews recent advances in the genetics of obsessive-compulsive disorder (OCD). We cover work on the following: genome-wide association studies, whole-exome sequencing studies, copy number variation studies, gene expression, polygenic risk scores, gene–environment interaction, experimental animal systems, human cell models, imaging genetics, pharmacogenetics, and studies of endophenotypes. Findings from this work underscore the notion that the genetic architecture of OCD is highly complex and shared with other neuropsychiatric disorders. Also, the latest evidence points to the participation of gene networks involved in synaptic transmission, neurodevelopment, and the immune and inflammatory systems in this disorder. We conclude by highlighting that further study of the genetic architecture of OCD, a great part of which remains to be elucidated, could benefit the development of diagnostic and therapeutic approaches based on the biological basis of the disorder. Studies to date revealed that OCD is not a simple homogeneous entity, but rather that the underlying biological pathways are variable and heterogenous. We can expect that translation from bench to bedside, through continuous effort and collaborative work, will ultimately transform our understanding of what causes OCD and thus how best to treat it.
Collapse
Affiliation(s)
- Leonardo Cardoso Saraiva
- Department & Institute of Psychiatry, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Carolina Cappi
- Department & Institute of Psychiatry, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Helen Blair Simpson
- Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
- The New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Dan J Stein
- SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry & Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Biju Viswanath
- Molecular Genetics Laboratory, National Institute of Mental Health & Neurosciences (NIMHANS); Accelerator Program for Discovery in Brain disorders using Stem cells (ADBS) Laboratory, NIMHANS, Bangalore, India
| | - Odile A van den Heuvel
- Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Department of Psychiatry, Department of Anatomy & Neuroscience, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - YC Janardhan Reddy
- Obsessive-Compulsive Disorder (OCD) Clinic, Department of Psychiatry, NIMHANS, Bangalore, India
| | - Euripedes C Miguel
- Department & Institute of Psychiatry, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Roseli G Shavitt
- Department & Institute of Psychiatry, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| |
Collapse
|
6
|
Mealer RG, Jenkins BG, Chen CY, Daly MJ, Ge T, Lehoux S, Marquardt T, Palmer CD, Park JH, Parsons PJ, Sackstein R, Williams SE, Cummings RD, Scolnick EM, Smoller JW. The schizophrenia risk locus in SLC39A8 alters brain metal transport and plasma glycosylation. Sci Rep 2020; 10:13162. [PMID: 32753748 PMCID: PMC7403432 DOI: 10.1038/s41598-020-70108-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/20/2020] [Indexed: 12/15/2022] Open
Abstract
A common missense variant in SLC39A8 is convincingly associated with schizophrenia and several additional phenotypes. Homozygous loss-of-function mutations in SLC39A8 result in undetectable serum manganese (Mn) and a Congenital Disorder of Glycosylation (CDG) due to the exquisite sensitivity of glycosyltransferases to Mn concentration. Here, we identified several Mn-related changes in human carriers of the common SLC39A8 missense allele. Analysis of structural brain MRI scans showed a dose-dependent change in the ratio of T2w to T1w signal in several regions. Comprehensive trace element analysis confirmed a specific reduction of only serum Mn, and plasma protein N-glycome profiling revealed reduced complexity and branching. N-glycome profiling from two individuals with SLC39A8-CDG showed similar but more severe alterations in branching that improved with Mn supplementation, suggesting that the common variant exists on a spectrum of hypofunction with potential for reversibility. Characterizing the functional impact of this variant will enhance our understanding of schizophrenia pathogenesis and identify novel therapeutic targets and biomarkers.
Collapse
Affiliation(s)
- Robert G Mealer
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- The Stanley Center for Psychiatric Research at Broad Institute of Harvard/MIT, Cambridge, MA, USA.
- National Center for Functional Glycomics, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Bruce G Jenkins
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Chia-Yen Chen
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- The Stanley Center for Psychiatric Research at Broad Institute of Harvard/MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark J Daly
- The Stanley Center for Psychiatric Research at Broad Institute of Harvard/MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- The Stanley Center for Psychiatric Research at Broad Institute of Harvard/MIT, Cambridge, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Sylvain Lehoux
- National Center for Functional Glycomics, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Thorsten Marquardt
- Klinik und Poliklinik für Kinder- und Jugendmedizin-Allgemeine Pädiatrie, Universitätsklinikum Münster, Münster, Germany
| | - Christopher D Palmer
- Laboratory of Inorganic and Nuclear Chemistry, Wadsworth Center, New York State Department of Health, Albany, NY, USA
- Department of Environmental Health Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - Julien H Park
- Klinik und Poliklinik für Kinder- und Jugendmedizin-Allgemeine Pädiatrie, Universitätsklinikum Münster, Münster, Germany
| | - Patrick J Parsons
- Laboratory of Inorganic and Nuclear Chemistry, Wadsworth Center, New York State Department of Health, Albany, NY, USA
- Department of Environmental Health Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - Robert Sackstein
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Sarah E Williams
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- National Center for Functional Glycomics, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Richard D Cummings
- National Center for Functional Glycomics, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Edward M Scolnick
- The Stanley Center for Psychiatric Research at Broad Institute of Harvard/MIT, Cambridge, MA, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- The Stanley Center for Psychiatric Research at Broad Institute of Harvard/MIT, Cambridge, MA, USA
| |
Collapse
|
7
|
Granot-Hershkovitz E, Wu P, Karasik D, Peter I, Peloso GM, Levy D, Vasan RS, Adrienne Cupples L, Liu CT, Meigs JB, Siscovick DS, Dupuis J, Friedlander Y, Hochner H. Searching for parent-of-origin effects on cardiometabolic traits in imprinted genomic regions. Eur J Hum Genet 2020; 28:646-655. [PMID: 31896779 PMCID: PMC7170899 DOI: 10.1038/s41431-019-0568-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 11/08/2022] Open
Abstract
Cardiometabolic traits pose a major global public health burden. Large-scale genome-wide association studies (GWAS) have identified multiple loci accounting for up to 30% of the genetic variance in complex traits such as cardiometabolic traits. However, the contribution of parent-of-origin effects (POEs) to complex traits has been largely ignored in GWAS. Family-based studies enable the assessment of POEs in genetic association analyses. We investigated POEs on a range of complex traits in 3 family-based studies. The discovery phase was carried out in large pedigrees from the Kibbutzim Family Study (n = 901 individuals) and in 872 parent-offspring trios from the Jerusalem Perinatal Study. Focusing on imprinted genomic regions, we examined parent-specific associations with 12 complex traits (i.e., body-size, blood pressure, lipids), mostly cardiometabolic risk traits. Forty five of the 11,967 SNPs initially found to have POE were evaluated for replication (p value < 1 × 10-4) in Framingham Heart Study families (max n = 8000 individuals). Three common variants yielded evidence of POE in the meta-analysis. Two variants, located on chr6 in the HLA region, showed a paternal effect on height (rs1042136: βpaternal = -0.023, p value = 1.5 × 10-8 and rs1431403: βpaternal = -0.011, p value = 5.4 × 10-6). The corresponding maternally-derived effects were statistically nonsignificant. The variant rs9332053, located on chr13 in RCBTB2 gene, demonstrated a maternal effect on hip circumference (βmaternal = -4.24, p value = 9.6 × 10-6; βpaternal = 1.29, p value = 0.23). These findings provide evidence for the utility of incorporating POEs into association studies of cardiometabolic traits, especially anthropometric traits. The study highlights the benefits of using family-based data for deciphering the genetic architecture of complex traits.
Collapse
Affiliation(s)
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Daniel Levy
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Ramachandran S Vasan
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- Sections of Preventive medicine and Epidemiology, and cardiovascular medicine, Departments of Medicine and Epidemiology, Boston University Schools of Medicine and Public health, Boston, MA, 02118, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - James B Meigs
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David S Siscovick
- Institute for Urban Health, New York Academy of Medicine, New York, NY, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Yechiel Friedlander
- Braun School of Public Health, The Hebrew University of Jerusalem, 99112102, Jerusalem, Israel
| | - Hagit Hochner
- Braun School of Public Health, The Hebrew University of Jerusalem, 99112102, Jerusalem, Israel.
| |
Collapse
|
8
|
Ryan FJ, Drew DP, Douglas C, Leong LEX, Moldovan M, Lynn M, Fink N, Sribnaia A, Penttila I, McPhee AJ, Collins CT, Makrides M, Gibson RA, Rogers GB, Lynn DJ. Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia. mSystems 2019; 4:e00484-19. [PMID: 31662429 PMCID: PMC6819732 DOI: 10.1128/msystems.00484-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/09/2019] [Indexed: 12/21/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a common chronic lung condition in preterm infants that results in abnormal lung development and leads to considerable morbidity and mortality, making BPD one of the most common complications of preterm birth. We employed RNA sequencing and 16S rRNA gene sequencing to profile gene expression in blood and the composition of the fecal microbiota in infants born at <29 weeks gestational age and diagnosed with BPD in comparison to those of preterm infants that were not diagnosed with BPD. 16S rRNA gene sequencing, performed longitudinally on 255 fecal samples collected from 50 infants in the first months of life, identified significant differences in the relative levels of abundance of Klebsiella, Salmonella, Escherichia/Shigella, and Bifidobacterium in the BPD infants in a manner that was birth mode dependent. Transcriptome sequencing (RNA-Seq) analysis revealed that more than 400 genes were upregulated in infants with BPD. Genes upregulated in BPD infants were significantly enriched for functions related to red blood cell development and oxygen transport, while several immune-related pathways were downregulated. We also identified a gene expression signature consistent with an enrichment of immunosuppressive CD71+ early erythroid cells in infants with BPD. Intriguingly, genes that were correlated in their expression with the relative abundances of specific taxa in the microbiota were significantly enriched for roles in the immune system, suggesting that changes in the microbiota might influence immune gene expression systemically.IMPORTANCE Bronchopulmonary dysplasia (BPD) is a serious inflammatory condition of the lung and is the most common complication associated with preterm birth. A large body of evidence now suggests that the gut microbiota can influence immunity and inflammation systemically; however, the role of the gut microbiota in BPD has not been evaluated to date. Here, we report that there are significant differences in the gut microbiota of infants born at <29 weeks gestation and subsequently diagnosed with BPD, which are particularly pronounced when infants are stratified by birth mode. We also show that erythroid and immune gene expression levels are significantly altered in BPD infants. Interestingly, we identified an association between the composition of the microbiota and immune gene expression in blood in early life. Together, these findings suggest that the composition of the microbiota may influence the risk of developing BPD and, more generally, may shape systemic immune gene expression.
Collapse
Affiliation(s)
- Feargal J Ryan
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Damian P Drew
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Chloe Douglas
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lex E X Leong
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Max Moldovan
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Miriam Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Naomi Fink
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Anastasia Sribnaia
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Irmeli Penttila
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew J McPhee
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Neonatal Medicine, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Carmel T Collins
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Maria Makrides
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Robert A Gibson
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- School of Agriculture, Food, and Wine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - David J Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| |
Collapse
|
9
|
Rauth M, Freund P, Orlova A, Grünert S, Tasic N, Han X, Ruan HB, Neubauer HA, Moriggl R. Cell Metabolism Control Through O-GlcNAcylation of STAT5: A Full or Empty Fuel Tank Makes a Big Difference for Cancer Cell Growth and Survival. Int J Mol Sci 2019; 20:E1028. [PMID: 30818760 PMCID: PMC6429193 DOI: 10.3390/ijms20051028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 12/23/2022] Open
Abstract
O-GlcNAcylation is a post-translational modification that influences tyrosine phosphorylation in healthy and malignant cells. O-GlcNAc is a product of the hexosamine biosynthetic pathway, a side pathway of glucose metabolism. It is essential for cell survival and proper gene regulation, mirroring the metabolic status of a cell. STAT3 and STAT5 proteins are essential transcription factors that can act in a mutational context-dependent manner as oncogenes or tumor suppressors. They regulate gene expression for vital processes such as cell differentiation, survival, or growth, and are also critically involved in metabolic control. The role of STAT3/5 proteins in metabolic processes is partly independent of their transcriptional regulatory role, but is still poorly understood. Interestingly, STAT3 and STAT5 are modified by O-GlcNAc in response to the metabolic status of the cell. Here, we discuss and summarize evidence of O-GlcNAcylation-regulating STAT function, focusing in particular on hyperactive STAT5A transplant studies in the hematopoietic system. We emphasize that a single O-GlcNAc modification is essential to promote development of neoplastic cell growth through enhancing STAT5A tyrosine phosphorylation. Inhibition of O-GlcNAcylation of STAT5A on threonine 92 lowers tyrosine phosphorylation of oncogenic STAT5A and ablates malignant transformation. We conclude on strategies for new therapeutic options to block O-GlcNAcylation in combination with tyrosine kinase inhibitors to target neoplastic cancer cell growth and survival.
Collapse
Affiliation(s)
- Manuel Rauth
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
| | - Patricia Freund
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
- Ludwig Boltzmann Institute for Cancer Research, 1090 Vienna, Austria.
| | | | | | - Xiaonan Han
- Key Laboratory of Human Disease Comparative Medicine, the Ministry of Health, Institute of Laboratory Animal Sciences (ILAS), Beijing 100730, China.
- Chinese Academy of Medical Science (CAMS) and Peking Union Medical College (PUMC), Beijing 100006, China.
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH 45229-3026, USA.
| | - Hai-Bin Ruan
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN 55455, USA.
| | - Heidi A Neubauer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
- Ludwig Boltzmann Institute for Cancer Research, 1090 Vienna, Austria.
- Medical University Vienna, Vienna 1090, Austria.
| |
Collapse
|