Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Abstract Background Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Funding GMP, PN, and CW are supported by NHLBI R01HL127564. GMP and PN are supported by R01HL142711. AG acknowledge support from the Wellcome Trust (201543/B/16/Z), European Union Seventh Framework Programme FP7/2007–2013 under grant agreement no. HEALTH-F2-2013–601456 (CVGenes@Target) & the TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation’s Grant number NNF15CC0018486. JMM is supported by American Diabetes Association Innovative and Clinical Translational Award 1–19-ICTS-068. SR was supported by the Academy of Finland Center of Excellence in Complex Disease Genetics (Grant No 312062), the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, and University of Helsinki HiLIFE Fellow and Grand Challenge grants. EW was supported by the Finnish innovation fund Sitra (EW) and Finska Läkaresällskapet. CNS was supported by American Heart Association Postdoctoral Fellowships 15POST24470131 and 17POST33650016. Charles N Rotimi is supported by Z01HG200362. Zhe Wang, Michael H Preuss, and Ruth JF Loos are supported by R01HL142302. NJT is a Wellcome Trust Investigator (202802/Z/16/Z), is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215–2001) and the MRC Integrative Epidemiology Unit (MC_UU_00011), and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A19169). Ruth E Mitchell is a member of the MRC Integrative Epidemiology Unit at the University of Bristol funded by the MRC (MC_UU_00011/1). Simon Haworth is supported by the UK National Institute for Health Research Academic Clinical Fellowship. Paul S. de Vries was supported by American Heart Association grant number 18CDA34110116. Julia Ramierz acknowledges support by the People Programme of the European Union’s Seventh Framework Programme grant n° 608765 and Marie Sklodowska-Curie grant n° 786833. Maria Sabater-Lleal is supported by a Miguel Servet contract from the ISCIII Spanish Health Institute (CP17/00142) and co-financed by the European Social Fund. Jian Yang is funded by the Westlake Education Foundation. Olga Giannakopoulou has received funding from the British Heart Foundation (BHF) (FS/14/66/3129). CHARGE Consortium cohorts were supported by R01HL105756. Study-specific acknowledgements are available in the Additional file 32: Supplementary Note. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services.Peer reviewedPublisher PD

Association between Dopamine Receptor D2 (DRD2) Variations rs6277 and rs1800497 and Cognitive Performance According to Risk Type for Psychosis : A Nested Case Control Study in a Finnish Population Sample

Background There is limited research regarding the association between genes and cognitive intermediate phenotypes in those at risk for psychotic disorders. Methods We measured the association between established psychosis risk variants in dopamine D2 receptor (DRD2) and cognitive performance in individuals at age 23 years and explored if associations between cognition and these variants differed according to the presence of familial or clinical risk for psychosis. The subjects of the Oulu Brain and Mind Study were drawn from the general population-based Northern Finland 1986 Birth Cohort (NFBC 1986). Using linear regression, we compared the associations between cognitive performance and two candidate DRD2 polymorphisms (rs6277 and rs1800497) between subjects having familial (n=61) and clinical (n=45) risk for psychosis and a random sample of participating NFBC 1986 controls (n=74). Cognitive performance was evaluated using a comprehensive battery of tests at follow-up. Results Principal components factor analysis supported a three-factor model for cognitive measures. The minor allele of rs6277 was associated with poorer performance on a verbal factor (p=0.003) but this did not significantly interact with familial or clinical risk for psychosis. The minor allele of rs1800497 was associated with poorer performance on a psychomotor factor (p=0.038), though only in those at familial risk for psychotic disorders (interaction p=0.049). Conclusion The effect of two DRD2 SNPs on cognitive performance may differ according to risk type for psychosis, suggesting that cognitive intermediate phenotypes differ according to the type (familial or clinical) risk for psychosis.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Funding Information: GMP, PN, and CW are supported by NHLBI R01HL127564. GMP and PN are supported by R01HL142711. AG acknowledge support from the Wellcome Trust (201543/B/16/Z), European Union Seventh Framework Programme FP7/2007–2013 under grant agreement no. HEALTH-F2-2013–601456 (CVGenes@Target) & the TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation’s Grant number NNF15CC0018486. JMM is supported by American Diabetes Association Innovative and Clinical Translational Award 1–19-ICTS-068. SR was supported by the Academy of Finland Center of Excellence in Complex Disease Genetics (Grant No 312062), the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, and University of Helsinki HiLIFE Fellow and Grand Challenge grants. EW was supported by the Finnish innovation fund Sitra (EW) and Finska Läkaresällskapet. CNS was supported by American Heart Association Postdoctoral Fellowships 15POST24470131 and 17POST33650016. Charles N Rotimi is supported by Z01HG200362. Zhe Wang, Michael H Preuss, and Ruth JF Loos are supported by R01HL142302. NJT is a Wellcome Trust Investigator (202802/Z/16/Z), is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215–2001) and the MRC Integrative Epidemiology Unit (MC_UU_00011), and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A19169). Ruth E Mitchell is a member of the MRC Integrative Epidemiology Unit at the University of Bristol funded by the MRC (MC_UU_00011/1). Simon Haworth is supported by the UK National Institute for Health Research Academic Clinical Fellowship. Paul S. de Vries was supported by American Heart Association grant number 18CDA34110116. Julia Ramierz acknowledges support by the People Programme of the European Union’s Seventh Framework Programme grant n° 608765 and Marie Sklodowska-Curie grant n° 786833. Maria Sabater-Lleal is supported by a Miguel Servet contract from the ISCIII Spanish Health Institute (CP17/00142) and co-financed by the European Social Fund. Jian Yang is funded by the Westlake Education Foundation. Olga Giannakopoulou has received funding from the British Heart Foundation (BHF) (FS/14/66/3129). CHARGE Consortium cohorts were supported by R01HL105756. Study-specific acknowledgements are available in the Additional file : Supplementary Note. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services. Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe

Predictors of psychosis risk and neurocognitive deficits

Abstract Psychotic disorders usually become evident during adolescence and early adulthood and are commonly preceded by psychosis risk states. Young people at risk for developing psychosis may already have cognitive deficits. This research examined factors associated with psychosis risk and adverse cognitive performance, particularly in those at risk for developing psychosis. We aimed to characterise genetic risk factors for psychosis risk and adverse cognitive performance. Additionally, early and later biological risk markers for adverse cognitive performance and psychosis risk were explored. Two longitudinal birth cohorts, the Northern Finland Birth Cohort 1986 (NFBC 1986, n=6,985 at 16 years) and Avon Longitudinal Study of Parents and Children (ALSPAC, n=5,217 at 17 years), two NFBC 1986 sub-studies, the Oulu Brain and Mind 1 (n=182 for these analyses) and Oulu Brain and Mind 2 (n=471 for these analyses) studies, and two Irish case control studies, the Adolescent Brain Development (n=212) and Challenging Times (n=211) studies, were utilised. Predictors of interest were selected Single Nucleotide Polymorphisms (SNPs at COMT, BDNF and DRD2), prenatal exposure to maternal cigarette smoking (PEMCS) and adolescent metabolic measures. Though not directly associated with psychotic experiences, the COMT-Val158Met Val-Val genotype interacted with experience of childhood trauma to predict more psychotic experiences. Two DRD2 SNPs were associated with poorer cognitive performance, though only in those with risk for psychotic disorders. PEMCS was associated with adult vocabulary and matrix reasoning performance in males, though not in males with adolescent psychotic experiences. Adolescent academic performance, but not psychotic experiences, were associated with metabolic measures, especially with ratios of omega-3 to total fatty acids. These findings impact on prevention strategies for long-term adverse outcomes. Some risk factors differ for those with psychotic experiences compared to the general population, while others do not. SNPs at COMT and DRD2 may be more relevant in those with psychotic experiences. Interventions targeting these groups may be particularly beneficial. Smoking in pregnancy, however, is harmful to male cognitive performance across the population, suggesting elimination of this risk is more broadly relevant. Fatty acid-related metabolic measures may mark risk for cognitive deficits or may represent a developmental feature that is potentially open to intervention.Tiivistelmä Psykoottiset häiriöt puhkeavat tavallisesti nuoruusiässä tai varhaisessa aikuisiässä. Varsinaista psykoosijaksoa edeltää usein psykoosialttiusvaihe. Nuoruusiän psykoosialttiusvaiheeseen liittyy kognitiivisia puutoksia. Tässä tutkimuksessa selvitettiin tekijöitä, jotka liittyvät psykoosialttiuteen ja heikkoon kognitiiviseen suoriutumiseen, etenkin nuorilla, jotka olivat psykoosiriskissä. Tutkimuksessa tarkasteltiin psykoosialttiuteen ja heikkoon kognitiiviseen suoriutumiseen liittyviä geneettisiä tekijöitä. Lisäksi tutkittiin biologisia varhaisia ja myöhempiä psykoosialttiutta ja heikkoa kognitiivista suoriutumista ennustavia tekijöitä. Tutkimusaineisto käsitti kaksi pitkittäistä syntymäkohorttia: Pohjois-Suomen syntymäkohortti 1986 (n=6,985 16-vuotiaana) ja englantilainen Avon Longitudinal Study of Parents and Children (ALSPAC, n=5,217 17-vuotiaana) -tutkimukset. Pohjois-Suomen syntymäkohortti 1986:sta analysoitiin kahta ala-otosta eli Aivot ja Mieli I (n=182) ja Aivot ja Mieli II (n=471) tutkimusta. Lisäksi tutkimusaineistoon kuului kaksi irlantilaista tapaus-verrokki tutkimusta: Adolescent Brain Development (n=212) ja Challenging Times (n=211) tutkimukset. Ennustavina tekijöinä tarkasteltiin yhden nukleotidin polymorfismia (Single Nucleotide Polymorphisms, SNP; COMT, BDNF ja DRD2 -geeneissä), äidin raskaudenaikaista tupakointia, lapsuuden traumaattisia kokemuksia ja nuoruusiän metabolisia arvoja. COMT-Val158Met geenin Val-Val genotyyppi ei ollut suoraan yhteydessä psykoottisiin kokemuksiin, mutta yhdessä lapsuuden traumaattisten kokemusten kanssa ennusti suurempaa psykoosioireiden määrää. Kaksi DRD2 SNP-varianttia assosioituivat heikompaan kognitiiviseen suoriutumiseen, vaikkakin vain tutkittavilla jotka olivat psykoosialttiita. Äidin raskaudenaikainen tupakointi ennusti huonompaa kognitiivista suoriutumista pojilla, tosin ei pojilla joilla oli nuoruusiässä psykoosioireita. Metaboliset tekijät, erityisesti omega-3 rasvahapon suhde kokonaisrasvahapon määrään oli yhteydessä koulumenestykseen. Tutkimuksen tulosten perusteella voidaan mahdollisesti suunnitella ennaltaehkäiseviä toimia myöhempien haittojen ehkäisemiseksi. Jotkut tutkituista riskitekijöistä assosioituivat eri tavalla kognitioon psykoosialttiilla kuin yleisväestössä. COMT ja DRD2 geenien variantit psykoosialttiilla saattavat olla keskeisiä. Interventiot nuorille, joilla on nämä variantit ja psykoosioireita, voisivat olla erityisesti hyödyllisiä. Äidin raskauden aikaisen tupakointi ennusti poikien kognitiivista suoriutumista. Äidin raskaudenaikaisen tupakoinnin vähentämisellä olisi suotuinen vaikutus tässäkin suhteessa. Rasvahappoihin liittyvät metaboliset suureet voivat olla riski kognitiivisille puutoksille tai ne voivat merkitä kehityksellistä piirrettä, joka voisi mahdollistaa varhaisen ennaltaehkäisyn