Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology

Publisher Copyright: © 2022, The Author(s).Back pain is a common and debilitating disorder with largely unknown underlying biology. Here we report a genome-wide association study of back pain using diagnoses assigned in clinical practice; dorsalgia (119,100 cases, 909,847 controls) and intervertebral disc disorder (IDD) (58,854 cases, 922,958 controls). We identify 41 variants at 33 loci. The most significant association (ORIDD = 0.92, P = 1.6 × 10−39; ORdorsalgia = 0.92, P = 7.2 × 10−15) is with a 3’UTR variant (rs1871452-T) in CHST3, encoding a sulfotransferase enzyme expressed in intervertebral discs. The largest effects on IDD are conferred by rare (MAF = 0.07 − 0.32%) loss-of-function (LoF) variants in SLC13A1, encoding a sodium-sulfate co-transporter (LoF burden OR = 1.44, P = 3.1 × 10−11); variants that also associate with reduced serum sulfate. Genes implicated by this study are involved in cartilage and bone biology, as well as neurological and inflammatory processes.Peer reviewe

Search for genetic variants influencing human height

Human growth and attained height are determined by a combination of genetic and environmental effects and in modern Western societies > 80% of the observed variation in height is determined by genetic factors. Height is a fundamental human trait that is associated with many socioeconomic and psychosocial factors and health measures, however little is known of the identity of the specific genes that influence height variation in the general population. This thesis work aimed to identify the genetic variants that influence height in the general population by genome-wide linkage analysis utilizing large family samples. The study focused on analysis of three separate sets of families consisting of: 1) 1,417 individuals from 277 Finnish families (FinnHeight), 2) 8,450 individuals from 3,817 families from Australia and Europe (EUHeight) and 3) 9,306 individuals from 3,302 families from the United States (USHeight). The most significant finding in this study was found in the Finnish family sample where we a locus in the chromosomal region 1p21 was linked to adult height. Several regions showed evidence for linkage in the Australian, European and US families with 8q21 and 15q25 being the most significant. The region on 1p21 was followed up with further studies and we were able to show that the collagen 11-alpha-1 gene (COL11A1) residing at this location was associated with adult height. This association was also confirmed in an independent Finnish population cohort (Health 2000) consisting of 6,542 individuals. From this population sample, we estimated that homozygous males and females for this gene variant were 1.1 and 0.6 cm taller than the respective controls. In this thesis work we identified a gene variant in the COL11A1 gene that influences human height, although this variant alone explains only 0.1% of height variation in the Finnish population. We also demonstrated in this study that special stratification strategies such as performing sex-limited analyses, focusing on dizygous twin pairs, analyzing ethnic groups within a population separately and utilizing homogenous populations such as the Finns can improve the statistical power of finding QTL significantly. Also, we concluded from the results of this study that even though genetic effects explain a great proportion of height variance, it is likely that there are tens or even hundreds of genes with small individual effects underlying the genetic architecture of height.Ihmisen kasvu ja aikuisiän pituus ovat tyypillisiä monitekijäisiä ominaisuuksia, joihin vaikuttavat sekä geneettiset tekijät että ympäristötekijät. Geneettisten tekijöiden merkitys pituuden määräytymisessä on huomattava ja on arvioitu, että kehittyneissä maissa nämä selittävät yli 80 % ihmisten välisistä pituuseroista. Aikuisiän pituudella on havaittu olevan yhteys lukuisiin sairauksiin sekä sosioekonomisiin, psykososiaalisiin ja terveydentilaa kuvaaviin muuttujiin, mutta pituuden määräytymiseen vaikuttavat geenit ovat pitkälti tuntemattomia toistaiseksi. Tässä väitöskirjatyössä pyrittiin paikantamaan pituuteen vaikuttavia kromosomialueita perimänlaajuisen kytkentäanalyysin avulla hyödyntäen poikkeuksellisen laajoja perheaineistoja. Lisäksi kytkeytyneiltä kromosomialueilta pyrittiin tunnistamaan assosiaatioanalyysin keinoin näillä alueilla sijaitsevia geenimuotoja, jotka vaikuttavat ihmisten välisiin pituuseroihin. Väitöskirjatyö koostui kolmesta osatyöstä, joissa kussakin hyödynnettiin suurta perheaineistoa: 1) FinnHeight, joka käsitti 1417 henkilöä 277 suomalaisesta perheestä, 2) EUHeight, joka sisälsi yhteensä 8450 henkilöä 3817 australialaisesta, tanskalaisesta, suomalaisesta, ruotsalaisesta ja englantilaisesta kaksosperheestä sekä 3) USHeight joka koostui yhteensä 9371 henkilöä 3032 yhdysvaltalaisesta perheestä. Tutkimuksen merkittävin tulos havaittiin ensimmäisessä osatyössä, jossa osoitettiin tilastollisesti merkitsevä kytkentä kromosomialueelle 1p21. Toisessa ja kolmannessa osatyössä puolestaan havaittiin usean kromosomialueen kytkeytyvän pituuteen, joista merkittävimmät olivat 8q21 ja 15q25. Kromosomialueen 1p21 jatkotutkimukset osoittivat alueella sijaitsevan kollageeni 11-alfa-1 (COL11A1) geenin assosioituvan pituuteen. Tämä assosiaatio toistettiin laajassa, 6542 yksilön suomalaisessa väestöaineistossa (Terveys 2000), jossa kyseisen geenimuodon suhteen samanperintäiset miehet olivat 1,1 cm ja naiset 0,6 cm pidempiä verrokkeihin nähden. Tässä tutkimuksessa paikannettiin ja tunnistettiin pituuteen vaikuttavan geenimuoto COL11A1-geenissä, joka selittää 0,1 % pituuden kokonaisvaihtelusta suomalaisväestössä. Lisäksi tutkimuksessa osoitettiin, että erityiset aineiston valikointitavat kuten sukupuolten, kaksosparien ja etnisten ryhmien erillisanalyysit voivat lisätä kytkentäanalyysin voimaa merkittävästi. Tutkimuksen merkittävin geenilöydös COL11A1-geenissä antaa myös viitteitä siitä, että vaikka suurin osa pituuden vaihtelusta on geneettisten tekijöiden määräämää, on todennäköistä, että tällaisia tekijöitä on hyvin suuri määrä ja kunkin yksittäinen geenimuodon vaikutus yksilön pituuteen on erittäin pieni

Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach.

Mineral contents in bovine muscle can affect meat quality, growth, health, and reproductive traits. To better understand the genetic basis of this phenotype in Nelore (Bos indicus) cattle, we analysed genome-wide mRNA and miRNA expression data from 114 muscle samples. The analysis implemented a new application for two complementary algorithms: the partial correlation and information theory (PCIT) and the regulatory impact factor (RIF), in which we included the estimated genomic breeding values (GEBVs) for the phenotypes additionally to the expression levels, originally proposed for these methods. We used PCIT to determine putative regulatory relationships based on significant associations between gene expression and GEBVs for each mineral amount. Then, RIF was adopted to determine the regulatory impact of genes and miRNAs expression over the GEBVs for the mineral amounts. We also investigated over-represented pathways, as well as pieces of evidences from previous studies carried in the same population and in the literature, to determine regulatory genes for the mineral amounts. For example, NOX1 expression level was positively correlated to Zinc and has been described as Zinc-regulated in humans. Based on our approach, we were able to identify genes, miRNAs and pathways not yet described as underlying mineral amount. The results support the hypothesis that extracellular matrix interactions are the core regulator of mineral amount in muscle cells. Putative regulators described here add information to this hypothesis, expanding the knowledge on molecular relationships between gene expression and minerals.Article: 8436

Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked DownloadBack pain is a common and debilitating disorder with largely unknown underlying biology. Here we report a genome-wide association study of back pain using diagnoses assigned in clinical practice; dorsalgia (119,100 cases, 909,847 controls) and intervertebral disc disorder (IDD) (58,854 cases, 922,958 controls). We identify 41 variants at 33 loci. The most significant association (ORIDD = 0.92, P = 1.6 × 10-39; ORdorsalgia = 0.92, P = 7.2 × 10-15) is with a 3'UTR variant (rs1871452-T) in CHST3, encoding a sulfotransferase enzyme expressed in intervertebral discs. The largest effects on IDD are conferred by rare (MAF = 0.07 - 0.32%) loss-of-function (LoF) variants in SLC13A1, encoding a sodium-sulfate co-transporter (LoF burden OR = 1.44, P = 3.1 × 10-11); variants that also associate with reduced serum sulfate. Genes implicated by this study are involved in cartilage and bone biology, as well as neurological and inflammatory processes.European Commission European Commission Joint Research Centre Novo Nordisk Foundation Novocure Limite

Epigenetic and integrative cross-omics analyses of cerebral white matter hyperintensities on MRI

Cerebral white matter hyperintensities on MRI are markers of cerebral small vessel disease, a major risk factor for dementia and stroke. Despite the successful identification of multiple genetic variants associated with this highly heritable condition, its genetic architecture remains incompletely understood. More specifically, the role of DNA methylation has received little attention. We investigated the association between white matter hyperintensity burden and DNA methylation in blood at approximately 450,000 CpG sites in 9,732 middle-aged to older adults from 14 community-based studies. Single-CpG and region-based association analyses were carried out. Functional annotation and integrative cross-omics analyses were performed to identify novel genes underlying the relationship between DNA methylation and white matter hyperintensities. We identified 12 single-CpG and 46 region-based DNA methylation associations with white matter hyperintensity burden. Our top discovery single CpG, cg24202936 (P = 7.6 × 10-8), was associated with F2 expression in blood (P = 6.4 × 10-5), and colocalized with FOLH1 expression in brain (posterior probability =0.75). Our top differentially methylated regions were in PRMT1 and in CCDC144NL-AS1, which were also represented in single-CpG associations (cg17417856 and cg06809326, respectively). Through Mendelian randomization analyses cg06809326 was putatively associated with white matter hyperintensity burden (P = 0.03) and expression of CCDC144NL-AS1 possibly mediated this association. Differentially methylated region analysis, joint epigenetic association analysis, and multi-omics colocalization analysis consistently identified a role of DNA methylation near SH3PXD2A, a locus previously identified in genome-wide association studies of white matter hyperintensities. Gene set enrichment analyses revealed functions of the identified DNA methylation loci in the blood-brain barrier and in the immune response. Integrative cross-omics analysis identified 19 key regulatory genes in two networks related to extracellular matrix organization, and lipid and lipoprotein metabolism. A drug repositioning analysis indicated antihyperlipidemic agents, more specifically peroxisome proliferator-activated receptor alpha, as possible target drugs for white matter hyperintensities. Our epigenome-wide association study and integrative cross-omics analyses implicate novel genes influencing white matter hyperintensity burden, which converged on pathways related to the immune response and to a compromised blood brain barrier possibly due to disrupted cell-cell and cell-extracellular matrix interactions. The results also suggest that antihyperlipidemic therapy may contribute to lowering risk for white matter hyperintensities possibly through protection against blood brain barrier disruption

The impact on meat quality of strategies to improve feed conversion efficiency in pigs and the functional networks underpinning the relationship

Feed efficiency (FE) is defined as a measure of efficiency in converting metabolizable energy acquired from macronutrients into body mass. The overall aims of this thesis were to identify genomic regions associated with FE in a commercial line of Maxgro boars, to evaluate the molecular and phenotypic relationship between FE and meat quality in Maxgro x (German Landrace x Large White) pigs and to investigate the molecular mechanisms contributing to differences in FE, in liver, fat and skeletal muscle tissue. Firstly, 952 boars having measures of FE traits were genotyped and used for a genome-wide association study. Most of the quantitative trait loci identified by this method were described for the first time, although some of them were located not far from previously associated genomic regions. Secondly, three metabolically important tissues, including muscle, adipose and liver were analysed. Significant differences in meat traits such as sensory profile, texture and cook loss suggest a minor impairment of meat quality from high-FE pigs. This group also exhibited leaner carcasses and greater muscle content. Ontology analysis predicted a more efficient immune defence in the muscle of high-FE pigs, which may indicate that these animals are also more efficient in conserving resources for growth. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the altered post-mortem muscle pH profiles between FE groups. Moreover, differences in amino acid metabolism may influence growth in FE-divergent muscle, whereas decreased degradation of fibroblasts could impact on collagen turnover and alter tenderness of meat. Transcriptomic profiling of adipose tissue of FE-divergent pigs suggested the establishment of a dense extracellular matrix and inhibition of capillary formation might be underlying mechanisms to achieve suppressed adipogenesis. Furthermore, gene expression patterns in the liver of high-FE pigs suggested improved hepatic absorption of carbohydrates and cholesterol, and enhanced reverse cholesterol transport. The liver of high-FE pigs may be characterised by higher protein turnover and increased epithelial cell differentiation, whilst enhanced quantity of invariant natural killer T-cells and viability of natural killer cells could induce a faster and more effective hepatic response to inflammatory stimuli.Strategien zur Verbesserung der Futterverwertung bei Schweinen und ihre Auswirkungen auf die Fleischqualität sowie Einblicke in die funktionellen Netzwerke, die dieser Beziehung zugrunde liegen Die Futterverwertung (FE) beschreibt die Effektivität der Umwandlung von metabolisierbarer Energie aus Makronährstoffen in Körpermasse. Die übergeordneten Ziele dieser Arbeit waren genomische Regionen zu bestimmen, die mit der Ausprägung von FE-Merkmalen in einer kommerziellen Linie von Maxgro Ebern in Zusammenhang stehen; molekulare und phänotypische Beziehung zwischen FE und Fleischqualität in einer Maxgro x (German Landrace x Large White) Population aufzuzeigen; und zugrundeliegende molekulare Mechanismen in drei FE-relevanten Geweben zu identifizieren. Im ersten Teil der Studie wurden 952 FE-getestete Eber genotypisiert und im Rahmen einer genomweiten Assoziationsstudie analysiert. Die meisten der mit dieser Methode identifizierten Quantitative Trait Loci wurden erstmals beschrieben, obwohl einige von ihnen in der Nähe von zuvor assoziierten genomischen Regionen lagen. Der zweite Teil dieser Dissertation betrachtet Muskel-, Fett- und Lebergewebe. Signifikante Unterschiede in den Fleischmerkmalen, wie zum Beispiel von sensorischen Profilen, Fleischtextur und Kochverlust, deuten auf eine geringfügige Verminderung der Fleischqualität bei Schweinen mit hoher FE hin. Andererseits wies diese Gruppe magerere Schlachtkörper und einen höheren Muskelanteil auf. Die Analyse der Genontologie prognostizierte eine erhöhte Effizienz der Immunabwehr im Muskel von Schweinen mit hoher FE, was darauf hindeuten könnte, dass diese Tiere auch effizienter in ihrer Ressourcennutzung für Wachstumsprozesse sind. Verschiebungen in der muskulären Umwandlung von Kohlenhydraten zu Glukose zwischen FE-divergenten Tieren wurden auch auf Ebene der post-mortalen pH-Profile zwischen den Gruppen abgebildet. Darüber hinaus könnten Unterschiede im Aminosäurestoffwechsel das Muskelwachstum beeinflussen, während ein verminderter Fibroblastenabbau den Kollagenumsatz und die Zartheit des Fleisches beeinflussen kann. Transkriptionelle Unterschiede im Fettgewebe FE-divergenter Schweine implizieren, dass die Bildung einer dichten extrazellulären Matrix und die Hemmung der Kapillarbildung grundlegende Mechanismen sein könnten, um die Adipogenese zu unterdrücken. Die Analyse der hepatischen Genontologie deutete auf eine verbesserte Aufnahme von Kohlenhydraten und Cholesterin sowie einen verbesserten Rücktransport von Cholesterin aus der Peripherie in Schweinen mit hoher FE hin. Zudem implizieren die Ergebnisse Unterschiede im Proteinumsatz und in der Reaktion auf Entzündungsreize

Proceedings...

The integration of national and international researchers is extremely important for the dissemination and perpetuation of knowledge in several areas of scientific research. The "Ist workshop on omics strategies applied to livestock science" aimed to promote discussion and experience exchange on innovative subjects and methods in livestock, addressing issues such as omics technologies for system biology, animal breeding, and genomic data integration for complex traits like meat quality and feed efficiency. This event was organized by the partnership between the College of Agriculture "Luiz de Queiroz" (ESALQ/USP) and the Brazilian Agricultural Research Corporation (EMBRAPA) Southeast Livestock Center, coordinated by Prof. Dr. Luiz Lehmann Coutinho, Dr. Luciana C. A. Regitano, Prof. Dr. Gerson Barreto Mourão and Dr. Adhemar Zerlotini Neto. The event took place in the city of Piracicaba/SP on April 24th - 26th, 2017. To attend these goals national and international speakers from partner institutions recognized in their areas of activity were invited, which enabled fruitful discussions on these themes, prompting new ideas for future research.bitstream/item/170582/1/Documentos125.pdfEditores: Luiz Lehmann Coutinho, ESALQ/USP; Luciana Correia de Almeida Regitano, Embrapa Pecuária Sudeste; Gerson Barreto Mourão, ESALQ/USP; Aline Silva Mello Cesar, ESALQ/USP; Bárbara Silva Vignato, FZEA/USP; Mirele Daiana Poleti, ESALQ/USP; Wellison Jarles da Silva Diniz, UFSCar

Analysis of the progeny of sibling matings reveals regulatory variation impacting the transcriptome of immune cells in commercial chickens

There is increasing recognition that the underlying genetic variation contributing to complex traits influences transcriptional regulation and can be detected at a population level as expression quantitative trait loci. At the level of an individual, allelic variation in transcriptional regulation of individual genes can be detected by measuring allele-specific expression in RNAseq data. We reasoned that extreme variants in gene expression could be identified by analysis of inbred progeny with shared grandparents. Commercial chickens have been intensively selected for production traits. Selection is associated with large blocks of linkage disequilibrium with considerable potential for co-selection of closely linked “hitch-hiker alleles” affecting traits unrelated to the feature being selected, such as immune function, with potential impact on the productivity and welfare of the animals. To test this hypothesis that there is extreme allelic variation in immune-associated genes we sequenced a founder population of commercial broiler and layer birds. These birds clearly segregated genetically based upon breed type. Each genome contained numerous candidate null mutations, protein-coding variants predicted to be deleterious and extensive non-coding polymorphism. We mated selected broiler-layer pairs then generated cohorts of F2 birds by sibling mating of the F1 generation. Despite the predicted prevalence of deleterious coding variation in the genomic sequence of the founders, clear detrimental impacts of inbreeding on survival and post-hatch development were detected in only one F2 sibship of 15. There was no effect on circulating leukocyte populations in hatchlings. In selected F2 sibships we performed RNAseq analysis of the spleen and isolated bone marrow-derived macrophages (with and without lipopolysaccharide stimulation). The results confirm the predicted emergence of very large differences in expression of individual genes and sets of genes. Network analysis of the results identified clusters of co-expressed genes that vary between individuals and suggested the existence of trans-acting variation in the expression in macrophages of the interferon response factor family that distinguishes the parental broiler and layer birds and influences the global response to lipopolysaccharide. This study shows that the impact of inbreeding on immune cell gene expression can be substantial at the transcriptional level, and potentially opens a route to accelerate selection using specific alleles known to be associated with desirable expression levels

Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs

Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype∗weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.</p

Developing computational tools and datasets to investigate the genomic loci associated with disease

The majority of genetic variants associated with complex diseases are located in non-coding, regulatory regions of the genome. Understanding the genetic mechanisms of the progression of these diseases has been largely advanced by sequencing-based genomic techniques including RNA-seq, ChIP-seq, Hi-C, genome-wide association studies (GWAS), and Quantitative Trait Locus (QTL) mapping. However, the genetic underpinnings of disease have been difficult to interpret largely because (1) currently available visualization software lacks the ability to efficiently and programmatically integrate large volumes of complex multi-omic data and (2) there are few datasets in disease-relevant cell types in which genomic changes are tracked in response to disease-specific stimuli. In the first part of this work I describe plotgardener, a new R programmatic library for efficiently and reproducibly plotting publication-quality, multi-panel genomic figures. Plotgardener provides customizable genomic plotting and annotation functions that allows users to size and arrange plots in precisely-defined coordinate systems based upon user-defined units of measurement. I include example use cases with plotgardener, both with genomic data and ggplot2 objects, and also have extensively documented and freely available code for the package through Bioconductor and GitHub. I then go on to create and investigate the first response allelic imbalance (AI) and eQTL (reQTL) datasets using an ex vivo model of osteoarthritis (OA) whereby chondrocytes are stimulated with fibronectin fragment (FN-f), a known OA trigger. AI analysis revealed 55 unique genetic variants exhibiting AI at 58 positional genes only after FN-f treatment, with some of these genes exhibiting differential expression. reQTL mapping identified 384 eGenes specific to FN-f treated samples, and colocalization of identified reQTLs with GWAS of various OA phenotypes revealed one robust colocalization of a reQTL with multiple OA phenotypes. I also use plotgardener to visualize these datasets within the context of the genes and linkage disequilibrium (LD) structure of the region. Overall, these studies have resulted in the creation of a broadly applicable genomic visualization tool and novel datasets to provide critical insights into the genetic basis of osteoarthritis.Doctor of Philosoph