Osteoarthritis affects over 300 million people worldwide. Here, we conduct a genome-wide association study meta-analysis across 826,690 individuals (177,517 with osteoarthritis) and identify 100 ...independently associated risk variants across 11 osteoarthritis phenotypes, 52 of which have not been associated with the disease before. We report thumb and spine osteoarthritis risk variants and identify differences in genetic effects between weight-bearing and non-weight-bearing joints. We identify sex-specific and early age-at-onset osteoarthritis risk loci. We integrate functional genomics data from primary patient tissues (including articular cartilage, subchondral bone, and osteophytic cartilage) and identify high-confidence effector genes. We provide evidence for genetic correlation with phenotypes related to pain, the main disease symptom, and identify likely causal genes linked to neuronal processes. Our results provide insights into key molecular players in disease processes and highlight attractive drug targets to accelerate translation.
Display omitted
•A multicohort study identifies 52 previously unknown osteoarthritis genetic risk variants•Similarities and differences in osteoarthritis genetic risk depend on joint sites•Osteoarthritis genetic components are associated with pain-related phenotypes•High-confidence effector genes highlight potential targets for drug intervention
A multicohort genome-wide association meta-analysis of osteoarthritis highlights the impact of joint site types on the features of genetic risk variants and the link between osteoarthritis genetics and pain-related phenotypes, pointing toward potential targets for therapeutic intervention.
Systematic data management and controlled data sharing aim at increasing reproducibility, reducing redundancy in work, and providing a way to efficiently locate complementing or contradicting ...information. One method of achieving this is collecting data in a central repository or in a location that is part of a federated system and providing interfaces to the data. However, certain data, such as data from biobanks or clinical studies, may, for legal and privacy reasons, often not be stored in public repositories. Instead, we describe a metadata cataloguing system and a software suite for reporting the presence of data from the life sciences domain. The system stores three types of metadata: file information, file provenance and data lineage, and content descriptions. Our software suite includes both graphical and command line interfaces that allow users to report and tag files with these different metadata types. Importantly, the files remain in their original locations with their existing access-control mechanisms in place, while our system provides descriptions of their contents and relationships. Our system and software suite thereby provide a common framework for cataloguing and sharing both public and private data. Database URL: http://bigr.medisin.ntnu.no/data/eGenVar/.
The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the ...humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150–500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here, we assess whether ancestry at mitochondrially targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome.
Display omitted
•Using SNP data, we find evidence for mitonuclear coevolution in hybrid African cattle•Increased taurine ancestry at mitochondrially targeted nuclear genes in several breeds•Observed for genes encoding proteins that interact with mtDNA-encoded proteins•Our results support the hypothesis of mitonuclear incompatibility in African cattle
Ecology, Biological sciences, Genetics, Genomics, Evolutionary biology
The objective of this study was to aggregate data for the first genomewide association study meta-analysis of cluster headache, to identify genetic risk variants, and gain biological insights.
A ...total of 4,777 cases (3,348 men and 1,429 women) with clinically diagnosed cluster headache were recruited from 10 European and 1 East Asian cohorts. We first performed an inverse-variance genomewide association meta-analysis of 4,043 cases and 21,729 controls of European ancestry. In a secondary trans-ancestry meta-analysis, we included 734 cases and 9,846 controls of East Asian ancestry. Candidate causal genes were prioritized by 5 complementary methods: expression quantitative trait loci, transcriptome-wide association, fine-mapping of causal gene sets, genetically driven DNA methylation, and effects on protein structure. Gene set and tissue enrichment analyses, genetic correlation, genetic risk score analysis, and Mendelian randomization were part of the downstream analyses.
The estimated single nucleotide polymorphism (SNP)-based heritability of cluster headache was 14.5%. We identified 9 independent signals in 7 genomewide significant loci in the primary meta-analysis, and one additional locus in the trans-ethnic meta-analysis. Five of the loci were previously known. The 20 genes prioritized as potentially causal for cluster headache showed enrichment to artery and brain tissue. Cluster headache was genetically correlated with cigarette smoking, risk-taking behavior, attention deficit hyperactivity disorder (ADHD), depression, and musculoskeletal pain. Mendelian randomization analysis indicated a causal effect of cigarette smoking intensity on cluster headache. Three of the identified loci were shared with migraine.
This first genomewide association study meta-analysis gives clues to the biological basis of cluster headache and indicates that smoking is a causal risk factor. ANN NEUROL 2023;94:713-726.
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 (OR
= 0.92, P = 1.6 × 10
; OR
= 0.92, P = 7.2 × 10
) 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
); 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.
The reactions of a series of Pd(II) methyl compounds of general formula LPd(NCCH3)CH3, where L is a bulky phenoxydiazene or phenoxyaldimine ligand with the polar olefin acrylonitrile (AN), are ...reported. The compounds react with an excess of AN to give the products of 2,1 insertion into the Pd−Me bond, yielding dimers and/or trimers which feature bridging α-cyano groups. The reactions were studied by low temperature 1H NMR spectroscopy, revealing an initial formation of compounds featuring N-bound AN, which isomerized to an (unobserved) π-bound species that rapidly underwent 2,1 insertion into the Pd−Me bond. Intermediate oligomeric complexes retaining a Pd−Me function were observed at low AN in these reactions. Under pseudo first-order conditions, k obs values of 8.5 × 10-5 to 2.68 × 10-3 M-1 (−22 °C to 10 °C, 100 equiv of AN) and activation parameters of ΔH ‡ = 14.4(5) kcal mol-1 and ΔS ‡ = −19(5) eu were obtained in one case. Comparison of the overall rates of insertion between two LPd(NCCH3)CH3, differing in the overall charge on the supporting ligand L, showed that the complex bearing a negatively charged ligand reacts with AN twice as fast as one with no anionic charge. The rates of insertion in both of these complexes are significantly faster than reported rates for analogous reactions in cationic Pd(II) derivatives, indicating that increasing the negative charge on the complex enhances the rate of AN insertion. These results provide fundamental mechanistic insights into a crucial reaction for incorporation of polar comonomers into alpha olefins via a coordination polymerization mechanism.
Chronic pain is often present at more than one anatomical location, leading to chronic overlapping pain conditions. Whether chronic overlapping pain conditions represent a distinct pathophysiology ...from the occurrence of pain at only one site is unknown. Using genome-wide approaches, we compared genetic determinants of chronic single-site versus multisite pain in the UK Biobank. We found that different genetic signals underlie chronic single-site and multisite pain with much stronger genetic contributions for the latter. Among 23 loci associated with multisite pain, nine loci replicated in the HUNT cohort, with the DCC netrin 1 receptor (DCC) as the top gene. Functional genomics identified axonogenesis in brain tissues as the major contributing pathway to chronic multisite pain. Finally, multimodal structural brain imaging analysis showed that DCC is most strongly expressed in subcortical limbic regions and is associated with alterations in the uncinate fasciculus microstructure, suggesting that DCC-dependent axonogenesis may contribute to chronic overlapping pain conditions via corticolimbic circuits.
Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace ...their origins to a wolf population that expanded during the last glacial maximum (LGM)1–3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.
Display omitted
•Pleistocene Siberian wolves represent multiple extinct evolutionary lineages•Pleistocene wolves share ancestry with arctic dogs and some East Asian wolves•A Paleolithic dog specimen is genetically similar to other Pleistocene wolves
Ramos-Madrigal et al. sequence the genomes of four Pleistocene Siberian wolves, two of which have divergent cranial morphologies. These canids represent multiple extinct lineages that dwelled in Siberia >50 ka ago and at least until 14.1 ka ago and that contributed to the genetic ancestry of arctic dogs and some East Asian wolves.
Metastatic colorectal cancer (mCRC) frequently occurs in elderly patients. However, data from a geriatric tailored randomized trial about tolerance to and the efficacy of doublet chemotherapy (CT) ...with irinotecan in the elderly are lacking. The benefit of first-line CT intensification remains an issue in elderly patients.
Elderly patients (75+) with previously untreated mCRC were randomly assigned in a 2 × 2 factorial design (four arms) to receive 5-FU (5-fluorouracil)-based CT, either alone (FU: LV5FU2 or simplified LV5FU2) or in combination with irinotecan IRI: LV5FU2–irinotecan or simplified LV5FU2–irinotecan (FOLFIRI). The CLASSIC arm was defined as LV5FU2 or LV5FU2–irinotecan and the SIMPLIFIED arm as simplified LV5FU2 or FOLFIRI. The primary end point was progression-free survival (PFS). Secondary end points were overall survival (OS), safety and objective response rate (ORR).
From June 2003 to May 2010, 71 patients were randomly assigned to LV5FU2, 71 to simplified LV5FU2, 70 to LV5FU2–irinotecan and 70 to FOLFIRI. The median age was 80 years (range 75–92 years). No significant difference was observed for the median PFS: FU 5.2 months versus IRI 7.3 months, hazard ratio (HR) = 0.84 (0.66–1.07), P = 0.15 and CLASSIC 6.5 months versus SIMPLIFIED 6.0 months, HR = 0.85 (0.67–1.09), P = 0.19. The ORR was superior in IRI (P = 0.0003): FU 21.1% versus IRI 41.7% and in CLASSIC (P = 0.04): CLASSIC 37.1% versus SIMPLIFIED 25.6%. Median OS was 14.2 months in FU versus 13.3 months in IRI, HR = 0.96 (0.75–1.24) and 15.2 months in CLASSIC versus 11.4 months in SIMPLIFIED, HR = 0.71 (0.55–0.92). More patients presented grade 3–4 toxicities in IRI (52.2% versus 76.3%).
In this elderly population, adding irinotecan to an infusional 5-FU-based CT did not significantly increase either PFS or OS. Classic LV5FU2 was associated with an improved OS compared with simplified LV5FU2.
NCT00303771.
PDF
