Collagen gene sequence variants in exercise-related traits

Collagens are major structural proteins of tendons, ligaments and other components of musculoskeletal tissues. Rare mutations in many of the genes, which encode for the collagen α-chains, result in serious musculoskeletal disorders, highlighting the importance of this protein family in the normal structure an d function of musculoskeletal tissues. Since these rare mutations cause severe disorders, it has been proposed that a lack of biological redundancy exists within the collagen fibril, and that collagen-encoding genes are therefore ideal candidates for association with less severe exercise-related traits. This review identifies a number of collagen gene variants which are associated with various exercise-related traits. Based on the evidence outlined in this review, we propose that a general genetic continuum exists for collagen genes and their associated traits. At one end of this general continuum model, a single mutation within one or more collagen genes will result in severe Mendelian disorders. At the other end of the continuum, functional variants within these collagen genes collectively contribute to the aetiology of anomalous multifactorial connective tissue traits, which arise as a result of the interaction of genetic and non-genetic factors which modulate physiological responses to environmental stimuli

Training volume and injury incidence in a professional rugby union team

Objective. To describe the incidence of injuries in a professional rugby team, and to identify any associations between injury rates and training volume. Methods. This retrospective, descriptive study included all injuries diagnosed as grade 1 and above in a South African Super 12 rugby team. Injury incidence and injury rates were calculated and compared with training volume and hours of match play. Results. Thirty-eight male rugby players were injured during the study period. The total number of annual injuries decreased from 50 (2002) to 38 (2004) (χ2=0.84, p=0.36). The number of new injuries showed a similar trend (χ2=2.81, p=0.09), while the number of recurring injuries increased over the 3-year period. There was a tendency for total in-season injury rates to decrease over the 3 years (χ2=2.89, p=0.09). The pre-season injury rate increased significantly over the 3 years (χ2=12.7, p<0.01), coupled with a reduction in training exposure over the pre-season phase. Conclusions. One has to be cognisant of the balance between performance improvement and injury risk when designing training programmes for elite rugby players. Although the reduction in training volume was associated with a slight reduction in the number of acute injuries and in-season injury rates over the three seasons, the performance of the team changed from 3rd to 7th (2002 and 2004, respectively). Further studies are required to determine the optimal training necessary to improve rugby performance while reducing injury rates

Application of anin silicoapproach identifies a genetic locus withinITGB2,and itsinteractions withHSPG2 and FGF9,to be associated with anterior cruciateligament rupture risk

We developed a Biomedical Knowledge Graph model that is phenotype and biological function-aware through integrating knowledge from multiple domains in a Neo4j, graph database. Allknown human genes were assessed through the model to identify potential new risk genes foranterior cruciate ligament (ACL) ruptures and Achilles tendinopathy (AT). Genes were prioritisedand explored in a case–control study comparing participants with ACL ruptures (ACL-R),including a sub-group with non-contact mechanism injuries (ACL-NON), to uninjured controlindividuals (CON). After genefiltering, 3376 genes, including 411 genes identified throughprevious whole exome sequencing, were found to be potentially linked to AT and ACL ruptures.Four variants were prioritised:HSPG2:rs2291826A/G,HSPG2:rs2291827G/A,ITGB2:rs2230528C/TandFGF9:rs2274296C/T. The rs2230528 CC genotype was over-represented in the CON groupcompared to ACL-R (p< 0.001) and ACL-NON (p< 0.001) and the TT genotype and T allele wereover-represented in the ACL-R group and ACL-NON compared to CON (p< 0.001) group. Severalsignificant differences in distributions were noted for the gene-gene interactions: (HSPG2:rs2291826, rs2291827 andITGB2:rs2230528) and (ITGB2:rs2230528 andFGF9:rs2297429)

Semantic interrogation of a multi knowledge domain ontological model of tendinopathy identifies four strong candidate risk genes

Tendinopathy is a multifactorial syndrome characterised by tendon pain and thickening, and impaired performance during activity. Candidate gene association studies have identified genetic factors that contribute to intrinsic risk of developing tendinopathy upon exposure to extrinsic factors. Bioinformatics approaches that data-mine existing knowledge for biological relationships may assist with the identification of candidate genes. The aim of this study was to data-mine functional annotation of human genes and identify candidate genes by ontology-seeded queries capturing the features of tendinopathy. Our BioOntological Relationship Graph database (BORG) integrates multiple sources of genomic and biomedical knowledge into an on-disk semantic network where human genes and their orthologs in mouse and rat are central concepts mapped to ontology terms. The BORG was used to screen all human genes for potential links to tendinopathy. Following further prioritisation, four strong candidate genes (COL11A2, ELN, ITGB3, LOX) were identified. These genes are differentially expressed in tendinopathy, functionally linked to features of tendinopathy and previously implicated in other connective tissue diseases. In conclusion, cross-domain semantic integration of multiple sources of biomedical knowledge, and interrogation of phenotypes and gene functions associated with disease, may significantly increase the probability of identifying strong and unobvious candidate genes in genetic association studies

Exploring new genetic variants within col5a1 intron 4‐exon 5 region and tgf‐β family with risk of anterior cruciate ligament ruptures

Variants within genes encoding structural and regulatory elements of ligaments have been associated with musculoskeletal soft tissue injury risk. The role of intron 4‐exon 5 variants within the α1 chain of type V collagen (COL5A1) gene and genes of the transforming growth factor‐β (TGF‐β) family, TGFBR3 and TGFBI, was investigated on the risk of anterior cruciate ligament (ACL) ruptures. A case‐control genetic association study was performed on 210 control (CON) and 249 participants with surgically diagnosed ruptures (ACL), of which 147 reported a noncontact mechanism of injury (NON). Whole‐exome sequencing data were used to prioritize variants of potential functional relevance

Variants within the COMP and THBS2 genes are not associated with Achilles tendinopathy in a case-control study of South African and Australian populations

Cartilage oligomeric matrix protein is a structural protein of the extracellular matrix, while thrombospondin-2 is a matricellular protein involved in cell–matrix interactions. Recent studies have shown that genetic variation is a significant risk factor for Achilles tendinopathy, and the genes encoding cartilage oligomeric matrix protein (COMP) and thrombospondin-2 (THBS2) were identified as good candidate genes for association with Achilles tendinopathy. This study aimed to test the association of sequence variants within these candidate genes with the risk of Achilles tendinopathy in participants from South Africa (SA) and Australia (AUS). Three-hundred and forty (133 SA; 207 AUS) control participants with no history of Achilles tendinopathy and 178 (94 SA; 84 AUS) participants clinically diagnosed with Achilles tendinopathy were genotyped for five single nucleotide polymorphisms within the COMP and THBS2 genes in this case-control study. There was no difference in genotype distributions between control and tendinopathy groups for either the THBS2 variants rs9505888, rs6422747 and rs9283850, or the COMP variants rs730079 and rs28494505 in the SA and AUS populations. As the selection of COMP and THBS2 as candidate genes was hypothesis driven, based on biological function, the possibility that other variants within these genes are associated with Achilles tendinopathy cannot be excluded.Web of Scienc

Defining the molecular signatures of Achilles tendinopathy and anterior cruciate ligament ruptures: A whole-exome sequencing approach

Musculoskeletal soft tissue injuries are complex phenotypes with genetics being one of many proposed risk factors. Case-control association studies using the candidate gene approach have predominately been used to identify risk loci for these injuries. However, the ability to identify all risk conferring variants using this approach alone is unlikely. Therefore, this study aimed to further define the genetic profile of these injuries using an integrated omics approach involving whole exome sequencing and a customised analyses pipeline. The exomes of ten exemplar asymptomatic controls and ten exemplar cases with Achilles tendinopathy were individually sequenced using a platform that included the coverage of the untranslated regions and miRBase miRNA genes. Approximately 200 000 variants were identified in the sequenced samples. Previous research was used to guide a targeted analysis of the genes encoding the tenascin-C (TNC) glycoprotein and the α1 chain of type XXVII collagen (COL27A1) located on chromosome 9. Selection of variants within these genes were; however, not predetermined but based on a tiered filtering strategy. Four variants in TNC (rs1061494, rs1138545, rs2104772 and rs1061495) and three variants in the upstream COL27A1 gene (rs2567706, rs2241671 and rs2567705) were genotyped in larger Achilles tendinopathy and anterior cruciate ligament (ACL) rupture sample groups. The CC genotype of TNC rs1061494 (C/T) was associated with the risk of Achilles tendinopathy (p = 0.018, OR: 2.5 95% CI: 1.2–5.1). Furthermore, the AA genotype of the TNC rs2104772 (A/T) variant was significantly associated with ACL ruptures in the female subgroup (p = 0.035, OR: 2.3 95% CI: 1.1–5.5). An inferred haplotype in the TNC gene was also associated with the risk of Achilles tendinopathy. These results provide a proof of concept for the use of a customised pipeline for the exploration of a larger genomic dataset. This approach, using previous research to guide a targeted analysis of the data has generated new genetic signatures in the biology of musculoskeletal soft tissue injuries.IS

Complete genome sequence of Candidatus Ruthia magnifica

The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Mollusca) is a member of the Vesicomyidae. Species within this family form symbioses with chemosynthetic Gammaproteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a rudimentary gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. The C. magnifica symbiont, Candidatus Ruthia magnifica, was the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced (Newton et al. 2007). Here we expand upon the original report and provide additional details complying with the emerging MIGS/MIMS standards. The complete genome exposed the genetic blueprint of the metabolic capabilities of the symbiont. Genes which were predicted to encode the proteins required for all the metabolic pathways typical of free-living chemoautotrophs were detected in the symbiont genome. These include major pathways including carbon fixation, sulfur oxidation, nitrogen assimilation, as well as amino acid and cofactor/vitamin biosynthesis. This genome sequence is invaluable in the study of these enigmatic associations and provides insights into the origin and evolution of autotrophic endosymbiosis