Application of an in silico approach identifies a genetic locus within ITGB2, and its interactions with HSPG2 and FGF9, to be associated with anterior cruciate ligament 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. All known human genes were assessed through the model to identify potential new risk genes for anterior cruciate ligament (ACL) ruptures and Achilles tendinopathy (AT). Genes were prioritised and 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 control individuals (CON). After gene filtering, 3376 genes, including 411 genes identified through previous 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/T and FGF9:rs2274296C/T. The rs2230528 CC genotype was over-represented in the CON group compared to ACL-R (p < 0.001) and ACL-NON (p < 0.001) and the TT genotype and T allele were over-represented in the ACL-R group and ACL-NON compared to CON (p < 0.001) group. Several significant differences in distributions were noted for the gene-gene interactions: (HSPG2:rs2291826, rs2291827 and ITGB2:rs2230528) and (ITGB2:rs2230528 and FGF9:rs2297429). This study substantiates the efficiency of using a prior knowledge-driven in silico approach to identify candidate genes linked to tendon and ACL injuries. Our biomedical knowledge graph identified and, with further testing, highlighted novel associations of the ITGB2 gene which has not been explored in a genetic case control association study, with ACL rupture risk. We thus recommend a multistep approach including bioinformatics in conjunction with next generation sequencing technology to improve the discovery potential of genomics technologies in musculoskeletal soft tissue injuries.HighlightsA biomedical knowledge graph was modelled for musculoskeletal soft tissue injuries to efficiently identify candidate genes for genetic susceptibility analyses.The biomedical knowledge graph and sequencing data identified potential biologically relevant variants to explore susceptibility to common tendon and ligament injuries. Specifically genetic variants within the ITGB2 and FGF9 genes were associated with ACL risk.Novel allele combinations (HSPG2-ITGB2 and ITGB2-FGF9) showcase the potential effect of ITGB2 in influencing risk of ACL rupture.

The effect of NucleoSpin® Forensic Filters on DNA recovery from trace DNA swabs.

Forensic DNA profiling is a globally accepted method for human identification, however, obtaining full DNA profiles from trace DNA can be challenging. The optimal recovery of DNA from trace DNA swabs is therefore crucial. Methods for extracting DNA from swabs often make use of a spin basket combined with a centrifugation step, to enhance the release of cells from the swab prior to DNA extraction. The NucleoSpin® Forensic Filter (Macherey-Nagel, Düren) is a type of spin basket, but it has not been thoroughly assessed on trace DNA samples. This study aimed to assess if the inclusion of the NucleoSpin® Forensic Filter significantly improved DNA recovery and DNA profiling success from cotton and flocked swabs used to collect trace DNA and buccal cells (control). Buccal cells and trace DNA samples were collected from 25 volunteers using each swab type (cotton and flocked) in duplicate. DNA was extracted from the samples using the NucleoSpin® DNA Forensic kit, one set with, and the other set without, NucleoSpin® Forensic Filters. DNA concentration was assessed using real time PCR, and DNA profiling was done using the PowerPlex® ESX 16 system. The inclusion of the NucleoSpin® Forensic Filters significantly improved DNA concentration for buccal cells that were collected using flocked swabs (p = 0.035). However, no significant differences were noted for trace DNA samples for either swab type. There was also no significant difference in DNA profiling success when NucleoSpin® Forensic Filters were used, regardless of swab and sample type. These results may be helpful for laboratories that are considering the NucleoSpin® Forensic Filters in the DNA extraction workflow, particularly for trace DNA samples.

Matrix Metalloproteinase Genes (MMP1, MMP10, MMP12) on Chromosome 11q22 and the Risk of Non-Contact Anterior Cruciate Ligament Ruptures.

BACKGROUND: Sequence variants within the matrix metalloproteinases genes remain plausible biological candidates for further investigation of anterior cruciate ligament (ACL) rupture risk. The aim of the present study was to establish whether variants within the MMP1 (rs1799750, ->G), MMP10 (rs486055, C > T) and MMP12 (rs2276109, T > C) genes were associated with non-contact ACL rupture in a Polish cohort. METHODS: The unrelated, self-reported Polish Caucasian participants consisted of 228 (157 male) individuals with primary non-contact ACL rupture and 202 (117 male) participants without any history of ACL rupture. All samples were genotyped in duplicate using the Applied Biosystems TaqMan® methodology. The statistical analyses were involved in determining the distribution of genotype and allele frequencies for the investigated polymorphisms between the diagnostic groups. Furthermore, pseudo-haplotypes were constructed to assess possible gene-gene interactions. RESULTS: All genotype frequencies in the ACL rupture and control groups conformed to Hardy Weinberg Equilibrium expectations. None of the polymorphisms were associated with risk of non-contact ACL rupture under the codominant, dominant, recessive and over-dominant genetic models. Likewise, no genotype-genotype combinations inferred as "haplotypes" as a proxy of gene-gene interactions were associated with the risk of non-contact ACL ruptures. CONCLUSIONS: Despite the fact that the current study did not support existing evidence suggesting that variants within the MMP1, MMP10, and MMP12 genes influence non-contact ACL rupture risk, future work should include high-throughput sequencing technologies to identify potential targeted polymorphisms to fully characterize the 11q22 region with susceptibility to non-contact ACL rupture susceptibility in a Polish cohort.

Functional COL1A1 variants are associated with the risk of acute musculoskeletal soft tissue injuries.

Studies have reported the association of the COL1A1 Sp1 binding site variant (rs1800012) with the risk of acute musculoskeletal soft tissue injuries. Interaction with the COL1A1 promoter variant (rs1107946) has also been proposed to modulate acute injury risk. Conversely, neither of these loci have been associated with chronic musculoskeletal soft tissue phenotypes. Therefore, the primary aim of this study involved characterizing these variants in a cohort of participants with chronic Achilles tendinopathy. Second, this study aimed to support the contribution of the rs1107946 and rs1800012 variants to the profile predisposing for acute musculoskeletal soft tissue injuries including Achilles tendon and anterior cruciate ligament (ACL) ruptures. A hypothesis-driven association study was conducted. In total, 295 control participants, 210 participants with clinically diagnosed Achilles tendinopathy, and 72 participants with Achilles tendon ruptures recruited independently from South Africa and the United Kingdom were genotyped for the prioritized variants. In addition, a cohort including 232 control participants and 234 participants with surgically diagnosed ACL ruptures was also analyzed. Although no associations were observed in the recruited cohorts, the rare rs1800012 TT genotype was associated with decreased ACL injury risk when the results from the current study were combined with that from previously published studies (P = .040, OR: 2.8, 95% CI: 1.0-11.0). In addition, the G-T (rs1107946-rs1800012) inferred haplotype was associated with decreased risk for Achilles tendon ruptures. These results support previous observations and reiterate the heterogeneity of musculoskeletal phenlotypes whereby certain markers may be common to the predisposing profiles while others may be unique.

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.

The association of genes involved in the angiogenesis-associated signaling pathway with risk of anterior cruciate ligament rupture.

Angiogenesis-associated signaling is a fundamental component in the remodeling of the extracellular matrix in response to loading. Genes encoding protein components within this signaling cascade are therefore suitable candidates for investigation into ACL injury susceptibility: namely, vascular endothelial growth factor A isoform (VEGFA), kinase insert-domain receptor (KDR), nerve growth factor (NGF), and hypoxia inducible factor-1α (HIF1A). A case-control genetic association study was conducted on 227 asymptomatic control participants and 227 participants with surgically diagnosed ACL ruptures of which 126 participants reported a non-contact mechanism of rupture. All participants were genotyped for seven polymorphisms within the four genes. The VEGFA rs699947 CC genotype (p=0.010, OR: 1.92, 95% CI: 1.17-3.17) was significantly over-represented within participants with non-contact ACL ruptures. The VEGFA rs1570360 GA genotype was significantly over-represented in the CON group (p=0.007, OR: 1.70, 95% CI: 1.16-2.50). Furthermore, the KDR rs2071559 GA genotype was significantly over-represented in the female controls (p=0.023, OR: 2.16, 95% CI: 1.11-4.22). Inferred haplotype analyses also implicated genomic regions spanning the VEGFA and KDR genes. These novel findings suggest that regions within VEGFA and KDR may be implicated in the pathophysiology of ACL ruptures; highlighting the potential biological significance of angiogenesis-associated signaling in the aetiology of ACL ruptures.