Field synopsis and synthesis of genetic association studies in osteoarthritis: the CUMAGAS-OSTEO information system

A combination of genome-wide association study and selection signature analysis dissects the genetic architecture underlying bone traits in chickens

The bones of chicken play an important role in supporting and protecting the body. The growth and development of bones have a substantial influence on the health and production performance in chickens. However, genetic architecture underlying chicken bone traits is not well understood. The objectives of this study are to dissect the genetic basis of bone traits in chickens and to identify valuable genes and genetic markers for chicken breeding. We performed a combination of genome-wide association study (GWAS) and selection signature analysis (fixation index values and nucleotide diversity ratios) in an F₂ crossbred experimental population with different genetic backgrounds (broiler × layer) to identify candidate genes and significant variants related to femur, shank, keel length, chest width, metatarsal claw weight, metatarsal length, and metatarsal circumference. A total of 545 individuals were genotyped based on the whole genome re-sequencing method (26 F₀ individuals were re-sequenced at 10 × coverage; 519 F₂ individuals were re-sequenced at 3 × coverage). A total of 2 028 112 single-nucleotide polymorphisms (SNPs) remained to carry out analysis after quality control and imputation. The integration of GWAS and selection signature analysis indicated that all significant SNPs responsible for bone traits were mainly localized on chicken chromosomes 1, 4, and 27. Finally, we identified 21 positional candidate genes that might regulate chicken bone growth and development, including LRCH1, RB1, FNDC3A, MLNR, CAB39L, FOXO1, LHFP, TRPC4, POSTN, SMAD9, RBPJ, PPARGC1A, SLIT2, NCAPG, NKX3-2, CPZ, SPOP, NGFR, SOST, ZNF652, and HOXB3. Additionally, an array of uncharacterized genes was identified. The findings provide an in-depth understanding of the genetic architecture of chicken bone traits and offer a molecular basis for applying genomics in practical chicken breeding.

Association of ADAM 12 polymorphisms with the risk of knee osteoarthritis: meta-analysis of 5048 cases and 6848 controls

Several studies have suggested the association between ADAM 12 polymorphisms and the risk of osteoarthritis (OA), but the results remained controversial. Therefore, we designed a meta-analysis to systematically evaluate the association on this issue. A literature search for eligible studies was conducted in PubMed, Web of Science and Google Scholar databases. The association between ADAM 12 polymorphisms and knee OA risk was calculated by odds ratios (ORs) and 95% confidence intervals (CIs). Study heterogeneity, sensitivity and publication bias analyses were also conducted. Ten articles covering 5048 cases and 6848 controls met our criteria for the final analysis. We found that the rs1871054 was significantly associated with the risk of knee OA (allele model OR 1.72, 95% CI 1.43-2.07, P < 0.001; additive model: OR 2.06, 95% CI 1.19-3.56, P = 0.010; dominant model: OR 2.45, 95% CI 1.85-3.25, P < 0.001; recessive model: OR 1.54, 95% CI 1.13-2.10, P = 0.007). rs1044122 was significantly associated with knee OA susceptibility in recessive model (OR 1.45, 95% CI 1.03-2.04, P = 0.031). For rs3740199 and rs1278279, no significant associations with knee OA were found. In the stratified analysis by gender, significant association was identified with the risk of knee OA for rs3740199 in men in allele model (OR 2.41, 95% CI 1.51-3.84, P < 0.001), dominant model (OR 2.68, 95% CI 1.17-6.14, P = 0.02) and recessive model (OR 3.51, 95% CI 1.68-7.36, P = 0.001), but not for additive model (OR 1.30, 95% CI 0.81-2.08, P = 0.28). This meta-analysis suggests that the ADAM 12 genetic polymorphisms rs1871054 and rs1044122 might be associated with risk of knee OA; rs3740199 might be associated with risk of knee OA in men. Further well-designed and large scale studies are warranted to validate these associations.

Millimeter Wave Treatment Inhibits Apoptosis of Chondrocytes via Regulation Dynamic Equilibrium of Intracellular Free Ca (2+)

The molecular mechanisms of TNF-α-induced apoptosis of chondrocyte and the role of Ca(2+) mediating the effects of MW on TNF-α-induced apoptosis of chondrocytes remained unclear. In this study, we investigated the molecular mechanism underlying inhibiting TNF-α-induced chondrocytes apoptosis of MW. MTT assay, DAPI, and flow cytometry demonstrated that MW significantly increased cell activity and inhibited chromatin condensation accompanying the loss of plasma membrane asymmetry and the collapse of mitochondrial membrane potential. Our results also indicated that MW reduced the elevation of [Ca(2+)] i in chondrocytes by LSCM. Moreover, MW suppressed the protein levels of calpain, Bax, cytochrome c, and caspase-3, while the expressions of Bcl-2, collagen II, and aggrecan were increased. Our evidences indicated that MW treatment inhibited the apoptosis of chondrocytes through depression of [Ca(2+)] i . It also inhibited calpain activation, which mediated Bax cleavage and cytochrome c release and initiated the apoptotic execution phase. In addition, MW treatment increased the expression of collagen II and aggrecan of chondrocytes.

A systematic appraisal of field synopses in genetic epidemiology: a HuGE review

Evidence from genetic association studies is accumulating rapidly. Field synopses have recently arisen as an unbiased way of systematically synthesizing this evidence. We performed a systematic review and appraisal of published field synopses in genetic epidemiology and assessed their main findings and methodological characteristics. We identified 61 eligible field synopses, published between January 1, 2007, and October 31, 2013, on 52 outcomes reporting 734 significant associations at the P < 0.05 level. The median odds ratio for these associations was 1.25 (interquartile range, 1.15-1.43). Egger's test was the most common method (n = 30 synopses) of assessing publication bias. Only 12 synopses (20%) used the Venice criteria to evaluate the epidemiologic credibility of their findings (n = 449 variants). Eleven synopses (18%) were accompanied by an online database that has been regularly updated. These synopses received more citations (P = 0.01) and needed a larger research team (P = 0.02) than synopses without an online database. Overall, field synopses are becoming a valuable tool for the identification of common genetic variants, especially when researchers follow relevant methodological guidelines. Our work provides a summary of the current status of the field synopses published to date and may help interested readers efficiently identify the online resources containing the relevant genetic evidence.

The insertion and deletion (I28005D) polymorphism of the angiotensin I converting enzyme gene is a risk factor for osteoarthritis in an Asian Indian population

INTRODUCTION

Angiotensin I converting enzyme (ACE) insertion and deletion (I/D) polymorphism has been implicated in the pathogenesis of osteoarthritis (OA). In recent years, numerous genetic factors have been identified and implicated in OA. In this Asian Indian population-based study, we aimed to evaluate the relationship between ACE (I28005D) gene polymorphism and primary OA. We performed a case-control association study to identify and explore the correlation between clinically, radiologically diagnosed individuals with primary knee OA and the ACE I/D polymorphism.

METHODS

Genomic DNA was isolated from 200 samples, including 100 OA cases and 100 healthy volunteers. DNA was amplified by polymerase chain reaction (PCR) using I and D allele-specific primers. PCR products were assessed via UV visualization of products electrophoresed on 2% agarose gels.

RESULTS

The groups differed significantly in genotype distributions (p < 0.05). The primary knee OA group showed a considerably higher incidence of the DD genotype and the D allele compared to the control group (OR = 2.14, 95% CI: 1.10-4.15, p = 0.02 and OR = 2.08, 95% CI: 1.39-3.10, p = 0.0003).

CONCLUSION

The ACE gene polymorphism I28005D was found to be associated with primary knee OA in Asian Indian populations. This is the first study in India to report that the ACE gene polymorphism is a risk factor for early onset primary knee OA.

Personalized medicine for osteoarthritis: where are we now?

Personalized medicine is a much talked about subject that is a timely and important development to healthcare in general and also specifically for patients affected by osteoarthritis. This review uses biomarker examples pertinent to osteoarthritis to highlight the current status of the field, while also highlighting probable future developments. It is not meant to be an exhaustive account. The BIPED(s) [Burden of disease, Investigative, Prognosis, Efficacy, Diagnosis (safety)] classification system is used to organize the discussion of examples. Biomarkers pertaining to burden, investigation, prognosis, efficacy, diagnosis and safety are highlighted. The examples are followed by a discussion of issues related to interpretation and application of biomarker results and approaches to solve the challenges interpretation faces, including graphical, mathematical and synthetic representations. Through this review, it is hoped that a better appreciation can be gained of the potential and pitfalls of personal medicine in the care of patients with osteoarthritis.

Heritability of chronic pain in 2195 extended families

Chronic pain is pathological, persisting beyond normal tissue healing time. Previous work has suggested ∼50% variation in chronic pain development is heritable. No data are currently available on the heritability of pain categorized using the Chronic Pain Grade (CPG). Furthermore, few existing studies have accounted for potential confounders that may themselves be under genetic control or indeed 'heritable' non-genetic traits. This study aimed to determine the relative contributions of genetic, measured and shared environmental and lifestyle factors to chronic pain. Chronic pain status was determined and CPG measured in participants from Generation Scotland: the Scottish Family Health Study, a large cohort of well-characterized, extended families from throughout Scotland, UK. Heritability estimates (h (2) ) for 'any chronic pain' and 'severe' chronic pain (CPG 3 or 4) were generated using SOLAR software, with and without adjustment for shared household effects and measured covariates age, body mass index, gender, household income, occupation and physical activity. Data were available for 7644 individuals in 2195 extended families. Without adjustment, h (2) for 'any chronic pain' was 29% [standard errors (SE) 6%; p < 0.001], and for 'severe' chronic pain was 44% (SE 3%; p <0.001). After adjustment, 'any chronic pain' h(2) = 16% (SE 7%; p = 0.02) and 'severe' chronic pain h(2) = 30% (SE 13%; p = 0.007). Co-heritability of both traits was 11% (SE 76%). This study supports the use of chronic pain as a phenotype in genetic studies, with adequate correction for confounders to specifically identify genetic risk factors for chronic pain.

Bone mineral density and genetic markers involved in three connected pathways (focal adhesion, actin cytoskeleton regulation and cell cycle): the CUMAGAS-BMD information system

The focal adhesion, the actin cytoskeleton and cell-cycle are connected pathways and their genes are implicated in the pathogenesis of low BMD. Data from 211 studies that investigated the association between BMD and gene variants involved in these pathways were catalogued in a web-based information system and analyzed. In individual studies, significant association was found for 16 variants in lumbar spine, 11 in femoral neck and 5 in hip. In meta-analysis, significant results were shown for the variants COL1A1 rs1800012 (in lumbar spine and femoral neck), COL1A1 rs1107946 (in lumbar spine), TGFB1 rs1982073 (in femoral neck and hip) and TGFB1 rs1800469 (in lumbar spine).

Osteoarthritis prevention

PURPOSE OF REVIEW

We discuss recent published epidemiologic data regarding risk factors for incident and progressive knee osteoarthritis and related knee pain to identify targets for primary and secondary prevention. We also discuss recently identified methodologic challenges to the study of knee osteoarthritis, particularly osteoarthritis progression.

RECENT FINDINGS

Recent epidemiologic studies and systematic reviews of knee osteoarthritis have confirmed that being overweight and obese, and knee injuries increase the risk for incident knee osteoarthritis. Biomechanical risk factors such as leg-length inequalities and malalignment require further study. Obesity also appears to play a role in accelerating osteoarthritis worsening. However, with the exception of malalignment, no risk factors for knee osteoarthritis progression have been identified. Novel approaches to the study of knee pain have demonstrated a strong association between structural abnormalities and knee pain, contrary to the 'so-called' structure-symptom discordance, as well as between fluctuations of knee pain with changes in specific structural lesions. A number of methodologic issues, including conditioning on an intermediate stage of disease and depletion of susceptibles may explain, in part, the difficulty in identifying risk factors for knee osteoarthritis.

SUMMARY

There is strong epidemiologic evidence that being overweight or obese and knee injury are associated with increased risk of developing knee osteoarthritis. Further study is required to confirm associations of leg-length inequality and malalignment with incident knee osteoarthritis. Few new risk factors for progression of knee osteoarthritis have been identified in the past few years. Without such knowledge, secondary prevention of osteoarthritis remains challenging.

Synopsis and meta-analysis of genetic association studies in osteoporosis for the focal adhesion family genes: the CUMAGAS-OSTEOporosis information system

BACKGROUND

Focal adhesion (FA) family genes have been studied as candidate genes for osteoporosis, but the results of genetic association studies (GASs) are controversial. To clarify these data, a systematic assessment of GASs for FA genes in osteoporosis was conducted.

METHODS

We developed Cumulative Meta-Analysis of GAS-OSTEOporosis (CUMAGAS-OSTEOporosis), a web-based information system that allows the retrieval, analysis and meta-analysis (for allele contrast, recessive, dominant, additive and codominant models) of data from GASs on osteoporosis with the capability of update. GASs were identified by searching the PubMed and HuGE PubLit databases.

RESULTS

Data from 72 studies involving 13 variants of 6 genes were analyzed and catalogued in CUMAGAS-OSTEOporosis. Twenty-two studies produced significant associations with osteoporosis risk under any genetic model. All studies were underpowered (<50%). In four studies, the controls deviated from the Hardy-Weinberg equilibrium. Eight variants were chosen for meta-analysis, and significance was shown for the variants collagen, type I, α1 (COL1A1) G2046T (all genetic models), COL1A1 G-1997T (allele contrast and dominant model) and integrin β-chain β3 (ITGB3) T176C (recessive and additive models). In COL1A1 G2046T, subgroup analysis has shown significant associations for Caucasians, adults, females, males and postmenopausal women. A differential magnitude of effect in large versus small studies (that is, indication of publication bias) was detected for the variant COL1A1 G2046T.

CONCLUSION

There is evidence of an implication of FA family genes in osteoporosis. CUMAGAS-OSTEOporosis could be a useful tool for current genomic epidemiology research in the field of osteoporosis.