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

Integration of single-cell and RNA-seq data to explore the role of focal adhesion-related genes in osteoporosis

Integrin-based focal adhesion is one of the major mechanosensory in osteocytes. The aim of this study was to mine the hub genes associated with focal adhesion and investigate their roles in osteoporosis based on the data of single-cell RNA sequencing and RNA-sequencing. Two hub genes (FAM129A and RNF24) with the same expression trend and AUC values greater than 0.7 in both GSE56815 and GSE56116 cohorts were uncovered. The nomogram was created to predict the risk of OP based on two hub genes. Subsequently, the competing endogenous RNA network was established based on two hub genes, 14 microRNAs and five long noncoding RNAs. Meanwhile, transcription factors-hub gene network was established based on two hub genes and 14 TFs. Finally, 73 drugs were predicted, of which there were 13 drugs targeting FAM129A and 66 drugs targeting RNF24. In both mouse and human blood samples, FAM129A expression was decreased in granulocytes and RNF24 expression was increased in monocytes. In the mouse experiment, FAM129A and anti-RNF24 were found to partially alleviate the progression of osteoporosis. In conclusion, two hub genes related to focal adhesion were identified by combined scRNA-seq and RNA-seq analyses, which might supply a new insight for the treatment and evaluation of OP.

Prevalence and factors associated with lumbopelvic pain among pregnant women in their third trimester: a cross-sectional study

Introduction

pregnancy related lumbopelvic pain, which refers to low back pain and pelvic girdle pain, is a common musculoskeletal disorder affecting quality of life. The purpose of this study was to establish the prevalence and the factors associated with lumbopelvic pain among pregnant women in their third trimester.

Methods

four hundred and nineteen pregnant women were included in this institutional-based cross-sectional study. The study was carried out from October 2018 to March 2019 at Kawempe national referral hospital in Uganda. Pregnant women in the third trimester participated in the study. Pregnant women with preexisting backache, a fracture or surgery to the back, hip or pelvic area in the preceding 12 months were excluded. Lumbopelvic pain was defined as low back pain and pelvic girdle pain. Bivariate and multivariable logistic regression were carried out to establish the factors associated with lumbopelvic pain. The presence of lumbopelvic pain was assessed for and diagnosed using the illustrations in the pelvic girdle questionnaire.

Results

the prevalence of pregnancy related lumbopelvic pain was 46% (95% CI: 40.8-50.4). Most women who had pregnancy related lumbopelvic pain experienced lumbar pain. The factors independently associated with pregnancy related lumbopelvic pain (PLPP) were being HIV sero positive [adjusted odds ratio (AOR) 2.25, 95% CI: 1.17-4.35] and having no monthly income (AOR 0.53, 95% CI: 0.30-0.94).

Conclusion

in this study, PLPP is common in women attending antenatal clinic in their third trimester. The factors associated with PLPP were being HIV positive and having no income. In future pregnant women who come for antenatal care with pregnancy related lumbopelvic pain should be given appropriate advice and support.

Association of rs12722 COL5A1 with pulmonary tuberculosis: a preliminary case-control study in a Kazakhstani population

Lung cavitation is the classic hallmark of TB, which facilitates the disease development and transmission. It involves the degradation of lung parenchyma which is mainly made up of collagen fibers by metalloproteinases (MMPs) produced by activated monocyte-derived cells, neutrophils and stromal cells. The following population-based preliminary case-control study of adults with TB (50) and controls (112) without TB was used to investigate possible association between rs1800012 in COL1A1, rs12722 in COL5A1 genes and pulmonary TB in Kazakhstan. We examined 162 samples (50 cases and 112 controls) to study the associations between TB disease status and demographic variables along with single nucleotide polymorphisms related to COLA1 and COL5A1. The unadjusted χ2 and multivariable logistic regression was performed to find out relationships between SNP and other predictors. Preliminary findings suggest that there is a statistically significant association of age (AOR = 0.97, 95% CI:0.94-0.99, p value = 0.049), social status (AOR = 2.41, 95% CI:1.16-5.02, p value = 0.018), HIV status (AOR = 7.12, 95% CI:1.90-26.7, p value = 0.004) and heterozygous rs12722 SNP (AOR = 2.47, 95% CI:1.17-5.19, p value = 0.018) polymorphism of COL5A1 gene with TB susceptibility. The association of collagen genes with TB pathogenesis indicates that anti TB programs can include development of new drug regimens that include MMP inhibitors which has been found to be helpful in collagen remodeling and repair. Therapeutic targeting of MMPs will prevent extracellular matrix and collagen degradation and granuloma maturation.

Parents' prioritised outcomes for trials investigating treatments for paediatric severe infection: a qualitative synthesis

OBJECTIVE

To identify parents' prioritised outcomes by combining qualitative findings from two trial feasibility studies of interventions for paediatric suspected severe infection.

DESIGN

Qualitative synthesis combining parent interview data from the Fluids in Shock (FiSh) and Fever feasibility studies. Parents had experience of their child being admitted to a UK emergency department or intensive care unit with a suspected infection.

PARTICIPANTS

n=: 85 parents. FiSh study: n=41 parents, 37 mothers, 4 fathers, 7 were bereaved. Fever study: n=44 parents, 33 mothers, 11 fathers, 7 were bereaved.

RESULTS

In addition to survival, parents prioritised short-term outcomes including: organ and physiological functioning (eg, heart rate, breathing rate and temperature); their child looking and/or behaving more like their normal self; and length of time on treatments or mechanical support. Longer term prioritised outcomes included effects of illness on child health and development. We found that parents' prioritisation of outcomes was influenced by their experience of their child's illness, survival and the point at which they are asked about outcomes of importance in the course of their child's illness.

CONCLUSIONS

Findings provide insight into parent prioritised outcomes to inform the design of future trials investigating treatments for paediatric suspected or proven severe infection as well as core outcome set development work.

How human factors affect escalation of care: a protocol for a qualitative evidence synthesis of studies

INTRODUCTION

Failure to rescue is defined as mortality after complications during hospital care. Incidence ranges 10.9%-13.3% and several national reports such as National Confidential Enquiry into Patient Outcomes and Death and National Institute of Clinical Excellence CG 50 highlight failure to rescue as a significant problem for safe patient care.To avoid failure to rescue events, there must be successful escalation of care. Studies indicate that human factors such as situational awareness, team working, communication and a culture promoting safety contribute to avoidance of failure to rescue events. Understanding human factors is essential to developing work systems that mitigate barriers and facilitate prompt escalation of care. This qualitative evidence synthesis will identify and synthesise what is known about the human factors that affect escalation of care.

METHODS AND ANALYSIS

We will search MEDLINE (Ovid), EMBASE (Ovid) and CINAHL, between database inception and 2018, for studies describing human factors affecting failure to rescue and/or care escalation. A search strategy was developed by two researchers and a medical librarian. Only studies exploring in-hospital (ward) populations using qualitative data collection methods will be included. Screening will be conducted by two researchers. We are likely to undertake a thematic synthesis, using the Thomas and Harden framework. Selected studies will be assessed for quality, rigour and limitations. Two researchers will extract and thematically synthesise codes using a piloted data extraction tool to develop analytical themes.

ETHICS AND DISSEMINATION

The qualitative evidence synthesis will use available published literature and no ethical approval is required. This synthesis will be limited by the quality of studies, rigour and reproducibility of study findings. Results will be published in a peer-reviewed journal, publicised at conferences and on social media.

PROSPERO REGISTRATION NUMBER

CRD42018104745.

Association between polymorphisms in folate metabolism genes and maternal risk for Down syndrome: A meta-analysis

Previous studies have focused on the association between polymorphisms of the genes involved in folate metabolism and Down syndrome (DS); however, the results remain inconclusive. The present meta-analysis was conducted to assess the association between RFC-1 A80G/MTR A2756G/CBS 844ins68 polymorphisms and the maternal risk of DS. Published studies were retrieved from PubMed, Embase, China National Knowledge Infrastructure and Chinese Biomedicine databases. Pooled odds ratios (ORs) with 95% confidence interval (CIs) were calculated using the fixed- or random-effects model. Additionally, test of heterogeneity, cumulative meta-analysis, sensitivity analysis and assessment of bias were also performed. Finally, 11, 11 and 6 studies were deemed eligible for meta-analyses of RFC-1 A80G, MTR A2756G and CBS 844ins68, respectively. A significant association between RFC-1 A80G polymorphism and DS risk was observed for G vs. A (OR=1.19, 95% CI: 1.004-1.40, P=0.04) and the recessive model (OR=1.28, 95% CI: 1.05-1.56, P=0.01). In the stratified analysis by source of control or sample size, a significantly increased risk was observed among hospital-based studies and large-sample groups (>200 subjects), respectively. In addition, the cumulative meta-analysis of the RFC-1 A80G variant revealed a trend toward an association as the amount of data increased. However, for the MTR A2756G and CBS 844ins68 polymorphisms, no obvious association was found for all genetic models. In summary, the present meta-analysis demonstrated that RFC-1 A80G, but not MTR A2756G or CBS 844ins68, was considered as a maternal risk factor for DS in the offspring.

Tissue-specific pathway association analysis using genome-wide association study summaries

MOTIVATION

Pathway association analysis has made great achievements in elucidating the genetic basis of human complex diseases. However, current pathway association analysis approaches fail to consider tissue-specificity.

RESULTS

We developed a tissue-specific pathway interaction enrichment analysis algorithm (TPIEA). TPIEA was applied to two large Caucasian and Chinese genome-wide association study summary datasets of bone mineral density (BMD). TPIEA identified several significant pathways for BMD [false discovery rate (FDR) < 0.05], such as KEGG FOCAL ADHESION and KEGG AXON GUIDANCE, which had been demonstrated to be involved in the development of osteoporosis. We also compared the performance of TPIEA and classical pathway enrichment analysis, and TPIEA presented improved performance in recognizing disease relevant pathways. TPIEA may help to fill the gap of classic pathway association analysis approaches by considering tissue specificity.

AVAILABILITY AND IMPLEMENTATION

The online web tool of TPIEA is available at https://sourceforge.net/projects/tpieav1/files CONTACT: fzhxjtu@mail.xjtu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.

Gene expression changes in human mesenchymal stem cells from patients with osteoporosis

The aim of the present study was to investigate the underlying molecular mechanisms of osteoporosis and to identify novel candidate genes involved in this disease. The gene expression profile of GSE35958 was downloaded from Gene Expression Omnibus, including five samples of human mesenchymal stem cells from patients with osteoporosis and four control samples. Differentially expressed genes (DEGs) were initially identified following an analysis using Student’s t-test. Subsequently, a protein-protein interaction (PPI) network of the significant pathways was constructed, based on the Human Protein Reference Database. In the significant pathways, DEGs were screened using cut-off criteria of FDR<0.1 and |log₂FC|>1.5. A co-change network for pathways was also constructed using the method of cumulative hypergeometric probability distribution. Finally, the transcriptional regulatory network for DEGs was constructed based on the TRANSFAC database. In total, 1,127 DEGs, including 554 upregulated and 573 downregulated DEGs, were screened. The constructed PPI network for the DEGs involved in the two significant pathways, including focal adhesion and lysosome, demonstrated that the five DEGs with a high degree (>60) were β-catenin, SHC-transforming protein 1, RAC-α serine/threonine-protein kinase, caveolin 1 and filamin A, with degrees of 135, 117, 117, 73 and 63, respectively. The pathway with the degree of 22 in the constructed co-change network was neuroactive ligand receptor interaction. The nine genes with a high (≥9) degree in the constructed transcriptional regulatory network were REL-associated protein, upstream stimulatory factor 1, specificity protein 1, Fos-related antigen 1, cyclin-dependent kinase inhibitor 1A, upstream stimulatory factor 2, ETS domain-containing protein Elk-1, JUND and retinoic acid receptor α, with degrees of 29, 27, 19, 18, 17, 13, 11, 11 and 9, respectively. The DEGs with high degree in the PPI and transcriptional regulatory networks may be candidate target molecules, which may be used to monitor, diagnose and treat osteoporosis.

Heritability of bone mineral density in a multivariate family-based study

There is evidence for a genetic contribution to bone mineral density (BMD×). Different loci affecting BMD have been identified by diverse linkage and genome-wide association studies. We studied the heritability of and the correlations among six densitometric phenotypes and four bone mass/fracture phenotypes. For this purpose, we used a family-based study of the genetics of osteoporosis, the Genetic Analysis of Osteoporosis Project. The primary aim of our study was to examine the roles of genetic and environmental factors in determining osteoporosis-related phenotypes. The project consisted of 11 extended families from Spain. All of them were selected through a proband with osteoporosis. BMD was measured using dual-energy X-ray absorptiometry. The proportion of variance of BMD attributable to significant covariates ranged from 25% (for femoral neck BMD) to 48% (for whole-body total BMD). The vast majority of the densitometric phenotypes had highly significant heritability, ranging from 0.252 (whole-body total BMD) to 0.537 (trochanteric BMD) after correcting for covariate effects. All of the densitometric phenotypes showed high and significant genetic correlations (from -0.772 to -1.000) with a low bone mass/osteopenia condition (Affected 3). Our findings provide additional evidence on the heritability of BMD and a strong genetic correlation between BMD and bone mass/fracture phenotypes in a Spanish population. Our results emphasize the importance of detecting genetic risk factors and the benefit of early diagnosis and especially therapeutic and preventive strategies.

Genetic variants in the folate pathway and the risk of neural tube defects: a meta-analysis of the published literature

BACKGROUND

Neural Tube Defects (NTDs) are among the most prevalent and most severe congenital malformations worldwide. Polymorphisms in key genes involving the folate pathway have been reported to be associated with the risk of NTDs. However, the results from these published studies are conflicting. We surveyed the literature (1996-2011) and performed a comprehensive meta-analysis to provide empirical evidence on the association.

METHODS AND FINDINGS

We investigated the effects of 5 genetic variants from 47 study populations, for a total of 85 case-control comparisons MTHFR C677T (42 studies; 4374 cases, 7232 controls), MTHFR A1298C (22 studies; 2602 cases, 4070 controls), MTR A2756G (9 studies; 843 cases, 1006 controls), MTRR A66G (8 studies; 703 cases, 1572 controls), and RFC-1 A80G (4 studies; 1107 cases, 1585 controls). We found a convincing evidence of dominant effects of MTHFR C677T (OR 1.23; 95%CI 1.07-1.42) and suggestive evidence of RFC-1 A80G (OR 1.55; 95%CI 1.24-1.92). However, we found no significant effects of MTHFR A1298C, MTR A2756G, MTRR A66G in risk of NTDs in dominant, recessive or in allelic models.

CONCLUSIONS

Our meta-analysis strongly suggested a significant association of the variant MTHFR C677T and a suggestive association of RFC-1 A80G with increased risk of NTDs. However, other variants involved in folate pathway do not demonstrate any evidence for a significant marginal association on susceptibility to NTDs.

Osteoporosis genetics: year 2011 in review

Increased rates of osteoporotic fractures represent a worldwide phenomenon, which result from a progressing aging in the population around the world and creating socioeconomic problems. This review will focus mostly on human genetic studies identifying genomic regions, genes and mutations associated with osteoporosis (bone mineral density (BMD) and bone loss) and related fractures, which were published during 2011. Although multiple genome-wide association studies (GWAS) were performed to date, the genetic cause of osteoporosis and fractures has not yet been found, and only a small fraction of high heritability of bone mass was successfully explained. GWAS is a successful tool to initially define and prioritize specific chromosomal regions showing associations with the desired traits or diseases. Following the initial discovery and replication, targeted sequencing is needed in order to detect those rare variants which GWAS does not reveal by design. Recent GWAS findings for BMD included WNT16 and MEF2C. The role of bone morphogenetic proteins in fracture healing has been explored by several groups, and new single-nucleotide polymorphisms present in genes such as NOGGIN and SMAD6 were found to be associated with a greater risk of fracture non-union. Finding new candidate genes, and mutations associated with BMD and fractures, also provided new biological connections. Thus, candidates for molecular link between bone metabolism and lactation (for example, RAP1A gene), as well as possible pleiotropic effects for bone and muscle (ACTN3 gene) were suggested. The focus of contemporary studies seems to move toward whole-genome sequencing, epigenetic and functional genomics strategies to find causal variants for osteoporosis.

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).