Lan-Juan Zhao

Genome-wide association study of copy number variation identified gremlin1 as a candidate gene for lean body mass.

Lean body mass (LBM) is a heritable trait predicting a series of health problems, such as osteoporotic fracture and sarcopenia. We aim to identify sequence variants associated with LBM by a genome-wide association study (GWAS) of copy number variants (CNVs). We genotyped genome-wide CNVs of 1627 individuals of the Chinese population with Affymetrix SNP6.0 genotyping platform, which comprised of 9 40 000 copy number probes. We then performed a GWAS of CNVs with lean mass at seven sites: left and right arms, left and right legs, total of limb, trunk and whole body. We identified a CNV that is associated with LBM variation at the genome-wide significance level (CNV2073, Bonferroni corrected P-value 0.002 at right arm). CNV2073 locates at chromosome 15q13.3, which has been implicated as a candidate region for LBM by our previous linkage studies. The nearest gene, gremlin1, has a key role in the regulation of skeletal muscle formation and repair. Our results suggest that the gremlin1 gene is a potentially important gene for LBM variation. Our findings also show the utility and efficacy of CNV as genetic markers in association studies.

Bivariate genome-wide association study suggests that the DARC gene influences lean body mass and age at menarche

Lean body mass (LBM) and age at menarche (AAM) are two important complex traits for human health. The aim of this study was to identify pleiotropic genes for both traits using a powerful bivariate genome-wide association study (GWAS). Two studies, a discovery study and a replication study, were performed. In the discovery study, 909622 single nucleotide polymorphisms (SNPs) were genotyped in 801 unrelated female Han Chinese subjects using the Affymetrix human genome-wide SNP array 6.0 platform. Then, a bivariate GWAS was performed to identify the SNPs that may be important for LBM and AAM. In the replication study, significant findings from the discovery study were validated in 1692 unrelated Caucasian female subjects. One SNP rs3027009 that was bivariately associated with left arm lean mass and AAM in the discovery samples (P=7.26×10−6) and in the replication samples (P=0.005) was identified. The SNP is located at the upstream of DARC (Duffy antigen receptor for chemokines) gene, suggesting that DARC may play an important role in regulating the metabolisms of both LBM and AAM.

Genome-wide association study of lncRNA polymorphisms with bone mineral density

Recent studies suggested that long noncoding RNAs (lncRNAs) were widely transcribed in the genome, but their potential roles in the genetic complexity of human disorders required further exploration. The purpose of the present study was to explore genetic polymorphisms of lncRNAs associated with bone mineral density (BMD) and its potential value. Based on the lncRNASNP database, 55,906 lncSNPs were selected to conduct a genome‐wide association study meta‐analysis among 11,140 individuals of seven independent studies for BMDs at femoral neck (FN), lumbar spine, and total hip (HIP). Promising results were replicated in Genetic Factors for Osteoporosis Consortium (GEFOS Sequencing, n = 32,965).

Race and socioeconomic effect on sarcopenia and sarcopenic obesity in the Louisiana Osteoporosis Study (LOS)

Sarcopenia and sarcopenic obesity are emerging public health issues. True prevalence rates are unknown and estimates differ substantially between studies. No large‐scale single study has compared prevalence rates between whites, blacks, Asians, and Hispanics, as we intend to do here. This study also examined the effects of race and socioeconomic factors on sarcopenia and sarcopenic obesity.

A joint analysis of metabolomic profiles associated with muscle mass and strength in Caucasian women

Both loss of muscle mass and strength are important sarcopenia-related traits. In this study, we investigated both specific and shared serum metabolites associated with these two traits in 136 Caucasian women using a liquid chromatography-mass spectrometry method. A joint analysis of multivariate traits was used to examine the associations of individual metabolites with muscle mass measured by the body mass index-adjusted appendicular lean mass (ALM/BMI) and muscle strength measured by hand grip strength (HGS). After adjusting for multiple testing, nine metabolites including two amino acids (aspartic acid and glutamic acid) and an amino acid derive (pipecolic acid), one peptide (phenylalanyl-threonine), one carbohydrate (methyl beta-D-glucopyranoside), and four lipids (12S-HETRE, arachidonic acid, 12S-HETE, and glycerophosphocholine) were significant in the joint analysis. Of them, the two amino acids (aspartic acid and glutamic acid) and two lipids (12S-HETRE and 12S-HETE) were associated with both ALM/BMI and HGS, and the other five were only associated with ALM/BMI. The pathway analysis showed the amino acid metabolism pathways (aspartic acid and glutamic acid) might play important roles in the regulation of muscle mass and strength. In conclusion, our study identified novel metabolites associated with sarcopenia-related traits, suggesting novel metabolic pathways for muscle regulation.

Multiple analyses indicate the specific association of NR1I3, C6 and TNN with low hip BMD risk

Low hip bone mineral density (BMD) is an important index for osteoporosis and is associated with hip fracture, which leads to more cases of disability and mortality than all other kinds of fractures (Kanis et al., 2007). BMDs heritability is more than 60% (Arden et al., 1996). A number of candidate loci for BMD have been previously identified by Genome Wide Association Studies (GWAS) (Xiong et al., 2009; Karasik et al., 2010; Zhang et al., 2013). Nevertheless, many significant signals based on GWAS are difficult to interpret because common single nucleotide polymorphisms (SNPs) selected for GWAS have small effects and explain less than 10% of BMD variation (Takai, 2005). Some low frequency SNPs and rare SNPs with larger effects may be missed by GWAS (Takai, 2005). Sequencing can provide detailed genetic variant information to identify low frequency variants that GWAS may have missed. Several sequencing studies have been conducted on osteoporosis. One study based on whole genome sequencing (WGS) found that a rare mutation in the leucine rich-repeat-containing G-proteincoupled receptor 4 (LGR4) gene is strongly associated with low BMD in Icelandic subjects (Styrkarsdottir et al., 2013). Another WGS study suggested that COL1A2 is associated with both low hip and spine BMD in Icelanders (Styrkarsdottir et al., 2015). A recent WGS indicated that EN1 is a determinant of bone density and fracture in Europeans (Zheng et al., 2015). All of these studies focused mainly on Western populations; so far, no sequencing study has been conducted for osteoporosis in the Asian population. As established by The International HapMap Consortium and others (Wang et al., 2013), different ethnic populations may have distinct allele frequencies and linkage disequilibrium patterns for specific potential functional variants. The results from one ethnic group may not hold true for other ethnic groups. Meta-analyses across different ethnic groups may have some advantages, because analyzing samples with diverse ancestries will increase statistical power to identify those responsible loci shared by different ethnic populations (Do et al., 2012). In this study, we performed whole exome sequencing (WES) with high sequencing depth (more than 40 ) in 101 Chinese individuals, carried out a meta-analysis for hip BMD by combiningWES and WGS (sequencing depth more than 50 ) analysis in 44 Caucasian individuals, and compared the genotypes of extremely high(top 20%) and low-hip BMD (bottom 20%) individuals. Moreover, other data were used to test the causality of variants in the metaanalysis, which include 1) GWAS with imputed genotype of 11,140 individuals in seven individual studies, 2) gene expression data with 40 extremely high-hip BMD (top 20%) versus 40