Because single genetic variants may have pleiotropic effects, one trait can be a confounder in a genome-wide association study (GWAS) that aims to identify loci associated with another trait. A ...typical approach to address this issue is to perform an additional analysis adjusting for the confounder. However, obtaining conditional results can be time-consuming. We propose an approximate conditional phenotype analysis based on GWAS summary statistics, the covariance between outcome and confounder, and the variant minor allele frequency (MAF). GWAS summary statistics and MAF are taken from GWAS meta-analysis results while the traits covariance may be estimated by two strategies: (i) estimates from a subset of the phenotypic data; or (ii) estimates from published studies. We compare our two strategies with estimates using individual level data from the full GWAS sample (gold standard). A simulation study for both binary and continuous traits demonstrates that our approximate approach is accurate. We apply our method to the Framingham Heart Study (FHS) GWAS and to large-scale cardiometabolic GWAS results. We observed a high consistency of genetic effect size estimates between our method and individual level data analysis. Our approach leads to an efficient way to perform approximate conditional analysis using large-scale GWAS summary statistics.
Hemoglobin A1c (HbA1c) is widely used to diagnose diabetes and assess glycemic control in individuals with diabetes. However, nonglycemic determinants, including genetic variation, may influence how ...accurately HbA1c reflects underlying glycemia. Analyzing the NHLBI Trans-Omics for Precision Medicine (TOPMed) sequence data in 10,338 individuals from five studies and four ancestries (6,158 Europeans, 3,123 African-Americans, 650 Hispanics, and 407 East Asians), we confirmed five regions associated with HbA1c (GCK in Europeans and African-Americans, HK1 in Europeans and Hispanics, FN3K and/or FN3KRP in Europeans, and G6PD in African-Americans and Hispanics) and we identified an African-ancestry-specific low-frequency variant (rs1039215 in HBG2 and HBE1, minor allele frequency (MAF) = 0.03). The most associated G6PD variant (rs1050828-T, p.Val98Met, MAF = 12% in African-Americans, MAF = 2% in Hispanics) lowered HbA1c (−0.88% in hemizygous males, −0.34% in heterozygous females) and explained 23% of HbA1c variance in African-Americans and 4% in Hispanics. Additionally, we identified a rare distinct G6PD coding variant (rs76723693, p.Leu353Pro, MAF = 0.5%; −0.98% in hemizygous males, −0.46% in heterozygous females) and detected significant association with HbA1c when aggregating rare missense variants in G6PD. We observed similar magnitude and direction of effects for rs1039215 (HBG2) and rs76723693 (G6PD) in the two largest TOPMed African American cohorts, and we replicated the rs76723693 association in the UK Biobank African-ancestry participants. These variants in G6PD and HBG2 were monomorphic in the European and Asian samples. African or Hispanic ancestry individuals carrying G6PD variants may be underdiagnosed for diabetes when screened with HbA1c. Thus, assessment of these variants should be considered for incorporation into precision medicine approaches for diabetes diagnosis.
Cardiometabolic traits pose a major global public health burden. Large-scale genome-wide association studies (GWAS) have identified multiple loci accounting for up to 30% of the genetic variance in ...complex traits such as cardiometabolic traits. However, the contribution of parent-of-origin effects (POEs) to complex traits has been largely ignored in GWAS. Family-based studies enable the assessment of POEs in genetic association analyses. We investigated POEs on a range of complex traits in 3 family-based studies. The discovery phase was carried out in large pedigrees from the Kibbutzim Family Study (n = 901 individuals) and in 872 parent-offspring trios from the Jerusalem Perinatal Study. Focusing on imprinted genomic regions, we examined parent-specific associations with 12 complex traits (i.e., body-size, blood pressure, lipids), mostly cardiometabolic risk traits. Forty five of the 11,967 SNPs initially found to have POE were evaluated for replication (p value < 1 × 10
) in Framingham Heart Study families (max n = 8000 individuals). Three common variants yielded evidence of POE in the meta-analysis. Two variants, located on chr6 in the HLA region, showed a paternal effect on height (rs1042136: β
= -0.023, p value = 1.5 × 10
and rs1431403: β
= -0.011, p value = 5.4 × 10
). The corresponding maternally-derived effects were statistically nonsignificant. The variant rs9332053, located on chr13 in RCBTB2 gene, demonstrated a maternal effect on hip circumference (β
= -4.24, p value = 9.6 × 10
; β
= 1.29, p value = 0.23). These findings provide evidence for the utility of incorporating POEs into association studies of cardiometabolic traits, especially anthropometric traits. The study highlights the benefits of using family-based data for deciphering the genetic architecture of complex traits.
DNA methylation, an epigenetic modification, can be affected by environmental factors and thus regulate gene expression levels that can lead to alterations of certain phenotypes. Network analysis has ...been used successfully to discover gene sets that are expressed differently across multiple disease states and suggest possible pathways of disease progression. We applied this framework to compare DNA methylation levels before and after lipid-lowering medication and to identify modules that differ topologically between the two time points, revealing the association between lipid medication and these triglyceride-related methylation sites.
We performed quality control using beta-mixture quantile normalization on 463,995 cytosine-phosphate-guanine (CpG) sites and deleted problematic sites, resulting in 423,004 probes. We identified 14,850 probes that were nominally associated with triglycerides prior to treatment and performed weighted gene correlation network analysis (WGCNA) to construct pre- and posttreatment methylation networks of these probes. We then applied both WGCNA module preservation and generalized Hamming distance (GHD) to identify modules with topological differences between the pre- and posttreatment. For modules with structural changes between 2 time points, we performed pathway-enrichment analysis to gain further insight into the biological function of the genes from these modules.
Six triglyceride-associated modules were identified using pretreatment methylation probes. The same 3 modules were not preserved in posttreatment data using both the module-preservation and the GHD methods. Top-enriched pathways for the 3 differentially methylated modules are sphingolipid signaling pathway, proteoglycans in cancer, and metabolic pathways (
values < 0.005). One module in particular included an enrichment of lipid-related pathways among the top results.
The same 3 modules, which were differentially methylated between pre- and posttreatment, were identified using both WGCNA module-preservation and GHD methods. Pathway analysis revealed that triglyceride-associated modules contain groups of genes that are involved in lipid signaling and metabolism. These 3 modules may provide insight into the effect of fenofibrate on changes in triglyceride levels and these methylation sites.
Building a gradient structure can achieve overall improvement of multiple properties of metal materials. However, the investigation on hydrogen embrittlement (HE) behavior of gradient structure ...alloys has not been reported so far. This study investigated HE of pure iron with gradient microstructure induced by pre-torsion. The results reveal that with an increase in pre-torsion angle, the resistance to HE of alloys decreases. Fracture surface observation demonstrates that hydrogen uncharged samples present ductile cup-shape fracture, whereas hydrogen charged samples exhibit brittle spiral patterns, mainly depending on pre-torsion level. Additionally, microscopical hydrogen-assisted cracking mechanism of gradient structured pure iron has been proposed.
•Pure iron with gradient microstructure is prepared by pre-torsion.•An increase in pre-torsion angle reduces the resistance to HE.•Adjacent grains orientated {110}//ND and {111}//ND are vulnerable to HE.•Hydrogen-assisted cracking mechanism of pre-torsioned pure iron is revealed.
Background
Leukocyte immunoglobulin-like receptor subfamily B2 (LILRB2) was reported to be an inhibitory molecule with suppressive functions. sEVs mediate communication between cancer cells and other ...cells. However, the existence of LILRB2 on sEVs in circulation and the function of sEVs-LILRB2 are still unknown. This study aims to investigate the role of LILRB2 in GBM and determine how LILRB2 in sEVs regulates tumor immunity.
Methods
LILRB2 expression in normal brain and GBM tissues was detected by immunohistochemistry, and the effect of LILRB2 on prognosis was evaluated in an orthotopic brain tumor model. Next, a subcutaneous tumor model was constructed to evaluate the function of pirb in vivo. The immune cells in the tumor sites and spleen were detected by immunofluorescence staining and flow cytometry. Then, the presence of pirb in sEVs was confirmed by WB. The percentage of immune cells after incubation with sEVs from GL261 (GL261-sEVs) or sEVs from GL261-pirb
+
(GL261-sEVs-pirb) was detected by flow cytometry. Then, the effect of pirb on sEVs was evaluated by a tumor-killing assay and proliferation assay. Finally, subcutaneous tumor models were constructed to evaluate the function of pirb on sEVs.
Results
LILRB2 was overexpressed in human GBM tissue and was closely related to an immunosuppressive TME in GBM. Then, a protumor ability of LILRB2 was observed in subcutaneous tumor models, which was related to lower CD8 + T cells and higher MDSCs (myeloid-derived suppressor cells) in the tumor and spleen compared to those of the control group. Next, we found that pirb on sEVs (sEVs-pirb) inhibits the function of CD8 + T cells by promoting the formation and expansion of MDSCs. Furthermore, the protumor function of sEVs-pirb was demonstrated in subcutaneous tumor models.
Conclusion
We discovered that LILRB2/pirb can be transmitted between GBM cells via sEVs and that pirb on sEVs induces the formation and expansion of MDSCs. The induced MDSCs facilitate the formation of an immunosuppressive TME.
Graphical Abstract
Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we ...aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 × 10
), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.
We focus on identifying genomics risk factors of higher body mass index (BMI) incorporating a priori information, such as biological pathways. However, the commonly used methods to incorporate prior ...information provide a model for the mean function of the outcome and rely on unmet assumptions. To address these concerns, we propose a method for nonparametric additive quantile regression with network regularization to incorporate the information encoded by known networks. To account for nonlinear associations, we approximate the unknown additive functional effect of each predictor with the expansion of a B‐spline basis. We implement the group Lasso penalty to obtain a sparse model. We define the network‐constrained penalty by the total ℓ2$$ {\ell}_2 $$ norm of the difference between the effect functions of any two linked genes in the known network. We further propose an efficient computation procedure to solve the optimization problem that arises in our model. Simulation studies show that our proposed method performs well in identifying more truly associated genes and less falsely associated genes than alternative approaches. We apply the proposed method to analyze the microarray gene‐expression dataset in the Framingham Heart Study and identify several 75 percentile BMI associated genes. In conclusion, our proposed approach efficiently identifies the outcome‐associated variables in a nonparametric additive quantile regression framework by leveraging known network information.
Patients with type 2 diabetes (T2D) are at two-fold increased risk of cardiovascular disease (CVD), which is the leading cause of T2D morbidity and mortality. Here, we conducted a time-to-event ...genome-wide association study (GWAS) to identify genetic variants associated with incident CVD among patients with T2D in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. Incident CVD was defined based on a composite of myocardial infarction, stroke, and cardiovascular death that occurred at least one year after the diagnosis of T2D. In each participating prospective cohort, we performed GWAS using a Cox proportional hazard survival model adjusting for age, and sex to identify genetic variants associated with incident CVD, and cohort-level estimated effect sizes were combined using inverse variance weighted fixed effects meta-analysis. A total of 37,327 participants were included in the analyses (26,928 European ancestry and 10,399 non-European ancestry) which comprised 6,012 primary event cases. We identified three distinct genetic loci associated with incident CVD among individuals with T2D that reached the threshold for genome-wide significance: rs231964 (intronic variant in NOX3, hazard ratio HR 1.4, P=8.3x10-9), rs139753656 (intronic variant in DCC, HR 2.0, P=2.4x10-8), and rs77202398 (intronic variant in TNS3, HR 1.4, P=4.4x10-8). Among 204 known coronary artery disease risk loci, 27 were associated with incident CVD with P<0.05 and rs6842241 upstream of EDNRA was associated with increased risk of CVD after Bonferroni correction (HR 1.1, P=1.2x10-4). The data provide evidence of novel and known genomic regions associated with incident CVD among individuals with T2D that require validation but point to novel targets.
Disclosure
S. Kwak: None. P. Wu: None. J. B. Meigs: Consultant; Self; Quest Diagnostics. On behalf of the charge diabetes working group: n/a.
Funding
National Institutes of Health (1R01HL151855-01)
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