Genetic architecture of cardiometabolic risks in people living with HIV

Regulatory elements in SEM1-DLX5-DLX6 (7q21.3) locus contribute to genetic control of coronal nonsyndromic craniosynostosis and bone density-related traits

Purpose

The etiopathogenesis of coronal nonsyndromic craniosynostosis (cNCS), a congenital condition defined by premature fusion of 1 or both coronal sutures, remains largely unknown.

Methods

We conducted the largest genome-wide association study of cNCS followed by replication, fine mapping, and functional validation of the most significant region using zebrafish animal model.

Results

Genome-wide association study identified 6 independent genome-wide-significant risk alleles, 4 on chromosome 7q21.3 SEM1-DLX5-DLX6 locus, and their combination conferred over 7-fold increased risk of cNCS. The top variants were replicated in an independent cohort and showed pleiotropic effects on brain and facial morphology and bone mineral density. Fine mapping of 7q21.3 identified a craniofacial transcriptional enhancer (eDlx36) within the linkage region of the top variant (rs4727341; odds ratio [95% confidence interval], 0.48[0.39-0.59]; P = 1.2E-12) that was located in SEM1 intron and enriched in 4 rare risk variants. In zebrafish, the activity of the transfected human eDlx36 enhancer was observed in the frontonasal prominence and calvaria during skull development and was reduced when the 4 rare risk variants were introduced into the sequence.

Conclusion

Our findings support a polygenic nature of cNCS risk and functional role of craniofacial enhancers in cNCS susceptibility with potential broader implications for bone health.

Polygenic Scores and Preclinical Cardiovascular Disease in Individuals With HIV: Insights From the REPRIEVE Trial

BACKGROUND

Coronary artery disease (CAD) is a leading cause of death among the 38.4 million people with HIV globally. The extent to which cardiovascular polygenic risk scores (PRSs) derived in non-HIV populations generalize to people with HIV is not well understood.

METHODS AND RESULTS

PRSs for CAD (GPSMult) and lipid traits were calculated in a global cohort of people with HIV treated with antiretroviral therapy with low-to-moderate atherosclerotic cardiovascular disease risk enrolled in REPRIEVE (Randomized Trial to Prevent Vascular Events in HIV). The PRSs were associated with baseline lipid traits in 4495 genotyped participants, and with subclinical CAD in a subset of 662 who underwent coronary computed tomography angiography. Among participants who underwent coronary computed tomography angiography (mean age, 50.9 [SD, 5.8] years; 16.1% women; 41.8% African, 57.3% European, 1.1% Asian), GPSMult was associated with plaque presence with odds ratio (OR) per SD in GPSMult of 1.42 (95% CI, 1.20-1.68; P=3.8×10-5), stenosis >50% (OR, 2.39 [95% CI, 1.48-3.85]; P=3.4×10-4), and noncalcified/vulnerable plaque (OR, 1.45 [95% CI, 1.23-1.72]; P=9.6×10-6). Effects were consistent in subgroups of age, sex, 10-year atherosclerotic cardiovascular disease risk, ancestry, and CD4 count. Adding GPSMult to established risk factors increased the C-statistic for predicting plaque presence from 0.718 to 0.734 (P=0.02). Furthermore, a PRS for low-density lipoprotein cholesterol was associated with plaque presence with OR of 1.21 (95% CI, 1.01-1.44; P=0.04), and partially calcified plaque with OR of 1.21 (95% CI, 1.01-1.45; P=0.04) per SD.

CONCLUSIONS

Among people with HIV treated with antiretroviral therapy without documented atherosclerotic cardiovascular disease and at low-to-moderate calculated risk in REPRIEVE, an externally developed CAD PRS was predictive of subclinical atherosclerosis. PRS for low-density lipoprotein cholesterol was also associated with subclinical atherosclerosis, supporting a role for low-density lipoprotein cholesterol in HIV-associated CAD.

REGISTRATION

URL: https://www.reprievetrial.org; Unique identifier: NCT02344290.

African American/Black race, apolipoprotein L1 , and serum creatinine among persons with HIV

OBJECTIVE

Accurate estimation of kidney function is critical among persons with HIV (PWH) to avoid under-dosing of antiretroviral therapies and ensure timely referral for kidney transplantation. Existing estimation equations for kidney function include race, the appropriateness of which has been debated. Given advancements in understanding of race and the necessity of accuracy in kidney function estimation, this study aimed to examine whether race, or genetic factors, improved prediction of serum creatinine among PWH.

DESIGN

This cross-sectional study utilized data from the Center for AIDS Research Network of Integrated Clinical Systems cohort (2008-2018). The outcome was baseline serum creatinine.

METHODS

Ordinary least squares regression was used to examine whether inclusion of race or genetic factors [ apolipoprotein-L1 ( APOL1 ) variants and genetic African ancestry] improved serum creatinine prediction. A reduction in root mean squared error (RMSE) greater than 2% was a clinically relevant improvement in predictive ability.

RESULTS

There were 4183 PWH included. Among PWH whose serum creatinine was less than 1.7 mg/dl, race was significantly associated with serum creatinine ( β  = 0.06, SE = 0.01, P  < 0.001) but did not improve predictive ability. African ancestry and APOL1 variants similarly failed to improve predictive ability. Whereas, when serum creatinine was at least 1.7 mg/dl, inclusion of race reduced the RMSE by 2.1%, indicating improvement in predictive ability. APOL1 variants further improved predictive ability by reducing the RMSE by 2.9%.

CONCLUSION

These data suggest that, among PWH, inclusion of race or genetic factors may only be warranted at higher serum creatinine levels. Work eliminating existing healthcare disparities while preserving the utility of estimating equations is needed.

Polygenic risk scores point toward potential genetic mechanisms of type 2 myocardial infarction in people with HIV

BACKGROUND

People with human immunodeficiency virus (HIV) infection (PWH) are at higher risk of myocardial infarction (MI) than those without HIV. About half of MIs in PWH are type 2 (T2MI), resulting from mismatch between myocardial oxygen supply and demand, in contrast to type 1 MI (T1MI), which is due to primary plaque rupture or coronary thrombosis. Despite worse survival and rising incidence in the general population, evidence-based treatment recommendations for T2MI are lacking. We used polygenic risk scores (PRS) to explore genetic mechanisms of T2MI compared to T1MI in PWH.

METHODS

We derived 115 PRS for MI-related traits in 9541 PWH enrolled in the Centers for AIDS Research Network of Integrated Clinical Systems cohort with adjudicated T1MI and T2MI. We applied multivariate logistic regression analyses to determine the association with T1MI and T2MI. Based on initial findings, we performed gene set enrichment analysis of the top variants composing PRS associated with T2MI.

RESULTS

We found that T1MI was strongly associated with PRS for cardiovascular disease, lipid profiles, and metabolic traits. In contrast, PRS for alcohol dependence and cholecystitis, significantly enriched in energy metabolism pathways, were predictive of T2MI risk. The association remained after the adjustment for actual alcohol consumption.

CONCLUSIONS

We demonstrate distinct genetic traits associated with T1MI and T2MI among PWH further highlighting their etiological differences and supporting the role of energy regulation in T2MI pathogenesis.

Epigenome-wide association study of plasma lipids in West Africans: the RODAM study

BACKGROUND

DNA-methylation has been associated with plasma lipid concentration in populations of diverse ethnic backgrounds, but epigenome-wide association studies (EWAS) in West-Africans are lacking. The aim of this study was to identify DNA-methylation loci associated with plasma lipids in Ghanaians.

METHODS

We conducted an EWAS using Illumina 450k DNA-methylation array profiles of extracted DNA from 663 Ghanaian participants. Differentially methylated positions (DMPs) were examined for association with plasma total cholesterol (TC), LDL-cholesterol, HDL-cholesterol, and triglycerides concentrations using linear regression models adjusted for age, sex, body mass index, diabetes mellitus, and technical covariates. Findings were replicated in independent cohorts of different ethnicities.

FINDINGS

We identified one significantly associated DMP with triglycerides (cg19693031 annotated to TXNIP, regression coefficient beta -0.26, false discovery rate adjusted p-value 0.001), which replicated in-silico in South African Batswana, African American, and European populations. From the top five DMPs with the lowest nominal p-values, two additional DMPs for triglycerides (CPT1A, ABCG1), two DMPs for LDL-cholesterol (EPSTI1, cg13781819), and one for TC (TXNIP) replicated. With the exception of EPSTI1, these loci are involved in lipid transport/metabolism or are known GWAS-associated loci. The top 5 DMPs per lipid trait explained 9.5% in the variance of TC, 8.3% in LDL-cholesterol, 6.1% in HDL-cholesterol, and 11.0% in triglycerides.

INTERPRETATION

The top DMPs identified in this study are in loci that play a role in lipid metabolism across populations, including West-Africans. Future studies including larger sample size, longitudinal study design and translational research is needed to increase our understanding on the epigenetic regulation of lipid metabolism among West-African populations.

FUNDING

European Commission under the Framework Programme (grant number: 278901).

Integrating Common Risk Factors with Polygenic Scores Improves the Prediction of Type 2 Diabetes

We tested associations between 13 established genetic variants and type 2 diabetes (T2D) in 1371 study participants from the Volga-Ural region of the Eurasian continent, and evaluated the predictive ability of the model containing polygenic scores for the variants associated with T2D in our dataset, alone and in combination with other risk factors such as age and sex. Using logistic regression analysis, we found associations with T2D for the CCL20 rs6749704 (OR = 1.68, P_FDR = 3.40 × 10^-5), CCR5 rs333 (OR = 1.99, P_FDR = 0.033), ADIPOQ rs17366743 (OR = 3.17, P_FDR = 2.64 × 10^-4), TCF7L2 rs114758349 (OR = 1.77, P_FDR = 9.37 × 10^-5), and CCL2 rs1024611 (OR = 1.38, P_FDR = 0.033) polymorphisms. We showed that the most informative prognostic model included weighted polygenic scores for these five loci, and non-genetic factors such as age and sex (AUC 85.8%, 95%CI 83.7-87.8%). Compared to the model containing only non-genetic parameters, adding the polygenic score for the five T2D-associated loci showed improved net reclassification (NRI = 37.62%, 1.39 × 10^-6). Inclusion of all 13 tested SNPs to the model with age and sex did not improve the predictive ability compared to the model containing five T2D-associated variants (NRI = -17.86, p = 0.093). The five variants associated with T2D in people from the Volga-Ural region are linked to inflammation (CCR5, CCL2, CCL20) and glucose metabolism regulation (TCF7L, ADIPOQ2). Further studies in independent groups of T2D patients should validate the prognostic value of the model and elucidate the molecular mechanisms of the disease development.

Associations between female birth sex and risk of chronic kidney disease development among people with HIV in the USA: A longitudinal, multicentre, cohort study

Background

Women represent a meaningful proportion of new HIV diagnoses, with Black women comprising 58% of new diagnoses among women. As HIV infection also increases risk of chronic kidney disease (CKD), understanding CKD risk among women with HIV (WWH), particularly Black women, is critical.

Methods

In this longitudinal cohort study of people with HIV (PWH) enrolled in CFAR Network of Integrated Clinical Systems (CNICS), a multicentre study comprised of eight academic medical centres across the United States from Jan 01, 1996 and Nov 01, 2019, adult PWH were excluded if they had ≤2 serum creatinine measurements, developed CKD prior to enrollment, or identified as intersex or transgendered, leaving a final cohort of 33,998 PWH. The outcome was CKD development, defined as estimated glomerular filtration rate (eGFR) <60 mL/min/1·73 m2 calculated using the CKD-EPI equation, for ≥90 days with no intervening higher values.

Findings

Adjusting for demographic and clinical characteristics, WWH were 61% more likely to develop CKD than men (adjusted hazard ratio [aHR]: 1·61, 95% CI: 1·46-1·78, p<0·001). This difference persisted after further adjustment for APOL1 risk variants (aHR female sex: 1·92, 95% CI: 1·63-2·26, p<0·001) and substance abuse (aHR female sex: 1·70, 95% CI: 1·54-1·87, p<0·001).

Interpretation

WWH experienced increased risk of CKD. Given disparities in care among patients with end-stage kidney disease, efforts to engage WWH in nephrology care to improve chronic disease management are critical.

Funding

US National Institutes of Health.

Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure

Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.

Cardiovascular risk assessment in people living with HIV compared to the general population

AIMS

We prospectively assessed and compared the accuracy of cardiovascular risk scores in people living with HIV (PLWH) and individuals from the general population.

METHODS AND RESULTS

The Systematic Coronary Risk Evaluation Score 2 (SCORE2), the Pooled Cohort Equations (PCE), and the HIV-specific Data Collection on Adverse events of Anti-HIV Drugs (D:A:D) score were calculated in participants free from atherosclerotic cardiovascular disease (ASCVD) between 2003 and 2009. In total, 6373 [mean age, 40.6 years (SD, 9.9)] PLWH from the Swiss HIV Cohort Study (SHCS) and 5403 [52.8 years (SD, 10.7)] individuals from the CoLaus|PsyCoLaus study were eligible for analysis. We tested discrimination and calibration, and the value of adding HIV-specific factors to scores using the net reclassification improvement (NRI). During mean follow-ups of 13.5 (SD, 4.1) in SHCS and 9.9 (SD, 2.3) years in CoLaus|PsyCoLaus study, 533 (8.4%) and 374 (6.9%) people developed an incident ASCVD, respectively. This translated into age-adjusted incidence rates of 12.9 and 7.5 per 1000 person-year, respectively. In SHCS, SCORE2, PCE, and D:A:D presented comparable discriminative capacities [area under the receiver operating characteristic curve of 0.745 (95% confidence interval, CI, 0.723-0.767), 0.757 (95% CI, 0.736-0.777), and 0.763 (95% CI, 0.743-0.783)]. Adding HIV-specific variables (CD4 nadir and abacavir exposure) to SCORE2 and PCE resulted in an NRI of -0.1% (95% CI, -1.24 to 1, P = 0.83) and of 2.7% (95% CI, 0.3-5.1, P = 0.03), respectively.

CONCLUSIONS

PLWH present a two-fold higher rate of incident ASCVD compared to individuals from the general population. SCORE2 and PCE, which are clinically easier to use (reduced set of variables without adding HIV-specific factors), are valid to predict ASCVD in PLWH.

HIV Protease Inhibitors and Insulin Sensitivity: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

Background: Protease inhibitors (PIs) are believed to affect insulin sensitivity. We aimed to analyze the effect of PIs on insulin sensitivity and the onset of diabetes mellitus (DM) in patients with HIV. Methodology: We searched PubMed, Google Scholar, ClinicalTrals.gov, and the WHO International Clinical Trials Registry Platform till November 2020 for randomized controlled trials (RCTs) that studied the effects of PIs on insulin sensitivity and DM in patients with HIV. We followed the PRISMA and PICOS frameworks to develop the search strategy. We used the random-effects meta-analysis model to estimate the mean difference (MD), standardized mean difference (SMD), and risk ratios for our outcomes, using Stata 14 software. Results: We included nine RCTs that enrolled 1,000 participants, with their ages ranging from 18 to 69 years. The parameters and investigations used in the studies to determine insulin sensitivity were glucose disposal rates, hyperglycemia, and mean glucose uptake. The majority of results showed an association between PIs and insulin sensitivity. The pooled analysis showed no statistically significant difference in insulin sensitivity with atazanavir, whether the study was performed on healthy individuals for a short term or long term in combination with other drugs like tenofovir or emtricitabine [SMD = 0.375, 95% CI (0.035, 0.714)]. The analysis showed reduced glucose disposal rates and hence reduced insulin sensitivity with lopinavir (heterogeneity chi-squared = 0.68, I-squared [variation in SMD attributable to heterogeneity] = 0.0%, p = 0.031). The heterogeneity with chi-squared was substantial (61-80%), while with I-squared was not significant (0-40%), p = 0.031). Less adverse events were observed with atazanavir than with lopinavir [RR = 0.987, 95% CI (0.849, 1.124)]. Darunavir and indinavir did not demonstrate any significant changes in insulin sensitivity. Most of the studies were found to have a low risk of bias. Conclusions: There are significant variations in the effects of PIs on insulin sensitivity and onsets of DM. Atazanavir, fosamprenavir, and darunavir did not demonstrate any significant changes in insulin sensitivity, compared to the rest of the group. There is a need to assess the benefits of PIs against the long-term risk of impaired insulin sensitivity. All patients newly diagnosed with HIV should have DM investigations before the start of ARVs and routinely. RCTs should focus on sub-Saharan Africa as the region is worst affected by HIV, but limited studies have been documented.

Correction to: Genetic architecture of cardiometabolic risks in people living with HIV

An amendment to this paper has been published and can be accessed via the original article.

HIV-1 and human genetic variation

Over the past four decades, research on the natural history of HIV infection has described how HIV wreaks havoc on human immunity and causes AIDS. HIV host genomic research, which aims to understand how human genetic variation affects our response to HIV infection, has progressed from early candidate gene studies to recent multi-omic efforts, benefiting from spectacular advances in sequencing technology and data science. In addition to invading cells and co-opting the host machinery for replication, HIV also stably integrates into our own genome. The study of the complex interactions between the human and retroviral genomes has improved our understanding of pathogenic mechanisms and suggested novel preventive and therapeutic approaches against HIV infection.