Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations

Mechanism of baricitinib supports artificial intelligence-predicted testing in COVID-19 patients

Baricitinib, is an oral Janus kinase (JAK)1/JAK2 inhibitor approved for the treatment of rheumatoid arthritis (RA) that was independently predicted, using artificial intelligence (AI)-algorithms, to be useful for COVID-19 infection via a proposed anti-cytokine effects and as an inhibitor of host cell viral propagation. We evaluated the in vitro pharmacology of baricitinib across relevant leukocyte subpopulations coupled to its in vivo pharmacokinetics and showed it inhibited signaling of cytokines implicated in COVID-19 infection. We validated the AI-predicted biochemical inhibitory effects of baricitinib on human numb-associated kinase (hNAK) members measuring nanomolar affinities for AAK1, BIKE, and GAK. Inhibition of NAKs led to reduced viral infectivity with baricitinib using human primary liver spheroids. These effects occurred at exposure levels seen clinically. In a case series of patients with bilateral COVID-19 pneumonia, baricitinib treatment was associated with clinical and radiologic recovery, a rapid decline in SARS-CoV-2 viral load, inflammatory markers, and IL-6 levels. Collectively, these data support further evaluation of the anti-cytokine and anti-viral activity of baricitinib and supports its assessment in randomized trials in hospitalized COVID-19 patients

Large Scale Association Analysis Identifies Three Susceptibility Loci for Coronary Artery Disease

Genome wide association studies (GWAS) and their replications that have associated DNA variants with myocardial infarction (MI) and/or coronary artery disease (CAD) are predominantly based on populations of European or Eastern Asian descent. Replication of the most significantly associated polymorphisms in multiple populations with distinctive genetic backgrounds and lifestyles is crucial to the understanding of the pathophysiology of a multifactorial disease like CAD. We have used our Lebanese cohort to perform a replication study of nine previously identified CAD/MI susceptibility loci (LTA, CDKN2A-CDKN2B, CELSR2-PSRC1-SORT1, CXCL12, MTHFD1L, WDR12, PCSK9, SH2B3, and SLC22A3), and 88 genes in related phenotypes. The study was conducted on 2,002 patients with detailed demographic, clinical characteristics, and cardiac catheterization results. One marker, rs6922269, in MTHFD1L was significantly protective against MI (OR = 0.68, p = 0.0035), while the variant rs4977574 in CDKN2A-CDKN2B was significantly associated with MI (OR = 1.33, p = 0.0086). Associations were detected after adjustment for family history of CAD, gender, hypertension, hyperlipidemia, diabetes, and smoking. The parallel study of 88 previously published genes in related phenotypes encompassed 20,225 markers, three quarters of which with imputed genotypes The study was based on our genome-wide genotype data set, with imputation across the whole genome to HapMap II release 22 using HapMap CEU population as a reference. Analysis was conducted on both the genotyped and imputed variants in the 88 regions covering selected genes. This approach replicated HNRNPA3P1-CXCL12 association with CAD and identified new significant associations of CDKAL1, ST6GAL1, and PTPRD with CAD. Our study provides evidence for the importance of the multifactorial aspect of CAD/MI and describes genes predisposing to their etiology

Association studies of calcium-sensing receptor (CaSR) polymorphisms with serum concentrations of glucose and phosphate, and vascular calcification in renal transplant recipients

BACKGROUND: Cardiovascular disease is the major cause of death in renal transplant recipients (RTRs) and linked to arterial calcification. The calcium-sensing receptor (CaSR), a G-protein coupled receptor, plays a pivotal role in extracellular calcium homeostasis and is expressed in the intimal and medial layers of the arterial wall. We investigated whether common CASR gene variants are predictors for aortic and coronary artery calcification or influence risk factors such as serum calcium, phosphate and glucose concentrations in RTRs. METHODS: Two hundred and eighty four RTRs were investigated for associations between three CASR promoter region single nucleotide polymorphisms (SNPs) (rs115759455, rs7652589, rs1501899), three non-synonymous CASR coding region SNPs (A986S, R990G, Q1011E), and aortic and coronary artery calcium mass scores, cardiovascular outcomes and calcification risk factors that included serum phosphate, calcium, total cholesterol and glucose concentrations. RESULTS: Multivariate analysis revealed that RTRs homozygous for the minor allele (SS) of the A986S SNP, when compared to those homozygous for the major allele (AA), had raised serum glucose concentrations (8.7±5.4 vs. 5.7±2.1 mmol/L, P<0.05). In addition, RTRs who were heterozygous (CT) at the rs115759455 SNP, when compared to those homozygous for the major allele (CC), had higher serum phosphate concentrations (1.1±0.3 vs. 1.0±0.2 mmol/L, P<0.05). CASR SNPs were not significant determinants for aortic or coronary artery calcification, and were not associated with cardiovascular outcomes or mortality in this RTR cohort. CONCLUSIONS: Common CASR SNPs may be independent predictors of serum glucose and phosphate concentrations, but are not determinants of vascular calcification or cardiovascular outcomes

Shared genetic variants between serum levels of high-density lipoprotein cholesterol and wheezing in a cohort of children from Cyprus

Background: In a cohort of children in Cyprus, we recently reported low levels of high density lipoprotein cholesterol (HDL-C) to be associated with asthma. We examined whether genetic polymorphisms that were previously linked individually to asthma, obesity, or HDL-C are associated with both asthma and HDL-C levels in the Cyprus cohort. Methods: We assessed genotypes frequencies in current-wheezers (n = 190) and non-asthmatic controls (n = 671) and HDL-C levels across several genotypes. Binary logistic regression models were used to assess the effect of genotypes on wheezing risk and examined whether this effect is carried out through changes of HDL-C. Results: Of the 16 polymorphisms tested, two polymorphisms TNFa rs3093664 and PRKCA rs9892651 presented significant differences in genotype distribution among current-wheezers and controls. Higher HDL-C levels were noted in carriers of genotype GG of polymorphism TNFa rs3093664 that was protective for wheezing Vs AG and AA genotypes (65.3 Vs 51.8 and 53.3 mg/dl, p-value < 0.001 and p-value for trend = 0.028). In polymorphism PRKCA rs9892651, HDL-C levels were lower in carriers of CC and TC genotypes that were more frequent in current-wheezers Vs TT genotype (52.2 and 52.7 Vs 55.2 mg/dl, p-value = 0.042 and p-value for trend = 0.02). The association of TNFa rs3093664 with wheezing is partly mediated by its effect on HDL-C whereas association of PRKCA rs9892651 with wheezing appeared to be independent of HDL-C. Conclusions: We found evidence that two SNPs located in different genetic loci, are associated with both wheezing and HDL-C levels, although more studies in other populations are needed to confirm our results

Univariate analysis of associations between <i>CASR</i> SNP genotypes and risk factors for aortic and coronary artery calcification.

<p>Results are shown as mean ± SD; −, indicates values not provided. Individual SNP genotypes that were present in N ≤3 individuals were excluded from analysis. Associations at the <i>P</i> ≤0.2 statistical level and used for multivariate modelling are highlighted in bold. Calcium, serum total calcium (mmol/L); Phosphate, serum phosphate (mmol/L); PTH, serum intact parathyroid hormone; Creatinine, serum creatinine; Glucose, serum glucose; Cholesterol, serum total cholesterol; 1,25 Vitamin D, 1,25-dihydroxyvitamin D. The genotypic alleles of the A986S, R990G and Q1011E coding region SNPs are represented by amino acids.</p><p>Univariate analysis of associations between <i>CASR</i> SNP genotypes and risk factors for aortic and coronary artery calcification.</p

Comparison of <i>CASR</i> SNP genotypes in patients with low and high levels of aortic calcification (AoC) and coronary artery calcification (CAC).

<p>Results are shown as N (%). P-values (<i>P</i>) represent a Chi-squared analysis of the <600mg AoC group (N = 204) versus the >600mg AoC group (N = 63) and <100mg CAC group (N = 168) versus the >100mg CAC group (N = 99), respectively. All values are shown following Bonferroni correction. −, indicates values not provided. The genotypic alleles of the A986S, R990G and Q1011E coding region SNPs are represented by amino acids.</p><p>Comparison of <i>CASR</i> SNP genotypes in patients with low and high levels of aortic calcification (AoC) and coronary artery calcification (CAC).</p

Baseline clinical, biochemical and radiological characteristics of the Brussels Renal Transplant Cohort.

<p>Results are presented as mean ± SD or the number of patients with the % of the total of number of patients shown in parentheses. AgS, Agatston score.</p><p>^aNormal serum ranges: creatinine, 53–124 μmol/L; glucose, 3.8–6.1 mmol/L; total cholesterol, <5.0 mmol/L; total calcium, 2.10–2.50 mmol/L; phosphate, 0.77–1.50 mmol/L; intact parathyroid hormone, 1.0–6.5 pmol/L; 25-hydroxyvitamin D, 75–250 nmol/L; 1,25-dihydroxyvitamin D, 47–117 pmol/L.</p><p>Baseline clinical, biochemical and radiological characteristics of the Brussels Renal Transplant Cohort.</p

<i>CASR</i> polymorphism genotype and allele frequencies in the Brussels Renal Transplant Cohort.

<p>Genotype frequencies are provided for homozygous major alleles, heterozygous alleles, and homozygous minor alleles, respectively in N = 284 subjects. Allelic frequencies are provided for major and minor alleles, respectively. UTR, untranslated region.</p><p><i>CASR</i> polymorphism genotype and allele frequencies in the Brussels Renal Transplant Cohort.</p

3D microperfusion of mesoscale human microphysiological liver models improves functionality and recapitulates hepatic zonation

Hepatic in vitro models that accurately replicate phenotypes and functionality of the human liver are needed for applications in toxicology, pharmacology and biomedicine. Notably, it has become clear that liver function can only be sustained in 3D culture systems at physiologically relevant cell densities. Additionally, drug metabolism and drug-induced cellular toxicity often follow distinct spatial micropatterns of the metabolic zones in the liver acinus, calling for models that capture this zonation. We demonstrate the manufacture of accurate liver microphysiological systems (MPS) via engineering of 3D stereolithography printed hydrogel chips with arrays of diffusion open synthetic vasculature channels at spacings approaching in vivo capillary distances. Chip designs are compatible with seeding of cell suspensions or preformed liver cell spheroids. Importantly, primary human hepatocytes (PHH) and hiPSC-derived hepatocyte-like cells remain viable, exhibit improved molecular phenotypes compared to isogenic monolayer and static spheroid cultures and form interconnected tissue structures over the course of multiple weeks in perfused culture. 3D optical oxygen mapping of embedded sensor beads shows that the liver MPS recapitulates oxygen gradients found in the acini, which translates into zone-specific acet-ami-no-phen toxicity patterns. Zonation, here naturally generated by high cell densities and associated oxygen and nutrient utilization along the flow path, is also documented by spatial proteomics showing increased concentration of periportal- versus perivenous-associated proteins at the inlet region and vice versa at the outlet region. The presented microperfused liver MPS provides a promising platform for the mesoscale culture of human liver cells at phenotypically relevant densities and oxygen exposures. Statement of significance: A full 3D tissue culture platform is presented, enabled by massively parallel arrays of high-resolution 3D printed microperfusion hydrogel channels that functionally mimics tissue vasculature. The platform supports long-term culture of liver models with dimensions of several millimeters at physiologically relevant cell densities, which is difficult to achieve with other methods. Human liver models are generated from seeded primary human hepatocytes (PHHs) cultured for two weeks, and from seeded spheroids of hiPSC-derived human liver-like cells cultured for two months. Both model types show improved functionality over state-of-the-art 3D spheroid suspensions cultured in parallel. The platform can generate physiologically relevant oxygen gradients driven by consumption rather than supply, which was validated by visualization of embedded oxygen-sensitive microbeads, which is exploited to demonstrate zonation-specific toxicity in PHH liver models.</p