Leslie J. Baier

Objective: To identify heritable factors that affect BMI among Indigenous Americans, we previously conducted a genome‐wide association study using 7.9 million imputed genetic variants from 6789 participants. This study sought to identify a mechanistic link between variants with the strongest association with BMI and adipocyte metabolism. Methods: Variants with the strongest association with BMI (rs114857151, rs187498396, and rs189879565; r ² = 0.99, 2.7% increase in BMI per risk allele, p = 4 × 10 ⁻⁷ , adjusted for age, sex, birth year, and the first five genetic principal components) were functionally analyzed using luciferase assays. Results: These variants map to CYP26B1 , which encodes an enzyme involved in retinoic acid (RA) metabolism. In vitro studies showed that the haplotype with the three risk (higher BMI) variants had a 23% decrease in CYP26B1 transcript variant 3 (TV3) promoter activity. RA response element reporter assays showed that the Cyp26b1 TV3 isoform might be important for RA homeostasis in adipocytes. Cyp26b1 TV3 knockdown in mouse OP9 adipocytes resulted in increased Aldh1a1 expression. Conclusion: Alleles carrying these three variants may have reduced expression of CYP26B1 TV3 which in turn influences RA signaling and adipocyte metabolism, providing a possible mechanistic link between CYP26B1 variation and BMI.

The strongest type 2 diabetes signal in Indigenous Americans from Arizona is in intron 15 of KCNQ1. We previously identified a functional region in this intron that contained four type 2 diabetes–associated single nucleotide polymorphisms (SNPs) (rs2299620, rs2237896, rs2237897, and rs74046911) and demonstrated functionality of this fragment using Indigenous American induced pluripotent stem cell (iPSC)-derived pancreatic islets (SC-islets). In the current study, we used isogenic iPSCs with targeted edits at these four SNPs, and three additional SNPs (rs2237895, rs60808706, and rs234864), to generate SC-islets and study the effect of these variants during different developmental stages. We identify an 11% reduction in stem cell–derived β-cells (SC-β-cells) in SC-islets with the risk alleles, suggesting an effect of these variants on β-cell mass. We further show premature endocrine commitment in cells with the risk allele and lower rate of β-cell commitment during the endocrine progenitor stages, likely due to differences in H19 and INS gene expression dynamics. We also show that the differential expression may be attributable to lower CpG methylation and higher chromatin accessibility in cells with the risk alleles. In summary, the type 2 diabetes SNPs at KCNQ1 affect SC-β-cell generation, and this effect is manifested early during development, likely via an epigenomic effect on gene regulation. Article Highlights: We previously developed an induced pluripotent stem cell–based model to study an intronic region of KCNQ1 that represents the strongest association signal with type 2 diabetes in Indigenous Americans from Arizona. The current study builds on this model by using CRISPR/Cas9-edited isogenic cells that differ only by targeted type 2 diabetes single nucleotide polymorphisms in this intronic region. The effect of KCNQ1 type 2 diabetes single nucleotide polymorphisms on pancreatic β-cell development and the probable mechanism of this effect were previously unknown. The current study shows an effect on INS and H19 gene expression dynamics specifically during the endocrine progenitor stage of pancreatic islet development likely via an epigenomic effect on gene regulation resulting in generation of lower β-like cells. Individuals carrying KCNQ1 risk alleles for type 2 diabetes will likely benefit from therapeutics that increase pancreatic β-cell mass.

Aims/hypothesis: An R1420H variation in sulfonylurea receptor 1 (SUR1), a subunit of the K _ATP channel, was previously identified in an Indigenous community in Arizona where a homozygous carrier (1420HH) had hyperinsulinaemic hypoglycaemia during infancy (HHI), suggestive of a K _ATP channel loss of function (LoF). Interestingly, heterozygous carriers of this variation (1420RH, occurring in 3% of the community), had a twofold increased risk of type 2 diabetes. We aimed to create an isogenic induced pluripotent stem cell (iPSC)-derived pancreatic islet (SC-islet)-based platform to test whether the R1420H variant results in K _ATP channel LoF, and to examine the distinct temporal effects of SUR1 1420HH and 1420RH K _ATP channel variations on insulin secretion from developing and mature SC-islets. Methods: Using CRISPR-Cas9, isogenic iPSCs with all three genotypes (SUR1 1420RR, 1420RH and 1420HH) were generated from two different parental Indigenous American iPSC lines (IS1, isogenic cell lines derived from parental cell line 1; and IS2, isogenic cell lines derived from parental cell line 2). These isogenic cell lines were used to generate immature SC-islets (resembling fetal islets) and mature SC-islets (resembling adult islets), which were used to assess insulin secretion dynamics during different stages of development and identify differences in gene expression by single-cell RNA-seq. This study was consistent with the CONSIDER statement for research studies among Indigenous American communities. Results: Immature SUR1 1420HH SC-islets secreted 3.4-fold (IS1, p p =0.001) more insulin under basal conditions than normal (SUR1 1420RR) SC-islets. Modest hyperinsulinaemia was also seen in immature SUR1 1420RH SC-islets (2.2-fold [IS1] and 2.3-fold [IS2]) but the results were not statistically significant. After maturation, the 1420HH SC-islets failed to achieve glucose responsiveness whereas the 1420RH SC-islets achieved biphasic insulin secretion but had significantly lower glucose responsiveness than normal SC-islets (AUC for insulin secretion [as a % of total insulin] under high glucose challenge: 1.04 vs 0.56 in normal vs 1420RH SC-islets, p p =0.01 [IS1, 11 mmol/l glucose ± dorzagliatin]; 5.5-fold vs 9.0-fold, p =0.13 [IS1, 20 mmol/l glucose ± dorzagliatin]). Single-cell RNA-seq identified dysregulated genes in SUR1 1420RH SC-beta cells, including lower expression of glycolytic genes and upregulation of G6PC2 , which could explain the lower insulin secretory response to glucose. Conclusions/interpretation: A SUR1 R1420H variant identified in an Indigenous American population causes hyperinsulinaemia in homozygous immature SC-islets during basal conditions and these SC-islets fail to achieve glucose responsiveness after maturation. In the heterozygous state, modest hyperinsulinaemia is observed in immature SC-islets, which after maturation have significantly lower glucose responsiveness. These results demonstrate that SUR1 R1420H is a K _ATP channel LoF variation and suggest that a lower insulin secretory response during adulthood is the cause of the higher type 2 diabetes risk in individuals heterozygous for this variation. We also show that the isogenic iPSC-based platform can be used to test therapeutic agents to treat HHI in infants homozygous for LoF K _ATP channels and screen for drugs that can improve glucose-responsive insulin secretion in adult heterozygous carriers. Data availability: See the database of Genotypes and Phenotypes (dbGaP; dbgap.ncbi.nlm.nih.gov/home; accession no.: phs002490.v1.p1) for details concerning data requests. All source codes can be found in the GitHub repository under https://github.com/Koushik-Cheranda/SC-islet-scRNAseq-analysis-R-codes . Graphical

Objective: Rare cases of monogenic obesity, which may respond to specific therapeutics, can remain undetected in populations in which polygenic obesity is prevalent. This study examined rare DNA variation in established monogenic obesity genes within a community using whole‐exome sequence data from 6803 longitudinally studied individuals.Methods: Exome data across 15 monogenic obesity genes were analyzed for nonsynonymous variants observed in any child with a maximum BMI z score > 2 (N = 279) but not observed in a child with a maximum BMI z score ≤ 0 (n = 1542) or that occurred in adults in the top 5th percentile of BMI (n = 263) but not in adults below the median BMI (n = 2629). Variants were then functionally analyzed using luciferase assays.Results: The comparisons between cases of obesity and controls identified eight missense variants in six genes: DYRK1B, KSR2, MC4R, NTRK2, PCSK1, and SIM1. Among these, MC4R p.A303P and p.R165G were previously shown to impair MC4R function. Functional analyses of the remaining six variants suggest that KSR2 p.I402F and p.T193I and NTRK2 p.S249Y alter protein function.Conclusions: In addition to MC4R, rare missense variants in KSR2 and NTRK2 may potentially explain the severe obesity observed for the carriers.

There is a collective push to diversify human genetic studies by including underrepresented populations. However, analyzing DNA sequence reads involves the initial step of aligning the reads to the GRCh38/hg38 reference genome which is inadequate for non-European ancestries. In this study, using long-read sequencing technology, we constructed de novo genome assemblies from two indigenous Americans from Arizona (IAZ). Each assembly included ∼17 Mb of DNA sequence not present [nonreference sequence (NRS)] in hg38, which consists mostly of repeat elements. Forty NRSs totaling 240 kb were uniquely anchored to the hg38 primary assembly generating a modified hg38-NRS reference genome. DNA sequence alignment and variant calling were then conducted with whole-genome sequencing (WGS) sequencing data from 387 IAZ using both the hg38 and modified hg38-NRS reference maps. Variant calling with the hg38-NRS map identified ∼50,000 single-nucleotide variants present in at least 5% of the WGS samples which were not detected with the hg38 reference map. We also directly assessed the NRSs positioned within genes. Seventeen NRSs anchored to regions including an identical 187 bp NRS found in both de novo assemblies. The NRS is located in HCN2 79 bp downstream of Exon 3 and contains several putative transcriptional regulatory elements. Genotyping of the HCN2-NRS revealed that the insertion is enriched in IAZ (minor allele frequency = 0.45) compared to other reference populations tested. This study shows that inclusion of population-specific NRSs can dramatically change the variant profile in an underrepresented ethnic groups and thereby lead to the discovery of previously missed common variations.

Context The locus CELSR2-PSRC1-SORT1, a primary genetic signal for lipids, has recently been implicated in different metabolic processes. Our investigation identified its association with energy metabolism. Objective This work aimed to determine biological mechanisms that govern diverse functions of this locus. Methods Genotypes for 491 265 variants in 7000 clinically characterized American Indians were previously determined using a custom-designed array specific for this longitudinally studied American Indian population. Among the genotyped individuals, 5205 had measures of fasting lipid levels and 509 had measures of resting metabolic rate (RMR) and substrate oxidation rate assessed through indirect calorimetry. A genome-wide association study (GWAS) for low-density lipoprotein cholesterol (LDL-C) levels identified a variant in CELSR2, and the molecular effect of this variant on gene expression was assessed in skeletal muscle biopsies from 207 participants, followed by functional validation in mouse myoblasts using a luciferase assay. Results A GWAS in American Indians identified rs12740374 in CELSR2 as the top signal for LDL-C levels (P = 1 × 10⁻²²); further analysis of this variant identified an unexpected correlation with reduced RMR (effect = −44.3 kcal/day/minor-allele) and carbohydrate oxidation rate (effect = −5.21 mg/hour/kg-EMBS). Tagged variants showed a distinct linkage disequilibrium architecture in American Indians, highlighting a potential functional variant, rs6670347 (minor-allele frequency = 0.20). Positioned in the glucocorticoid receptor's core binding motif, rs6670347 is part of a skeletal muscle-specific enhancer. Human skeletal muscle transcriptome analysis showed CELSR2 as the most differentially expressed gene (P = 1.9 × 10⁻⁷), with the RMR-lowering minor allele elevating gene expression. Experiments in mouse myoblasts confirmed enhancer-based regulation of CELSR2 expression, dependent on glucocorticoids. Rs6670347 was also associated with increased oxidative phosphorylation gene expression; CELSR2, as a regulator of these genes, suggests a potential influence on energy metabolism through muscle oxidative capacity. Conclusion Variants in the CELSR2/PSRC1/SORT1 locus exhibit tissue-specific effects on metabolic traits, with an independent role in muscle metabolism through glucocorticoid signaling.

Genetic determinants of interindividual differences in energy expenditure (EE) are largely unknown. Sphingolipids, such as ceramides, have been implicated in the regulation of human EE via mitochondrial uncoupling. In this study, we investigated whether genetic variants within enzymes involved in sphingolipid synthesis and degradation affect EE and insulin-related traits in a cohort of American Indians informative for 24-h EE and glucose disposal rates during a hyperinsulinemic-euglycemic clamp. Association analysis of 10,084 genetic variants within 28 genes involved in sphingolipid pathways identified a missense variant (rs267738, A>C, E115A) in exon 4 of CERS2 that was associated with higher sleeping EE (116 kcal/day) and increased rates of endogenous glucose production during basal (5%) and insulin-stimulated (43%) conditions, both indicators of hepatic insulin resistance. The rs267738 variant did not affect ceramide synthesis in HepG2 cells but resulted in a 30% decrease in basal mitochondrial respiration. In conclusion, we provide evidence that the CERS2 rs267738 missense variant may influence hepatic glucose production and postabsorptive sleeping metabolic rate. Article Highlights:

We sought to identify genetic/immunologic contributors of type 2 diabetes (T2D) in an indigenous American community by genotyping all study participants for both high-resolution HLA-DRB1 alleles and SLC16A11 to test their risk and/or protection for T2D. These genes were selected based on independent reports that HLA-DRB1*16:02:01 is protective for T2D and that SLC16A11 associates with T2D in individuals with BMI <35 kg/m2. Here, we test the interaction of the two loci with a more complete data set and perform a BMI sensitivity test. We defined the risk protection haplotype of SLC16A11, T-C-G-T-T, as allele 2 of a diallelic genetic model with three genotypes, SLC16A11*11, *12, and *22, where allele 1 is the wild type. Both earlier findings were confirmed. Together in the same logistic model with BMI ≥35 kg/m2, DRB1*16:02:01 remains protective (odds ratio [OR] 0.73), while SLC16A11 switches from risk to protection (OR 0.57 [*22] and 0.78 [*12]); an added interaction term was statistically significant (OR 0.49 [*12]). Bootstrapped (b = 10,000) statistical power of interaction, 0.4801, yielded a mean OR of 0.43. Sensitivity analysis demonstrated that the interaction is significant in the BMI range of 30–41 kg/m2. To investigate the epistasis, we used the primary function of the HLA-DRB1 molecule, peptide binding and presentation, to search the entire array of 15-mer peptides for both the wild-type and ancient human SLC16A11 molecules for a pattern of strong binding that was associated with risk and protection for T2D. Applying computer binding algorithms suggested that the core peptide at SLC16A11 D127G, FSAFASGLL, might be key for moderating risk for T2D with potential implications for type 1 diabetes. Article Highlights: