Genome-wide association studies (GWAS) have identified thousands of variants associated with complex traits, yet the majority lie in noncoding regions, making it difficult to determine their functional impact. Alterations to the three-dimensional (3D) spatial interactions among gene regulatory elements are increasingly recognized as a mechanism by which genetic variants influence gene expression. However, experimentally evaluating whether variants disrupt 3D-genome structure is not feasible at GWAS scale. To address this, we developed a computational framework that integrates GWAS summary statistics with predictions from the Akita sequence-based deep learning model of 3D chromatin contacts. We applied the framework to 9,917 genomic regions associated with human height, assessing both individual variants and haplotypes for their predicted impact on 3D genome architecture. Only a small fraction of height-associated haplotypes had substantial predicted disruption of 3D folding (17 regions, 0.17%, exceeded a disruption score of 0.1). Considering all common variants in a haplotype together generally produced greater perturbations than individual variants, but several highly divergent regions were driven by single variants. We highlight a variant that disrupts the binding motif at a confirmed CTCF binding site and is predicted to modify 3D genome contacts with the LCOR promoter, suggesting that 3D-genome-mediated disruption of gene regulation underlies the association with height. This work presents a scalable and interpretable strategy for integrating 3D genome modeling with GWAS, enabling investigation of this important regulatory mechanism in the connection of non-coding genetic variation to complex traits. ### Competing Interest Statement The authors have declared no competing interest.

Relatedness within genomic cohorts is a potential source of bias for many genetic analyses. Existing tools to break relatedness are phenotype-naïve; they indiscriminately remove subjects to break relationship, risking the loss of valuable data, especially in studies targeting uncommon and rare phenotypes. To address this limitation, we developed the Kinship Decouple and Phenotype Selection (KDPS) tool, with a novel algorithm designed to enhance the precision of subject selection in genetic and epidemiological research by incorporating phenotype prioritization. KDPS separates related individuals by considering relatedness (kinship or identity by descent) scores and allows prioritizing subjects based on phenotypes of interest. This approach enables the retention of valuable subjects for analysis, even in the face of necessary exclusions due to relatedness. Furthermore, KDPS accommodates a wide range of phenotypes, including quantitative and categorical, and allows for customization to either prioritize specific phenotypes or maximization of sample size. In simulations based on the UK Biobank dataset and real-world datasets, KDPS demonstrated significant improvements in retention of subjects with prioritized phenotypes and computational efficiency compared to previously published software. The ability of this method to process biobank-scale studies within practical timeframes marks the ability of this method to process biobank-scale studies within practical timeframes and marks a considerable advancement over existing techniques. KDPS offers tailored solutions for complex analytical challenges and broad applicability in genetics and epidemiology research. To our knowledge, KDPS is the first tool to perform phenotype-aware decoupling, paving the way for more powerful genetic and epidemiological analyses.

Accurately identifying and quantifying human blood circular RNAs (circRNAs) from RNA-seq data is a critical bioinformatics challenge in biomarker discovery for human diseases. In this study, we present AQUARIUM-HB, a comprehensive bioinformatics pipeline for identifying, quantifying, annotating, and analyzing circRNAs from human blood transcriptomes. AQUARIUM-HB includes three functional modules. First, it identifies and annotates circRNAs from rRNA-depleted RNA-seq datasets of human blood samples. Second, it performs an in-depth expression analysis of blood circRNAs. Third, it constructs a reference set of full-length blood circRNAs. We demonstrate the application of AQUARIUM-HB using a human blood RNA-seq dataset from COVID-19 patients, showcasing its potential for improving the accuracy and depth of circRNA biomarker discovery.

ObjectiveChikungunya virus (CHIKV) is a re-emerging mosquito-borne human pathogen, which poses critical threats to the public health. However, an effective diagnostic method for early CHIKV infection remains scarce. Circular RNAs (CircRNAs) are a novel class of RNAs with important biological functions. They have been shown to be promising biomarkers for many human diseases. In this study, we sought to identify circRNA biomarkers in human peripheral whole blood for the early diagnosis of CHIKV infection.DesignCandidate circRNA biomarkers were identified by group comparison using a case-control study, which was further validated using an independent cohort. The performance of this signature and its correlation with clinical factors were estimated in both cohorts.ResultsUsing two public RNA-seq datasets of CHIKV infection, we developed and validated a 13-circRNA based blood signature that can discriminate CHIKV infectious patients from healthy controls. Furthermore, this blood circRNA signature was correlated with viral load in patients with CHIKV infection. Functional analysis implicated that these biomarker circRNAs were involved in the activation and regulation of immune processes against CHIKV infection.ConclusionCollectively, our findings indicated that peripheral blood circRNAs were potential biomarkers for the early diagnosis of CHIKV infection.

Blood circular RNAs (circRNAs) are stable noncoding RNAs with diverse functions, yet a comprehensive blood-derived circRNA resource is lacking. We developed BloodCircR, a database of circRNAs from human peripheral blood, integrating 5,430 RNA-seq samples across 58 diseases. Using CIRI-full and public datasets, we identified ∼2.3 million circRNAs, including >1.7 million exonic, most at full length. BloodCircR offers transcript-level annotation, expression and differential analysis, and functional insights into circRNA-miRNA and circRNA-RBP interactions. This resource supports circRNA research in disease and biomarker discovery, with potential therapeutic relevance.

Highland groups have adapted to the extreme selective pressures of hypoxia at high altitude via alterations in the oxygen-transport cascade. PRKAA1, which encodes the catalytic subunit of the AMP-activated protein kinase (AMPK), is a notable target of natural selection in Andeans and has been associated with protective fetal phenotypes in this population. AMPK is a universal cellular energy sensor involved in a multitude of physiological processes, including ventilation and the hypoxic ventilatory response (HVR) in animal models. We localized a signal of positive selection and identified a regulatory promoter variant (rs10035235, C>T) of adaptive significance that is associated with ventilatory and sleep phenotypes in male Andean highlanders as well as sleep phenotypes in publicly available lowland cohorts. This work identifies a functional, adaptive, and likely pleiotropic regulatory variant in PRKAA1 in Andeans that may accentuate hypoxia-induced ventilation and provide protection from sleep-disordered breathing in both high- and lowland populations.

Advancements in genetic research have greatly enhanced our understanding of human adaptation to high-altitude environments through the identification of genetic markers linked to hypoxia tolerance. Our recent studies identify key genes associated with haematological and ventilatory traits in Andeans. Adaptive variation at EPAS1, encoding endothelial PAS domain protein 1, a key regulator in the hypoxia-inducible factor (HIF) pathway (the alpha subunit of HIF2), has been associated with relatively low haematocrit at high altitude, which may be linked directly or indirectly to improvements in oxygen transport and/or delivery, while PRKAA1, encoding the AMP-activated protein kinase (AMPK) alpha-1 subunit, has been linked to ventilatory responses during wakefulness that are further associated with sleep phenotypes with metabolic implications. The relevance of these genetic adaptations extends beyond adult physiology; e.g. other studies have associated an adaptive genetic signature at PRKAA1 with pregnancy outcomes in Andean populations. Understanding how adaptive genetic variations in EPAS1 and PRKAA1 contribute to hypoxia tolerance offers a foundation for investigating broader evolutionary mechanisms of high-altitude adaptation, particularly in the contexts of pregnancy and fetal development, where oxygen availability is crucial. Integrative studies that combine molecular, physiological, and evolutionary perspectives offer promise in revealing the complexities of high-altitude adaptation and its relevance to hypoxia-related health challenges in both highland and lowland populations.This article is part of the discussion meeting issue 'Pregnancy at high altitude: the challenge of hypoxia'.

High-altitude pregnancy presents the complex physiological challenge of fulfilling maternal, placental, and fetal metabolic demands under chronic ambient hypoxia. Highland Andeans exhibit signs of adaptation to high-altitude hypoxia, showing relative protection against altitude-associated fetal growth restriction (FGR) and the positive selection of metabolic genes linked to placental mitochondrial capacity. Not all infants are protected, with both FGR and preeclampsia occurring among highland-resident Andeans. In Andeans, placental metabolic dysfunction is evident. By integrating metabolomic studies of maternal-placental-fetal triads with adaptive genetic signals in the fetal genome, we sought to identify adaptive and maladaptive placental metabolic phenotypes in highland Andeans (La Paz, Bolivia; 3850 m), including normotensive and preeclamptic pregnancies. Widespread differences in metabolite abundance were evident between normotensive and preeclamptic pregnancy across maternal, placental, and fetal compartments. Preeclampsia was characterized by a pronounced accumulation of fatty acid derivatives, specifically medium and long-chain acylcarnitines; these were also associated with low birth weight. Genotype-phenotype association analyses revealed novel links between putatively adaptive fetal haplotypes and placental metabolite abundance. Carriers of specific adaptive fetal haplotypes comprising genes linked to lipid metabolism had a greater abundance of placental short-chain acetyl-carnitine alongside decreased levels of linolenic acid (CPT2/LRP8), lower levels of the medium-chain octanoylcarnitine (EXOC4), and greater abundance of free carnitine (LIPG). Collectively, our study reveals a distinct metabolic phenotype in Andean preeclampsia characterized by incomplete fatty acid oxidation and highlights novel links between putatively adaptive fetal haplotypes and healthy placental metabolic phenotypes.

Hypoxia-inducible factor pathway genes are linked to adaptation in both human and nonhuman highland species. EPAS1 , a notable target of hypoxia adaptation, is associated with relatively lower hemoglobin concentration in Tibetans. We provide evidence for an association between an adaptive EPAS1 variant (rs570553380) and the same phenotype of relatively low hematocrit in Andean highlanders. This Andean-specific missense variant is present at a modest frequency in Andeans and absent in other human populations and vertebrate species except the coelacanth. CRISPR-base-edited human cells with this variant exhibit shifts in hypoxia-regulated gene expression, while metabolomic analyses reveal both genotype and phenotype associations and validation in a lowland population. Although this genocopy of relatively lower hematocrit in Andean highlanders parallels well-replicated findings in Tibetans, it likely involves distinct pathway responses based on a protein-coding versus noncoding variants, respectively. These findings illuminate how unique variants at EPAS1 contribute to the same phenotype in Tibetans and a subset of Andean highlanders despite distinct evolutionary trajectories.

A 'grammar of graphics' approach for visualizing summary statistics from multiple Genome-wide Association Studies (GWAS). It offers geneticists, bioinformaticians, and researchers a powerful yet flexible tool for illustrating complex genetic associations using data from various GWAS datasets. The visualizations can be extensively customized, facilitating detailed comparative analysis across different genetic studies. Reference: Uffelmann, E. et al. (2021) .

BACKGROUND:Three-dimensional weightbearing CT (WBCT) has been widely used to assess foot and ankle alignment. However, most current measurement methods are based on 2-dimensional concepts-distance, long axis, angulation, etc-and are sensitive to changes in orientation of the WBCT images. This study demonstrated how changes in positioning of the image can significantly influence the evaluation of hindfoot alignment. METHODS:WBCT scans of 10 feet without deformities were used. In the horizontal view, the long axis of the foot image was aligned to a neutral position and then rotated 5, 10, 15, and 20 degrees both internally and externally to simulate malposition. The Calcaneal Moment Arm (CMA) was measured by 2 investigators independently in the above positions. An intraclass correlation coefficient (ICC) model was used to assess the intra- and interobserver reliabilities. The correlation between the CMA and the rotation angle of the foot images was analyzed using linear regression. RESULTS:The CMA measurements demonstrated that internal rotation of the image changed the neutral hindfoot into valgus, whereas external rotation led to varus. A 1-degree internal or external rotation of the image correlated with 0.48 (±0.03) mm increase or decrease in the modified WBCT-CMA value (P < .0001, R2 = 0.6406). CONCLUSION:This study demonstrated that although 3D WBCT provides the ability to observe the foot from different perspectives, current alignment evaluation tools are limited to 2 dimensions. Therefore, positioning the WBCT images in a consistent orientation is important to generate correct data.

Objective: This study introduced a modified weight-bearing computed tomography to measure the calcaneal moment arm (WBCTCMA) and compared the CMA values between the original and modified techniques. Methods: The WBCT scans of 10 healthy feet were loaded in the CubeVue software, correctly oriented in the transverse plane. Instead of using a specific single coronal cut of the tibia, as in the original WBCT-CMA method, the modified method includes the full thickness of the tibia in the coronal plane to better define the tibia axis. The CMA of each foot was evaluated using both methods. Intraclass correlation coefficient (ICC) model was used to assess the intra- and interobserver reliabilities of both techniques. Results: There was no statistically significant difference between the CMA values generated from the two measurement techniques (p = 0.99). Both methods demonstrated excellent intra- and interobserver reliabilities (0.93 and 0.97 for the modified WBCT-CMA, and 0.93 and 0.94 for the original WBCT-CMA). Conclusion: The modified WBCT-CMA is equivalent to the original WBCT-CMA in both intra- and interobserver reliabilities. Instead of using a relatively shorter tibia from one specific single cut, as in the original technique, the modified WBCT-CMA provides a reconstructed tibia with a longer and clearer shaft for measurement. This has the potential advantages of being easy to perform and less time-consuming, also reducing errors. Level of Evidence III; Retrospective comparative study.

Kawasaki Disease (KD) affects young children less than five years old with severe blood vessel inflammation. Despite being treatable, the causes and mechanisms remain elusive. This study conducted a meta-analysis of RNA sequencing (RNA-seq) data from human and animal models to explore KD's transcriptomic profile and evaluate animal models. We retrieved bulk and single-cell RNA-seq data from Gene Expression Omnibus, with blood and coronary artery samples from KD patients, aorta samples from KD mouse models (Lactobacillus casei cell wall extract-injected mice), and their controls. Upon consistent quality control, we applied Fisher's exact test to assess differential gene expression, followed by an enrichment analysis of overlapping genes. These studies identified 400 differentially expressed genes in blood samples of KD patients compared to controls and 413 genes in coronary artery samples. The data from KD blood and KD coronary artery samples shared only 16 differentially expressed genes. Eighty-one genes overlapped between KD human coronary arteries and KD mouse aortas, and 67 of these 81 genes were regulated in parallel in both humans and mice: 30 genes were up-regulated, and 37 were down-regulated. These included previously identified KD-upregulated genes: CD74, SFRP4, ITGA4, and IKZF1. Gene enrichment analysis revealed significant alterations in the cardiomyopathy pathway. Single-cell RNAseq showed a few significant markers, with known KD markers like S100A9, S100A8, CD74, CD14, IFITM2, and IFITM3, being overexpressed in KD cohorts. Gene profiles obtained from KD human coronary artery are more compatible with data from aorta samples of KD mice than blood samples of KD humans, validating KD animal models for identifying therapeutic targets. Although blood samples can be utilized to discover novel biomarkers, more comprehensive single-cell sequencing is required to detail gene expression in different blood cell populations. This study identifies critical genes from human and mouse tissues to help develop new treatment strategies for KD.

Hypobaric hypoxia exerts a significant evolutionary pressure on highlanders who have resided at high altitude for thousands of years. This evolutionary pressure has resulted in signatures of natural selection within native highlanders’ genomes, some of which associate with adaptive physiological traits. Our recent analyses examined the overlap of a priori functional candidate genes and genes identified in the composite of multiple signals test of selection in 40 Andean genomes. We identified ICAM1, which encodes the intercellular adhesion molecule 1 protein, as one of the top 10 candidate genes of positive selection in this highland population. We utilized LDproxy and CADD score analysis to prioritize variants of functional relevance in this gene. The single-nucleotide variant (SNV) rs1799969, located in exon 4, exhibited the highest CADD score of 22.0. We genotyped rs1799969 in a larger cohort of 255 Andean highlanders and found that 68% of Andeans have at least one copy of the SNV, compared to 6% and 20% in worldwide and American populations, respectively, from the 1000 Genomes data set. Given the soluble form of ICAM1 is elevated in patients with COPD, atherosclerosis, coronary heart disease, and other cardiometabolic phenotypes, and rs1799969 is associated with less soluble ICAM1 in larger, worldwide cohorts, we tested the hypothesis that putatively adaptive copies of ICAM1 would be associated with blood pressure in the high-altitude Andean cohort. We found that more copies of the putatively adaptive haplotype containing rs1799969 is associated with lower systolic blood pressure (p-value = 0.012 for 0 vs 2 alleles, 0.028 for 0 vs 1 allele; effect size = 7.1mmHg for males, 13.5mmHg for females; NS diastolic blood pressure), whereby the effect size of the number of adaptive gene copies on systolic blood pressure is comparable to commonly prescribed medications and orders of magnitude larger than previous genetic association studies of blood pressure (~1.5mmHg for rare variants, ~0.5mmHg for common variants). Because ICAM1 is activated by hypoxia, it is plausible that rs1799969 may play a protective physiological role in the context of chronic hypoxia in Andean highlanders. Hypertension is one of the strongest modifiable risk factors for cardiometabolic disease, and this may be especially relevant in hypobaric hypoxia, where chronic activation of sympathetic activity can increase blood pressure. Additionally, elevated blood pressure is a known causative agent for diseases that are exacerbated at high altitude, such as pre-eclampsia. However, studies of hypertension in native highland populations have mixed results, often reporting conflicting associations depending on the population being studied, warranting further investigations into hypertension prevalence in various highland populations and genetic factors that may impact blood pressure. Supported by NIH 1R01HL145470 to TSS This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Background: To investigate the relationship between dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) radiomic features and the expression activity of hallmark pathways and to develop prediction models of pathway-level heterogeneity for breast cancer (BC) patients. Methods: Two radiogenomic cohorts were analyzed (n = 246). Tumor regions were segmented semiautomatically, and 174 imaging features were extracted. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were performed to identify significant imaging-pathway associations. Random forest regression was used to predict pathway enrichment scores. Five-fold cross-validation and grid search were used to determine the optimal preprocessing operation and hyperparameters. Results: We identified 43 pathways, and 101 radiomic features were significantly related in the discovery cohort (p-value < 0.05). The imaging features of the tumor shape and mid-to-late post-contrast stages showed more transcriptional connections. Ten pathways relevant to functions such as cell cycle showed a high correlation with imaging in both cohorts. The prediction model for the mTORC1 signaling pathway achieved the best performance with the mean absolute errors (MAEs) of 27.29 and 28.61% in internal and external test sets, respectively. Conclusions: The DCE-MRI features were associated with hallmark activities and may improve individualized medicine for BC by noninvasively predicting pathway-level heterogeneity.

Andean highlanders living at high altitude (>4200 m) for hundreds of generations exhibit distinct cardiovascular and ventilatory traits in response to environmental stress. Adrenergic Receptor Alpha-1A ( ADRA1A), a gene coding for the Alpha 1-A adrenergic receptor, has been previously shown to be under positive natural selection in the Andeans. ADRA1A has also been demonstrated to have a protective effect against cardiovascular complications in other lowland populations. We hypothesized that putatively adaptive single nucleotide variants (SNVs) of strong functional impact can be found in ADRA1A and associated with cardiovascular traits in the Andean highlanders.We examined data from the Composite of Multiple Signals test in 40 high-coverage whole genomes of Andean highlanders living in Cerro de Pasco, Peru (~4340 m), specifically focusing on SNVs with strong predicted functional impact. Genetic variants of interests were then genotyped and tested for phenotypic associations in an extended Andean cohort (132 males, 46 females). The presence of Chronic Mountain Sickness (CMS), a maladaptive syndrome observed in Andean highlanders characterized by excessive erythrocytosis, and resting heart rate during hypoxia were prioritized for the regression analysis. The genotype-phenotype association analysis adapted a multivariate linear model with sex as a stratum and age as a covariate.A missense variant (rs1048101, A>G) in the second exon of ADRA1A with strong predicted functional impact was tagged by the Composite of Multiple Signals analysis. In Andean males, the rs1048101 A allele was associated with 1.52-fold decreased risk for CMS (p<0.018) and attenuated resting heart rate at room air (~10% inspired O 2 ) and at 21% inspired O 2 (room air: p<0.019, 21% O 2 : p<0.012). In women, the association between ADRA1A rs1048101 and CMS was not significant (p>0.917). In addition, women with more copies of the putatively adaptive A allele demonstrated increased heart rate both at room air and 21% inspired O 2 (room air: p<0.033, 21% O 2 : p<0.044) in contrast to observations in men.In conclusion, the putatively adaptive missense variant rs1048101 at ADRA1A demonstrated a protective effect against Chronic Mountain Sickness and was further associated with decreased resting heart rate in Andean males. The lack of replicability of these associations in females suggests potential sex-dependent effect of ADRA1A. Further experiments functionalizing the variant and validating the associations in large genome cohorts may shed light on the mechanisms of the gene. This project is funded by R01HL145470. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Highly transcribed noncoding elements (HTNEs) are critical noncoding elements with high levels of transcriptional capacity in particular cohorts involved in multiple cellular biological processes. Investigation of HTNEs with persistent aberrant expression in abnormal tissues could be of benefit in exploring their roles in disease occurrence and progression. Breast cancer is a highly heterogeneous disease for which early screening and prognosis are exceedingly crucial. In this study, we developed a HTNE identification framework to systematically investigate HTNE landscapes in breast cancer patients and identified over ten thousand HTNEs. The robustness and rationality of our framework were demonstrated via public datasets. We revealed that HTNEs had significant chromatin characteristics of enhancers and long noncoding RNAs (lncRNAs) and were significantly enriched with RNA-binding proteins as well as targeted by miRNAs. Further, HTNE-associated genes were significantly overexpressed and exhibited strong correlations with breast cancer. Ultimately, we explored the subtype-specific transcriptional processes associated with HTNEs and uncovered the HTNE signatures that could classify breast cancer subtypes based on the properties of hormone receptors. Our results highlight that the identified HTNEs as well as their associated genes play crucial roles in breast cancer progression and correlate with subtype-specific transcriptional processes of breast cancer.

The extrathoracic oral airway is not only a major mechanical barrier for pharmaceutical aerosols to reach the lung but also a major source of variability in lung deposition. Using computational fluid dynamics, deposition of 1–30 µm particles was predicted in 11 CT-based models of the oral airways of adults. Simulations were performed for mouth breathing during both inspiration and expiration at two steady-state flow rates representative of resting/nebulizer use (18 L/min) and of dry powder inhaler (DPI) use (45 L/min). Consistent with previous in vitro studies, there was a large intersubject variability in oral deposition. For an optimal size distribution of 1–5 µm for pharmaceutical aerosols, our data suggest that >75% of the inhaled aerosol is delivered to the intrathoracic lungs in most subjects when using a nebulizer but only in about half the subjects when using a DPI. There was no significant difference in oral deposition efficiency between inspiration and expiration, unlike subregional deposition, which shows significantly different patterns between the two breathing phases. These results highlight the need for incorporating a morphological variation of the upper airway in predictive models of aerosol deposition for accurate predictions of particle dosimetry in the intrathoracic region of the lung.

BACKGROUND: The chronic hypoxia of high-altitude residence poses challenges for tissue oxygen supply and metabolism. Exposure to high altitude during pregnancy increases the incidence of hypertensive disorders of pregnancy and fetal growth restriction and alters placental metabolism. High-altitude ancestry protects against altitude-associated fetal growth restriction, indicating hypoxia tolerance that is genetic in nature. Yet, not all babies are protected and placental pathologies associated with fetal growth restriction occur in some Andean highlanders. METHODS: We examined placental metabolic function in 79 Andeans (18–45 years; 39 preeclamptic and 40 normotensive) living in La Paz, Bolivia (3600–4100 m) delivered by unlabored Cesarean section. Using a selection-nominated approach, we examined links between putatively adaptive genetic variation and phenotypes related to oxygen delivery or placental metabolism. RESULTS: Mitochondrial oxidative capacity was associated with fetal oxygen delivery in normotensive but not preeclamptic placenta and was also suppressed in term preeclamptic pregnancy. Maternal haplotypes in or within 200 kb of selection-nominated genes were associated with lower placental mitochondrial respiratory capacity ( PTPRD [protein tyrosine phosphatase receptor-δ]), lower maternal plasma erythropoietin ( CPT2 [carnitine palmitoyl transferase 2], proopiomelanocortin, and DNMT3 [DNA methyltransferase 3]), and lower VEGF (vascular endothelial growth factor) in umbilical venous plasma ( TBX5 [T-box transcription factor 5]). A fetal haplotype within 200 kb of CPT2 was associated with increased placental mitochondrial complex II capacity, placental nitrotyrosine, and GLUT4 (glucose transporter type 4) protein expression. CONCLUSIONS: Our findings reveal novel associations between putatively adaptive gene regions and phenotypes linked to oxygen delivery and placental metabolic function in highland Andeans, suggesting that such effects may be of genetic origin. Our findings also demonstrate maladaptive metabolic mechanisms in the context of preeclampsia, including dysregulation of placental oxygen consumption.

Andeans have resided at high altitude for thousands of years and exhibit distinct physiological phenotypes to maintain homeostasis under the selective pressure of hypoxia. Based on previous whole-genome sequence data generated in 40 Andeans from Cerro De Pasco, Peru, at an altitude of 4340m, we utilized the composite of multiple signals (CMS) test of selection and identified an adaptive signal at PRKAA1, the gene which encodes the alpha-1 subunit of the AMP-activated protein kinase (AMPK). We hypothesize that genetic variants in PRKAA1 are associated with control of breathing in highland populations exposed to chronic hypoxia.While no protein-coding variants were identified as potential functional targets of selection, we identified several putatively adaptive variants within epigenetic regulatory regions of PRKAA1. The variants identified were in high linkage-disequilibrium (LD) with our selection scan markers as well as previously reported PRKAA1 variants associated with uterine artery diameter and other fetal phenotypes in Andeans. Our in-silico analyses reveal that the epigenetic landscape within the gene promoter region containing rs10035235 strongly implicates the role of rs10035235 in transcriptional regulation of PRKAA1.We demonstrated genotype-phenotype associations between a PRKAA1 promoter variant rs10035235 (chr5:40798644, C>T) and control of breathing phenotypes in Andeans. Males with copies of the putatively adaptive T allele were shown to have increased hypoxic ventilatory response (p < 0.03). The variant was also associated with end-tidal CO2 (p < 0.01), ventilation (p < 0.05), and heart rate (p < 0.05). We further examined the effect of rs10035235 on PRKAA1 gene expression using a luciferase assay in HEK293 cells and found the T allele resulted in a 203% increase in expression relative to cells with the non-adaptive C allele (p < 0.05).To assess whether rs10035235 was associated with other phenotypes, we tested for associations with a subset of phenotypes from the Hispanic Community Health Study, Study of Latinos (HCHS-SOL) (n = 11,893). We identified associations with apneic events (FDR < 3.30E-3), total time spent in apnea (FDR < 7.90E-4) as well as the apnea/hypopnea index (FDR < 3.09E-3). These findings suggest that adaptation at the PRKAA1 locus is associated with increased breathing responses to hypoxia in Andean highlanders and may underlie variation in sleep-apnea related phenotypes in the Hispanic/Latino population.In conclusion, we indentify rs10035235 as a positively selected, functional regulatory variant in the promoter of PRKAA1 using in-silico prediction and cellular models. We also utilized our prior genotype-phenotype associations and the HCHS-SOL cohort data to demonstrate novel association of rs10035235 with pulmonary, cardiac, and sleep phenotypes. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.