Leveraging drug perturbation to reveal genetic regulators of hepatic gene expression in African Americans.

Expression quantitative locus (eQTL) studies have paved the way in identifying genetic variation impacting gene expression levels. African Americans (AAs) are disproportionately underrepresented in eQTL studies, resulting in a lack of power to identify population-specific regulatory variants especially related to drug response. Specific drugs are known to affect the biosynthesis of drug metabolism enzymes as well as other genes. We used drug perturbation in cultured primary hepatocytes derived from AAs to determine the effect of drug treatment on eQTL mapping and to identify the drug response eQTLs (reQTLs) that show altered effect size following drug treatment. Whole-genome genotyping (Illumina MEGA array) and RNA sequencing were performed on 60 primary hepatocyte cultures after treatment with six drugs (Rifampin, Phenytoin, Carbamazepine, Dexamethasone, Phenobarbital, and Omeprazole) and at baseline (no treatment). eQTLs were mapped by treatment and jointly with Meta-Tissue. We found varying transcriptional changes across different drug treatments and identified Nrf2 as a potential general transcriptional regulator. We jointly mapped eQTLs with gene expression data across all drug treatments and baseline, which increased our power to detect eQTLs by 2.7-fold. We also identified 2,988 reQTLs (eQTLs with altered effect size after drug treatment). reQTLs were more likely to overlap transcription factor binding sites, and we uncovered reQTLs for drug metabolizing genes such as CYP3A5. Our results provide insights into the genetic regulation of gene expression in hepatocytes through drug perturbation and provide insight into SNPs that effect the liver's ability to respond to transcription upregulation.

Balancing selection maintains ancient polymorphisms at conserved enhancers for the olfactory receptor genes of a Chinese marine fish.

The study of balancing selection, as a selective force maintaining adaptive genetic variation in gene pools longer than expected by drift, is currently experiencing renewed interest due to the increased availability of new data, methods of analysis, and case studies. In this investigation, evidence of balancing selection operating on conserved enhancers of the olfactory receptor (OR) genes is presented for the Chinese sleeper (Bostrychus sinensis), a coastal marine fish that is emerging as a model species for evolutionary studies in the Northwest Pacific marginal seas. Coupled with tests for Gene Ontology enrichment and transcription factor binding, population genomic data allow for the identification of an OR cluster in the sleeper with a downstream flanking region containing three enhancers that are conserved with human and other fish species. Phylogenetic and population genetic analyses indicate that the enhancers are under balancing selection as evidenced by their translineage polymorphisms, excess common alleles, and increased within-group diversities. Age comparisons between the translineage polymorphisms and most recent common ancestors of neutral genealogies substantiate that the former are old, and thus, due to ancient balancing selection. The survival and reproduction of vertebrates depend on their sense of smell, and thereby, on their ORs. In addition to locus duplication and allelic variation of structural genes, this study highlights a third mechanism by which receptor diversity can be achieved for detecting and responding to the huge variety of environmental odorants (i.e., by balancing selection acting on OR gene expression through their enhancer variability).

Correction : Characterization of hybridization within a secondary contact region of the inshore fish, Bostrychus sinensis, in the East China Sea.

Following the publication of this article, the authors have requested that the Acknowledgements section be amended to thank Weidi Yang for his assistance with their Bostrychus sinensis photograph that was chosen for the front cover of the January 2018 issue of the journal. This error has been corrected in both the PDF and HTML versions of the paper. Also, the legends for Supplementary Figures 1 and 2 were not posted online. This error has been corrected in the HTML version of the paper.

Diversity and Dynamics of "Candidatus Endobugula" and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina.

Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, "Candidatus Endobugula sertula" continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. "Ca. Endobugula sertula" is confirmed as the symbiont of the Chinese "Ca. Endobugula"/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, "Ca. Endobugula," and bryostatins more globally.

Characterization of hybridization within a secondary contact region of the inshore fish, Bostrychus sinensis, in the East China Sea.

The northwest Pacific marginal seas are a primary center of phylogeographic and evolutionary research, because of their dynamic geographic history of falling and rising sea levels during the glaciations and interglaciations of the last one million years. Here we present new molecular and morphological data for geographic samples of the four-eyed sleeper (Bostrychus sinensis), which reinforce the evidence for secondary contact and hybridization between two phylogeographic lineages in the East China Sea. Specifically, we find that the secondary contact region is characterized by a low frequency of hybridization, where mitochondrial DNA introgression is relatively common, whereas F1 hybrids are correspondingly scarce. Furthermore, the adult standard lengths of the two phylogeographic lineages vary geographically in a manner that is consistent with reproductive character displacement. Collectively, the molecular and morphological data document that sleeper hybridization conforms to the classic "tension zone" model, where alleles are lost via reduced hybrid viability and/or positive assortative mating but are then replenished by dispersal from south of the secondary contact region. They also indicate that the two phylogeographic lineages are at an incipient stage of the speciation process. These results and conclusions for the four-eyed sleeper are presented as a case study for future research on the vicariance, secondary contact, and hybridization of marine groups in the northwest Pacific marginal seas.

Pantoea intestinalis sp. nov., isolated from the human gut.

A novel bacterial strain, 29Y89BT, was isolated from a faecal sample of a healthy human subject. Cells were Gram-stain-negative, motile, non-spore-forming and rod-shaped. Strain 29Y89BT formed cream-coloured colonies 2 mm in diameter on trypticase soy agar and showed optimum growth at 35 °C. Strain 29Y89BT showed highest 16S rRNA gene sequence similarity to Pantoea gaviniae A18/07T (98.4 %) followed by Pantoea calida 1400/07T (97.2 %). Multi-locus sequence analysis using atpD (ATP synthase ß subunit), gyrB (DNA gyrase), infB (initiation translation factor 2) and rpoB (RNA polymerase ß subunit) genes also supported the result of 16S rRNA gene sequence based phylogeny. Strain 29Y89BT showed 62 and 40.7 % DNA-DNA relatedness with P. calida DSM 22759T and P. gaviniae DSM 22758T. Strain 29Y89BT contained C17 : 0 cyclo, C19 : 0 cyclo ω8c, C16 : 0, C14 : 0 and C12 : 0 as predominant fatty acids. In addition, strain 29Y89BT showed physiological and phenotypic differences from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T. The polar lipid profile mainly comprised phospholipids. The DNA G+C content was 59.1 mol%. Thus, based on the findings of the current study, strain 29Y89BT showed clear delineations from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T, and is thus considered to represent a novel species of the genus Pantoea, for which the name Pantoea intestinalis sp. nov. is proposed. The type strain is 29Y89BT ( = DSM 28113T = MCC 2554T).

LA-GEM: imputation of gene expression with incorporation of Local Ancestry.

Gene imputation and TWAS have become a staple in the genomics medicine discovery space; helping to identify genes whose regulation effects may contribute to disease susceptibility. However, the cohorts on which these methods are built are overwhelmingly of European Ancestry. This means that the unique regulatory variation that exist in non-European populations, specifically African Ancestry populations, may not be included in the current models. Moreover, African Americans are an admixed population, with a mix of European and African segments within their genome. No gene imputation model thus far has incorporated the effect of local ancestry (LA) on gene expression imputation. As such, we created LA-GEM which was trained and tested on a cohort of 60 African American hepatocyte primary cultures. Uniquely, LA-GEM include local ancestry inference in its prediction of gene expression. We compared the performance of LA-GEM to PrediXcan trained the same dataset (with no inclusion of local ancestry) We were able to reliably predict the expression of 2559 genes (1326 in LA-GEM and 1236 in PrediXcan). Of these, 546 genes were unique to LA-GEM, including the CYP3A5 gene which is critical to drug metabolism. We conducted TWAS analysis on two African American clinical cohorts with pharmacogenomics phenotypic information to identity novel gene associations. In our IWPC warfarin cohort, we identified 17 transcriptome-wide significant hits. No gene reached are prespecified significance level in the clopidogrel cohort. We did see suggestive association with RAS3A to P2RY12 Reactivity Units (PRU), a clinical measure of response to anti-platelet therapy. This method demonstrated the need for the incorporation of LA into study in admixed populations.

Multi-Omics Studies in Historically Excluded Populations: The Road to Equity.

Over the past few decades, genomewide association studies (GWASs) have identified the specific genetics variants contributing to many complex diseases by testing millions of genetic variations across the human genome against a variety of phenotypes. However, GWASs are limited in their ability to uncover mechanistic insight given that most significant associations are found in non-coding region of the genome. Furthermore, the lack of diversity in studies has stymied the advance of precision medicine for many historically excluded populations. In this review, we summarize most popular multi-omics approaches (genomics, transcriptomics, proteomics, and metabolomics) related to precision medicine and highlight if diverse populations have been included and how their findings have advance biological understanding of disease and drug response. New methods that incorporate local ancestry have been to improve the power of GWASs for admixed populations (such as African Americans and Latinx). Because most signals from GWAS are in the non-coding region, other machine learning and omics approaches have been developed to identify the potential causative single-nucleotide polymorphisms and genes that explain these phenotypes. These include polygenic risk scores, expression quantitative trait locus mapping, and transcriptome-wide association studies. Analogous protein methods, such as proteins quantitative trait locus mapping, proteome-wide association studies, and metabolomic approaches provide insight into the consequences of genetic variation on protein abundance. Whereas, integrated multi-omics studies have improved our understanding of the mechanisms for genetic association, we still lack the datasets and cohorts for historically excluded populations to provide equity in precision medicine and pharmacogenomics.