Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

In a recent project, Farhad Hormozdiari and Eleazar Eskin contributed data analysis and interpretation to a project identifying new genes and genomic regions associated with metabolic function in mice. Our paper presents a comprehensive picture of the transcriptome of the mouse hypothalamus and its genetic variation and regulation. This project, which was published in eLife, was led by fellow UCLA researchers Yehudit Hasin-Brumshtein, Jake Lusis, and Desmond Smith.

Mice and humans share virtually the same set of genes; thus, mapping the mouse genome is an important step toward understanding genetic factors in common, complex human diseases such as obesity, heart disease, and diabetes. In metabolic tissues, the integration of genome-wide expression profiles with genetic and phenotypic variance can provide valuable insight into a disease’s underlying molecular mechanism. Measuring gene activity can reveal new molecules that clinical translation efforts may target to treat metabolic disorders.

Our project uses RNA-Seq to characterize transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. Mice were fed a high, high sugar diet, and all strains were comprehensively genotyped and phenotyped for 150 metabolic traits. Our study examines tissues relevant to the hypothalmus, the brain region that controls metabolism and regulates body weight and appetite.

We sequenced 285 samples from all 99 strains of the HMDP. Using methods described in our paper, we identified thousands of new isoforms and >400 new genes. The HMDP allowed us to map Quantitative Trait Loci (eQTLs) with high resolution and power, identifying both local and trans acting variants—or, variants that affect a molecule from within and from outside, respectively.

Groups of genes are associated with multiple related phenotypes in HMDP, although not necessarily enriched for GO ontology or specific pathways. For more information, see our paper.

We report numerous novel transcripts supported by proteomic analyses, as well as novel non-coding RNAs. High resolution genetic mapping of transcript levels in HMDP reveals both local and trans expression eQTLs, identifying two trans eQTL ’hotspots’ associated with expression of hundreds of genes. We also report thousands of alternative splicing events regulated by genetic variants. We further showed that the genes associated with trans eQTL hotspots correlate to physiological phenotypes, such as HDL and triglyceride levels. This discovery provides insight into the mechanism behind correlation of these genotypes with complex traits.

Our data capture the various non-neuronal cell types, such as microglia or astrocytes, which are often overlooked in the mostly neuron focused studies of the hypothalamus. These cells are important mediators of hypothalamic inflammation and other processes induced by a high fat diet. Regulation of gene expression in these cell types impacts every aspect of metabolism, and our data provide a robust framework recapitulating transcriptional processes affecting multiple cell populations. Our approach is thus complementary to on-going cell type-specific transcriptomic efforts.

For more information, see our paper, which is available for download through eLife: https://elifesciences.org/content/5/e15614.

The full citation to our paper is: 

Hasin-Brumshtein, Yehudit; Hormozdiari, Farhad ; Martin, Lisa ; van Nas, Atila ; Eskin, Eleazar ; Lusis, Aldons J; Drake, Thomas A

Allele-specific expression and eQTL analysis in mouse adipose tissue. Journal Article

In: BMC Genomics, 15 (1), pp. 471, 2014, ISSN: 1471-2164.

Abstract | Links | BibTeX

See our blog post on a recent paper reviewing the HMDP data set: http://www.zarlab.xyz/the-hybrid-mouse-diversity-panel-a-resource-for-systems-genetics-analyses-of-metabolic-and-cardiovascular-traits/

The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis

We recently published the first study to report a genetic component to host choice behavior in the major malaria vector Anopheles arabiensis. In a collaboration with the University of California Davis, University of Glasgow, and the Environmental Health and Ecological Sciences Group, Ifakara Health Institute, Ifakara, United Republic of Tanzania, we assess the genetic basis for An. arabiensis host choice and resting behavior. We link human-fed behavior to allelic variation between the 3Ra inversion states. This effort was led by researchers at UC Davis, including Bradley Main, Yoosook Lee, Travis Collier, Anthony Cornel, Catelyn Nieman, Allison Weakley, and Gregory Lanzaro. Eleazar Eskin and Eun Yong Kang contributed data analysis and interpretation.

Mosquitoes that feed on human blood pose an enormous public health threat by transmitting numerous pathogens, such as dengue virus, Zika virus, and malaria. Together, these mosquito-borne diseases kill more than one million people per year. Human exposure to malaria is driven by variable mosquito behaviors such as: (1) propensity to feed on humans relative to other animals (anthropophily) and (2) preference for living in close proximity to humans, as reflected by biting and residing inside houses (endophily).

Our project focused on the potential for An. arabiensis, the only remaining malaria vector in many parts of Africa, to adapt its behavior to avoid control measures such as insecticide-treated nets and indoor residual sprays. To investigate the genetic basis of host choice and resting behavior, we sequenced the genomes of 23 human-fed and 25 cattle-fed mosquitoes collected both in-doors and out-doors in the Kilombero Valley, Tanzania. We tested for genetic associations with each of the four phenotypes: human-fed, cow-fed, resting indoors, and resting outdoors.

With these genomes, we identified a set of 4,820,851 segregating SNPs after imposing a minor allele frequency threshold of 10%. We estimated the genetic component (or “SNP heritability”) for each phenotype. Results suggest a genetic component for host choice and no genetic component for resting behavior.

To test for the existence of genetic structure within our set of 48 sequenced genomes, individuals were partitioned by genetic relatedness using a Principle Component Analysis (Genome-Wide Complex Trait Analysis software, GCTA) applied to all SNPs. Using this approach, we observed three discrete genetic clusters. We used a novel population-scale inversion genotyping method to identify an association between the standard arrangement of 3Ra (3R+) and cattle-fed An. arabiensis. We highlight two intriguing candidate genes within the 3Ra, including the odorant binding protein Obp5, and the odorant receptor Or65. The enrichment of 3R+ among cattle-fed mosquitoes provides support for a genetic component to host choice, which is consistent with the report that zoophily can be selected for.

Genetic variation explained by the 2Rb and 3Ra inversions. For more information, see our paper.

Our multiplex genotyping assays allowed us to directly estimate relationships between host choice and genotype in wild mosquitoes in a high-throughput and economical fashion. Given the importance of mosquito feeding and resting behavior to the effectiveness of malaria control and transmission, there is an urgent need to understand the underlying biological determinants of these behaviors and their short- and long-term impact on the effectiveness of current public health interventions.

For more information, see our paper, which is available for download through PLoS Genetics: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006303.

The full citation to our paper is:
Main, B.J., Lee, Y., Ferguson, H.M., Kreppel, K.S., Kihonda, A., Govella, N.J., Collier, T.C., Cornel, A.J., Eskin, E., Kang, E.Y. and Nieman, C.C., 2016. The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis. PLoS Genet, 12(9), p.e1006303.