Precise genetic mapping and integrative bioinformatics in Diversity Outbred mice reveals Hydin as a novel pain gene

Abstract

Mouse genetics is a powerful approach for discovering genes and other genome features influencing human pain sensitivity. Genetic mapping studies have historically been limited by low mapping resolution of conventional mouse crosses, resulting in pain-related quantitative trait loci (QTL) spanning several megabases and containing hundreds of candidate genes. The recently developed Diversity Outbred (DO) population is derived from the same eight inbred founder strains as the Collaborative Cross, including three wild-derived strains. DO mice offer increased genetic heterozygosity and allelic diversity compared to crosses involving standard mouse strains. The high rate of recombinatorial precision afforded by DO mice makes them an ideal resource for high-resolution genetic mapping, allowing the circumvention of costly fine-mapping studies. We utilized a cohort of ~300 DO mice to map a 3.8 Mbp QTL on chromosome 8 associated with acute thermal pain sensitivity, which we have tentatively named Tpnr6. We used haplotype block partitioning to narrow Tpnr6 to a width of ~230 Kbp, reducing the number of putative candidate genes from 44 to 3. The plausibility of each candidate gene’s role in pain response was assessed using an integrative bioinformatics approach, combining data related to protein domain, biological annotation, gene expression pattern, and protein functional interaction. Our results reveal a novel, putative role for the protein-coding gene, Hydin, in thermal pain response, possibly through the gene’s role in ciliary motility in the choroid plexus–cerebrospinal fluid system of the brain. Real-time quantitative-PCR analysis showed no expression differences in Hydin transcript levels between pain-sensitive and pain-resistant mice, suggesting that Hydin may influence hot-plate behavior through other biological mechanisms.

Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection

“…At 21 generations, the DO mouse population has proven to be a valuable resource for genetic mapping (Recla et al 2014; Smallwood et al 2014; Church et al 2015; French et al 2015; Gu et al 2016) and systems genetics (Kelly et al 2015; Chick et al 2016). However, an ongoing selective sweep driven by the R2d2 locus occurred in the DO breeding colony and threatened to eliminate genetic variation across a large region of chromosome 2.…”

Systems genetic and pharmacological analysis identifies candidate genes underlying mechanosensation in the von Frey test

“…Moreover, ciliary function in other cell types, namely keratinocytes (Elofsson et al 1984) and Schwann cells (Grillo & Palay 1963), could also play a role in mechanosensation. Recent genetic analysis of thermal nociception in the Diversity Outbred mapping population showed hydin , which encodes a ciliary protein as a likely candidate gene (Recla et al 2014), further highlighting the potential role of variation within ciliary structure and function in peripheral sensory processing. Given the lack of pharmacological agents capable of selectively targeting the protein product of Ift27 , we could not further evaluate its role at this time.…”

Association of novelty-related behaviors and intravenous cocaine self-administration in Diversity Outbred mice

“…The Collaborative Cross inbred strains (CC), DO mouse population, and related populations (Ghazalpour et al 2012; Iancu et al 2010) complement these resources with a wealth of allelic variation, high mapping precision and a greater range of behavioral diversity (reviewed in Chesler 2014). Allelic variants can be identified using a QTL mapping approach in combination with functional genomic data resources (Recla et al 2014). We have successfully mapped several additive behavioral QTLs in the DO using approximately 300 mice, though more power will enable reliable detection of a larger number of loci and more complex genetic effects (Logan et al 2013).…”