QTL Mapping of Intestinal Neutrophil Variation in Threespine Stickleback Reveals Possible Gene Targets Connecting Intestinal Inflammation and Systemic Health

Abstract

Selection, via host immunity, is often required to foster beneficial microbial symbionts and suppress deleterious pathogens. In animals, the host immune system is at the center of this relationship. Failed host immune system-microbial interactions can result in a persistent inflammatory response in which the immune system indiscriminately attacks resident microbes, and at times the host cells themselves, leading to diseases such as Ulcerative Colitis, Crohn’s Disease, and Psoriasis. Host genetic variation has been linked to both microbiome diversity and to severity of such inflammatory disease states in humans. However, the microbiome and inflammatory states manifest as quantitative traits, which encompass many genes interacting with one another and the environment. The mechanistic relationships among all of these interacting components are still not clear. Developing natural genetic models of host-microbe interactions is therefore fundamental to understanding the complex genetics of these and other diseases. Threespine stickleback (Gasterosteus aculeatus) fish are a tractable model for attacking this problem because of abundant population-level genetic and phenotypic variation in the gut inflammatory response. Previous work in our laboratory identified genetically divergent stickleback populations exhibiting differences in intestinal neutrophil activity. We took advantage of this diversity to genetically map variation in an emblematic element of gut inflammation - intestinal neutrophil recruitment - using an F2-intercross mapping framework. We identified two regions of the genome associated with increased intestinal inflammation containing several promising candidate genes. Within these regions we found candidates in the Coagulation/Complement System, NFkB and MAPK pathways along with several genes associated with intestinal diseases and neurological diseases commonly accompanying intestinal inflammation as a secondary symptom. These findings highlight the utility of using naturally genetically diverse ‘evolutionary mutant models’ such as threespine stickleback to better understand interactions among host genetic diversity and microbiome variation in health and disease states.

Anti-inflammatory, anti-apoptotic, and antioxidant effects of obestatin on the colonic mucosa following acetic acid–induced colitis

“…Similar results were reported [53]. In NFkB immune stain as a marker of coordination of chronic inflammatory condition of the colon also reported a marked increase in the AA-induced colitis and an apparent decrease in NFkB immunoreactivity with the use of obestatin indicating tissue induced anti-inflammatory effect [5]. At the same time, the indicator of apoptosis, Caspase-3, was also markedly decreased in the obestatin treated group after induction of U.C.…”

Threespine Stickleback: A Model System For Evolutionary Genomics

“…This pointed to natural variation within threespine stickleback ecotypes that could be used to further investigate the genomic architecture of the host's immune response. Indeed, a genetic mapping study comparing oceanic and freshwater sticklebacks and examining intestinal neutrophil activity identified two moderate-effect QTLs on chromosome III (15.84% PVE) and chromosome VIII (15.77% PVE) that span several candidate genes (14 genes for the QTL on chromosome III and 13 for the one on chromosome VIII) (12). Intriguingly, some of the same pathways and biological functions for genes identified in the RNA-seq study by Small et al (149) appeared also to be enriched among the genes at these two QTLs.…”

Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

“…Here, we show that ScISOr-Seq in the context of a scRNAseq experiment allows rapid 3′-UTR annotation in threespine stickleback fish ( Gasterosteus aculeatus ). This fish has long been a focus of study in behavior, ecology, and evolution ( Bell and Foster 1994 ; Colosimo et al 2004 ; Cresko et al 2004 , 2007 ; Shapiro et al 2004 ; Hohenlohe et al 2010 ; Reid et al 2021 ), and is now a nascent system for biomedical research ( Miller et al 2007 ; Gardell et al 2017 ; Small et al 2017 ; Beck et al 2020 , 2021 ; Fuess et al 2021 ). Although stickleback has a well-assembled genome, its 3′-UTR annotations are incomplete which limits scRNAseq’s utility.…”