Biology subjects

Despins, C. A.

Publications and source records attributed to Despins, C. A..

5 recordsLinked to original sources

bioRxiv2025

Self-multimerization of mRNA LNP-derived antigen improves antibody responses

BackgroundmRNA LNP technology is now being widely applied as a highly effective vaccine platform. Antigen multimerization is a well-established approach to enhance antibody titers and protective efficacy of several protein subunit vaccines. However, this approach has been less explored for mRNA LNP vaccines. MethodsHere, within the context of mRNA LNP vaccination, we used mStrawberry (mSb) as a model antigen to conduct a comprehensive, head-to-head comparison of the ability of the foldon (3-mer), IMX313 (7-mer), and ferritin (24-mer) multimerization domains to enhance immunogenicity in mice. ResultsWe compared multimerized antigen to monomeric secreted antigen and monomeric surface-displayed antigen and observed that the IMX313 domain efficiently multimerized mSb protein and enhanced anti-mSb antibody titers to a degree greater than surface-display, whereas the foldon and ferritin domains failed to multimerize or improve antibody levels. ConclusionsOur results extend the observation of enhanced immunogenicity from antigen multimerization to mRNA LNP vaccines and indicate the 7-mer forming IMX313 multimerization domain may be an ideal candidate for multimer formation in the context of mRNA LNP vaccination.

immunology↗

bioRxiv2022

Isolation-by-distance and population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome

Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated two chromosome-level genome assemblies and sequenced 24 RNA-seq libraries to better annotate the coho salmon genome assemblies. We also resequenced the genomes of 83 coho salmon across their North American range to identify nucleotide variants, characterize the broad effects of isolation-by-distance using a genome-wide association analysis approach, and understand the demographic histories of these salmon by modeling population size from genome-wide data. We observed that more than 13% of all SNPs were associated with latitude (before multiple test correction), likely an affect of isolation-by-distance. From demographic history modeling, we estimated that the SNP latitudinal gradient likely developed as recently as 8,000 years ago. In addition, we identified four genes each harboring multiple SNPs associated with latitude; all of these SNPs were also predicted to modify the function of the gene. Three of these genes have roles in cell junction maintenance and may be involved in osmoregulation. This signifies that ocean salinity may have been a factor influencing coho salmon recolonization after the last glaciation period - generating the current pattern of variation in these three genes.

genomics↗

bioRxiv2021

Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)

Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on a regional, rather than at a stock-specific, level. Within British Columbia, chum salmon regional groupings were described at the conservation unit (CU) level, and there may be substructure within particular CUs. Genome wide associations of phenotypic sex to SNP genetic markers identified two clear peaks, a very strong peak on Linkage Group 15, and another on Linkage Group 3. With these new resources, we were better able to characterize the sex-determining region and gain further insights into sex determination in chum salmon and the general biology of this species.

genomics↗

bioRxiv2021

Modulation of the host cell transcriptome and epigenome by Fusobacterium nucleatum

Fusobacterium nucleatum (Fn) is a ubiquitous opportunistic pathogen with an emerging role as an oncomicrobe in colorectal and other cancer types. Fn can adhere to and invade host cells in a manner that varies across Fn strains and host cell phenotypes. Here we performed pairwise co-cultures between three Fn strains and two immortalized primary host cell types (colonic epithelial cells and vascular endothelial cells) followed by RNA-seq and ChIP-seq to investigate transcriptional and epigenetic host cell responses. We observed that Fn-induced host cell transcriptional modulation involves strong upregulation of genes related to immune migration and inflammatory processes, such as TNF, CXCL8, CXCL1, and CCL20. Further, we identified genes strongly upregulated specifically in conditions of host cell invasion, including overexpression of both EFNA1 and LIF, two genes commonly upregulated in colorectal cancer and associated with poor patient outcomes, and PTGS2 (COX2), a gene associated with the protective effect of aspirin in the colorectal cancer setting. Interestingly, we also observed downregulation of numerous histone modification genes upon Fn exposure. To further explore this relationship, we used the ChIP-seq data to annotate chromatin states genome-wide. We found significant chromatin remodeling following Fn exposure in conditions of host cell invasion, with substantial increases in the frequency of states corresponding to active enhancers as well as low signal or quiescent states. Thus, our results highlight increased inflammation and chemokine gene expression as conserved host cell responses to Fn exposure, and extensive host cell epigenomic changes associated with Fn host cell invasion. These results extend our understanding of Fn as an emerging pathogen and highlight the importance of considering strain heterogeneity and host cell phenotypic variation when exploring pathogenic mechanisms of Fn.

genomics↗

bioRxiv2020

Population genomics of North American northern pike: variation and sex-specific signals from a chromosome-level, long read genome assembly

The northern pike Esox lucius is a freshwater fish renowned for having low genetic diversity but ecological success throughout the Northern Hemisphere. Here we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds using long-reads and chromatin capture technology. We then align whole-genome resequencing data against this reference to genotype northern pike from Alaska through New Jersey (n = 47). A striking decrease in genetic diversity occurs along the sampling range, whereby samples to the west of the North American Continental Divide have substantially higher diversity than populations to the east. As an example, individuals from Interior Alaska in the west and St. Lawrence River in the east have on average 181K and 64K heterozygous SNPs per individual, respectively (i.e., a SNP variant every 3.2 kbp and 11.2 kbp, respectively). Even with such low diversity, individuals clustered with strong support within each population, and this may be related to numerous private alleles in each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajimas D = -1.07 and -1.30, respectively). Non-uniform patterns of diversity were observed across the genome, with large regions showing elevated diversity in several chromosomes, including LG24. In populations with the master sex determining gene amhby still present in the genome, amhby is in LG24. As expected, amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we also document some amhby(-) males in Alaska and amhby(+) males in the Columbia River. This indicates that rather than a discrete boundary after which amhby was lost in North America, there is a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity including the loss of the sex determination system.

genomics↗