Psoriasis: A Study of the Skin Transcriptome and Microbiome

Psoriasis is a complex autoimmune skin disorder characterized by dry, scaly plaques and painful flares. Even though genetic contribution and environmental factors are suspected, the exact trigger of psoriasis is not well understood. The chronic condition of the disease and the lack of effective and definitive treatments are burdens on the patients. Recent emergence of transcriptome and genomic datasets for the host, as well as the taxonomic datasets for the microbiome has enabled the use of bioinformatics approaches to investigate altered gene circuits in psoriasis. As a first step, open source microarray datasets of psoriasis were analyzed in context of other skin conditions. The analysis showed that upregulated genes in the psoriasis transcriptome included those involved in epidermal differentiation complex and antimicrobial processes, while the top downregulated genes were involved in lipid metabolism. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were enriched with significantly altered genes point to the upregulation of both innate and adaptive immune responses. The psoriasis gene signature was distinctive from other inflammatory skin conditions and it resembled the wound healing process in terms of keratinization and immune response signals. On the microbiome side, over-abundance of opportunistic bacteria on the psoriasis microbiome was observed compared to controls. Virulence genes were consistently in high abundance across different body sites. Bacterial invasion of epithelial cells gene pathway was crowded with both significantly altered genes on the host side and high-abundance orthologs on the microbiome side. The findings suggested bacterial involvement in the initiation or maintenance of psoriasis flares. Genetic components also play a role in susceptibility to psoriasis. Human Leukocyte Antigen (HLA) is one of the regions that has previously been associated with psoriasis through Genome Wide Association studies. The Single Nucleotide Polymorphisms (SNPs) typed in the HapMap dataset (11 ethnic populations) within the HLA region have been analyzed using extended haplotype homozygosity based tests to identify positive selection on polymorphisms that have not yet reached fixation. Results showed regional specificity of positive selection signals on the sub-classes of HLA. The positive selection signals in Class I sub-region showed European ancestry specificity with intronic SNPs on a psoriasis related gene PSORS1C1 as well as on TCF19, MUC22, TRIM10, and TRIM15. The region specific selection signals were also seen in the Class III region for the East Asian populations and in the Class II region for African ancestry populations. Similar to single population tests, the cross population tests showed that the significant SNPs were concentrated in the Class II region for African ancestry populations, whereas for European ancestry populations, they were concentrated in the Class I region. The results show how positive selection of a SNP can encourage genetic hitchhiking of the susceptibility SNPs for a disease along with a SNP that is under positive selection. This research thesis bridges large scale transcriptome datasets of the host and operational taxonomy unit abundance datasets of the microbiome, opening up new avenues for drug repositioning studies by pointing out specific host-microbiome genes as drug targets.Ph.D., Biomedical Engineering -- Drexel University, 201

Antigen presenting ILC3 regulate T cell-dependent IgA responses to colonic mucosal-associated bacteria

Intestinal immune homeostasis is dependent upon tightly regulated and dynamic host interactions with the commensal microbiota. Immunoglobulin A (IgA) produced by mucosal B cells dictates the composition of commensal bacteria residing within the intestine. While emerging evidence suggests the majority of IgA is produced innately and may be polyreactive, mucosal-dwelling species can also elicit IgA via T cell-dependent mechanisms. However, the mechanisms that modulate the magnitude and quality of T cell-dependent IgA responses remain incompletely understood. Here we demonstrate that group 3 innate lymphoid cells (ILC3) regulate steady state interactions between T follicular helper cells (TfH) and B cells to limit mucosal IgA responses. ILC3 used conserved migratory cues to establish residence within the interfollicular regions of the intestinal draining lymph nodes, where they act to limit TfH responses and B cell class switching through antigen presentation. The absence of ILC3-intrinsic antigen presentation resulted in increased and selective IgA coating of bacteria residing within the colonic mucosa. Together these findings implicate lymph node resident, antigen-presenting ILC3 as a critical regulatory checkpoint in the generation of T cell-dependent colonic IgA and suggest ILC3 act to maintain tissue homeostasis and mutualism with the mucosal-dwelling commensal microbiota

Establishing a mucosal gut microbial community in vitro using an artificial simulator.

The Twin Simulator of the Human Intestinal Microbial Ecosystem (TWINSHIME®) was initially developed to study the luminal gut microbiota of the ascending (AC), transverse (TC), and descending (DC) colon regions. Given the unique composition and potential importance of the mucosal microbiota for human health, the TWINSHIME was recently adapted to simulate the mucosal microbiota as well as the luminal community. It has been previously demonstrated that the luminal community in the TWINSHIME reaches a steady state within two weeks post inoculation, and is able to differentiate into region specific communities. However, less is known regarding the mucosal community structure and dynamics. During the current study, the luminal and mucosal communities in each region of the TWINSHIME were evaluated over the course of six weeks. Based on 16S rRNA gene sequencing and short chain fatty acid analysis, it was determined that both the luminal and mucosal communities reached stability 10-20 days after inoculation, and remained stable until the end of the experiment. Bioinformatics analysis revealed the formation of unique community structures between the mucosal and luminal phases in all three colon regions, yet these communities were similar to the inoculum. Specific colonizers of the mucus mainly belonged to the Firmicutes phylum and included Lachnospiraceae (AC/TC/DC), Ruminococcaceae and Eubacteriaceae (AC), Lactobacillaceae (AC/TC), Clostridiaceae and Erysipelotrichaceae (TC/DC). In contrast, Bacteroidaceae were enriched in the gut lumen of all three colon regions. The unique profile of short chain fatty acid (SCFA) production further demonstrated system stability, but also proved to be an area of marked differences between the in vitro system and in vivo reports. Results of this study demonstrate that it is possible to replicate the community structure and composition of the gut microbiota in vitro. Through implementation of this system, the human gut microbiota can be studied in a dynamic and continuous fashion

Comparison of relative abundance at the family level between the mucosal phase of the AC, TC, and DC regions of the SHIME 1 system.

<p>The relative abundance at the family level for each region at each all time points after stabilization (Day10-Day 43) were averaged and plotted together. Only families with at least a .01% relative abundance in at least one region were considered. The error bars represent the standard deviation between the percent abundance at these time points. The P values based on a 2 tailed student <i>t-</i>test between regions are listed in the bottom chart. P values were corrected for multiple comparison. A green box indicates that the p value was less than 0.05.</p

Alpha diversity measurements over time for the mucosal and luminal phase of the AC, TC, and DC regions.

<p>The black dotted line represents the Shannon diversity of the fecal sample used to inoculate the system. (A) The number of OTUs identified (B) Shannon diversity index.</p

Comparison of the combined communities for each SHIME system to the fecal inoculum.

<p>SHIME 1 combined and SHIME 2 combined is the sum of the luminal phases for the AC, TC, and DC regions from day 10–43; SHIME 1 combined (M+L) is the sum of the luminal and mucosal phases of the AC, TC, and DC regions from day 10–43.</p