Presentation Title

A γδ T cell-focused analysis of published RNA-seq data from skin biopsies of Alopecia Areata patients

Presenter Information

Matilde MacedoFollow

Faculty Mentor

Julie Jameson

Start Date

23-11-2019 8:45 AM

End Date

23-11-2019 9:30 AM

Location

86

Session

poster 2

Type of Presentation

Poster

Subject Area

biological_agricultural_sciences

Abstract

γδ T cells reside in the epithelial tissues of the human body, and are responsible for regulating skin homeostasis. Many studies have examined the transcriptome of cells isolated from alopecia areata (AA) patients, but few have focused on studying the activity of γδ T cells using RNA sequencing. For this, a public RNA sequence dataset was used to examine gene signatures associated with γδ T cells. Gene signatures refers to those that showed activity compared to a control. Public RNA sequence data used in this analysis are from skin biopsies taken from patients with alopecia areata with and without 8 weeks of treatment with Tofacitinib citrate. The computer program Galaxy was used to analyze the RNA-sequence data, and investigate if the signature genes were upregulated or downregulated. The RNA-sequence data was first checked for quality, aligned to the reference human genome h19, and measured for the level of gene expression. Tools such Tophat, Cufflinks, and Cuffdiff proved difficult to measure gene expression levels due to fragment distribution errors and reads larger than the limited analyzed sequence. Tools HISAT2, htseq-count, and DEseq2 were then used to more effectively measure differential gene expression using a smaller sample size. Htseq-count was used to measure the amount of reads the sample had according to the reference genome, and DEseq2 was used to compare the before and after treatment groups and run statistical analysis of differentially expressed genes. The γδ-specific gene signature were then identified in these results, but showed no statistically significant difference between the treatments groups. Although these genes were not differentially expressed in the datasets, the methodology can be used to examine changes in keratinocytes and immune-relevant gene expression.

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Nov 23rd, 8:45 AM Nov 23rd, 9:30 AM

A γδ T cell-focused analysis of published RNA-seq data from skin biopsies of Alopecia Areata patients

86

γδ T cells reside in the epithelial tissues of the human body, and are responsible for regulating skin homeostasis. Many studies have examined the transcriptome of cells isolated from alopecia areata (AA) patients, but few have focused on studying the activity of γδ T cells using RNA sequencing. For this, a public RNA sequence dataset was used to examine gene signatures associated with γδ T cells. Gene signatures refers to those that showed activity compared to a control. Public RNA sequence data used in this analysis are from skin biopsies taken from patients with alopecia areata with and without 8 weeks of treatment with Tofacitinib citrate. The computer program Galaxy was used to analyze the RNA-sequence data, and investigate if the signature genes were upregulated or downregulated. The RNA-sequence data was first checked for quality, aligned to the reference human genome h19, and measured for the level of gene expression. Tools such Tophat, Cufflinks, and Cuffdiff proved difficult to measure gene expression levels due to fragment distribution errors and reads larger than the limited analyzed sequence. Tools HISAT2, htseq-count, and DEseq2 were then used to more effectively measure differential gene expression using a smaller sample size. Htseq-count was used to measure the amount of reads the sample had according to the reference genome, and DEseq2 was used to compare the before and after treatment groups and run statistical analysis of differentially expressed genes. The γδ-specific gene signature were then identified in these results, but showed no statistically significant difference between the treatments groups. Although these genes were not differentially expressed in the datasets, the methodology can be used to examine changes in keratinocytes and immune-relevant gene expression.