Genome science in high school classrooms: inflammation, glutamate, and methylation

Abstract

Incorporating genome science into high school classrooms allows students to participate in authentic research, developing a pipeline for a new generation of STEM leaders. Since 2018, ‘Iolani School is one of the few schools in the United States actively integrating nanopore sequencing into their curriculum. While the previous curriculum has answered community questions using bacterial whole-genome sequencing, 16S, and eDNA, we recently introduced DNA methylation studies into the classroom by examining a member of the community, who has been diagnosed with psoriatic arthritis (PA) and experiences chronic inflammation following glutamate consumption despite taking TNFα inhibitors. She was the subject of a novel study investigating the use of gene-body methylation (GbM) as a proxy for inflammatory gene expression. Currently, the connection between inflammation, GbM, and glutamate consumption in a patient with PA is unclear. Venous blood was drawn from the individual before and after glutamate consumption. A Human Cytokine Luminex panel was performed, targeting 16 inflammatory cytokines. DNA from peripheral blood mononuclear cells was sequenced using Oxford Nanopore MinION R10 Flow Cells with adaptive sampling, targeting a custom panel of 227 inflammatory genes. Methylated CpGs were aggregated using the wf-human-variation workflow and further analysed using R. We found the genes encoding CXCL8 and IL6 to be differentially methylated, showing an increase in the amount of methylated CpGs within the gene body following the consumption of glutamate, corresponding with an increase in both CXCL8 and IL6 cytokines. This novel finding has the future potential to inform additional treatment targets for individuals with PA who experience chronic inflammation following glutamate consumption.

Biography

Ethan Hill is the bioinformatician for the ‘Iolani School Office of Community Science where he is actively developing bioinformatic tools that are easily accessible for high school students and the greater community in Hawaii. He is currently involved in answering community-based questions in Hawaii using 16S, eDNA, and WGS in collaboration with students from different schools around the state. Ethan also teaches a senior-level bioinformatics course where students are introduced to the world of bioinformatics through directed research projects. He earned his bachelor’s and master’s degrees in biology and microbiology from the University of Hawaii at Manoa.