Diana Lin

Diana Lin

Research Programmer - Data Scientist at Canada's Michael Smith Genome Sciences Centre @ BC Cancer

Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage

Published in Antibiotics, 2022

Recommended citation: Lin, D., Sutherland, D., Aninta, S.I., Louie, N., Nip, K.M., Li, C., Yanai, A., Coombe, L., Warren, R.L., Helbing, C.C., Hoang, L.M.N., & Birol, I. (2022). "Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage." Antibiotics 11(7):952. https://doi.org/10.3390/antibiotics11070952

Abstract: Antibiotic resistance is a global health crisis increasing in prevalence every day. To combat this crisis, alternative antimicrobial therapeutics are urgently needed. Antimicrobial peptides (AMPs), a family of short defense proteins, are produced naturally by all organisms and hold great potential as effective alternatives to small molecule antibiotics. Here, we present rAMPage, a scalable bioinformatics discovery platform for identifying AMP sequences from RNA sequencing (RNA-seq) datasets. In our study, we demonstrate the utility and scalability of rAMPage, running it on 84 publicly available RNA-seq datasets from 75 amphibian and insect species—species known to have rich AMP repertoires. Across these datasets, we identified 1137 putative AMPs, 1024 of which were deemed novel by a homology search in cataloged AMPs in public databases. We selected 21 peptide sequences from this set for antimicrobial susceptibility testing against Escherichia coli and Staphylococcus aureus and observed that seven of them have high antimicrobial activity. Our study illustrates how in silico methods such as rAMPage can enable the fast and efficient discovery of novel antimicrobial peptides as an effective first step in the strenuous process of antimicrobial drug development.