Proteogenomics Analysis Reveals Novel Micropeptides in Primary Human Immune Cells

• Published in: Immuno Vol. 2; no. 2; pp. 283 - 292
• Main Authors: Subbannayya, Yashwanth, Bhatta, Ankit, Pinto, Sneha M., Fitzgerald, Katherine A., Kandasamy, Richard K.
• Format: Journal Article
• Language: English
• Published: Sapporo MDPI AG 01.06.2022
• Subjects: Antigen presentation; autoimmune disorders; Datasets; Gene expression; Genomes; immunoproteogenomics; Inflammation; Mass spectrometry; micropeptides; Peptides; Proteomics; Scientific imaging; systems immunology; systems inflammation; therapeutic peptides
• ISSN: 2673-5601; 2673-5601
• DOI: 10.3390/immuno2020018

Short open reading frames (sORFs) encoding functional peptides have emerged as important mediators of biological processes. Recent studies indicate that sORFs of long non-coding RNAs (lncRNAs) can encode functional micropeptides regulating immunity and inflammation. However, large-scale identification of potential micropeptide-encoding sequences is a significant challenge. We present a data analysis pipeline that uses immune cell-derived mass spectrometry-based proteomic data reanalyzed using a rigorous proteogenomics-based workflow. Our analysis resulted in the identification of 2815 putative lncRNA-encoded micropeptides across three human immune cell types. Stringent score cut-off and manual verification confidently identified 185 high-confidence putative micropeptide-coding events, of which a majority have not been reported previously. Functional validation revealed the expression and localization of lnc-MKKS in both nucleus and cytoplasmic compartments. Our pilot analysis serves as a resource for future studies focusing on the role of micropeptides in immune cell response.