Illuminating the Dark MicroProteome in Innate Immunity

Introduction

Genome annotation, transcriptomic and proteomic pipelines have traditionally dismissed proteins encoded by short open reading frames (sORF) known as microproteins. This provides a pool of unexplored functional genes. Despite the increasing body of work in identifying the microproteome in different model organisms and cell lines, only a few have been functionally studied, showing diverse regulatory roles in multiple cellular pathways.

Project Overview

In MicroIMMUNE, I present a 3-aim workflow combining computational and synthetic biology, protein and genetic engineering approaches designed to systematically uncover the microproteome atlas and investigate its interactome and functional role in innate immune cells.

Aims

We aim to:

1. Identify microproteins expressed in innate immune cells under resting and stimulating conditions, using state-of-the-art computational and experimental approaches to study the microproteome.
2. Develop genetic code expansion technologies in innate immune cells to incorporate non-canonical amino acids to study the localization and binding partners of microproteins.
3. Elucidate the function of microproteins in innate immune cells by combining genetic engineering with an array of high-throughput functional assays and automated analysis pipelines.

Research Questions

Our research output will address key questions such as:

• What is the microproteome atlas in innate immune cells and how does it vary upon activation?
• Where are the microproteins localized and in which protein-protein interactions are they involved?
• What functions do different microproteins play in innate immune cells?

Significance

Understanding the role of microproteins in innate immune cells can revolutionize our understanding of the immune response at a fundamental level and open new avenues for therapeutic interventions in which new antimicrobial peptides or druggable targets could be discovered.