Alternative Splicing and Protein Isoforms in the Human Proteome

Project contributors:

By enabling multiple protein isoforms to be encoded in one gene, alternative pre-mRNA processing such as alternative splicing (AS) constitutes a major source of proteome complexity in eukaryotes. Differential isoform expression is a critical feature of human diseases from cancer to heart failure, as well as responses to environmental stress including alcohol and oxidative damage. Their importance notwithstanding, current knowledge remains poor on the functional consequences of alternative protein isoforms. In this project, our goal is to develop new multi-omics strategies by integrating RNA-seq and shotgun proteomics approaches, to determine the differential expression of protein alternative isoforms in normal physiology and pathophysiology.

Questions we are interested in addressing:

  • What drives protein isoform expression in the heart?
  • How do alternative exons affect protein modifications?
  • How do protein splicing patterns change in cardiac disease and aging?

Figure: An alternative splice region in a cardiac protein intersects with an intrinsically disordered region of the protein.

Proteome Dynamics Under Oxidative Stress and ER Stress

Project contributors:

Proteins in the cell are finely balanced in a dynamic equilibrium of synthesis and degradation to maintain protein integrity and protein homeostasis (“proteostasis”). When protein dynamics becomes disrupted, endoplasmic reticulum stress (ER stress) results and prompts potent response pathways that can either restore proteostasis or precipitate cell death.

Mounting evidence now implicates ER stress as a central and conserved feature in multiple cardiac diseases, including cardiac hypertrophy and failure. Inhibition of ER stress shows therapeutic promise in reversing pathological aspects of cardiac remodeling in animals, suggesting proteostasis is causally linked to pathogenesis. However, relatively little is currently known about the quantitative parameters that describe the proteostasis of cardiac proteins, which encompasses proper protein synthesis, folding, glycosylation, and other dynamic processes that cannot be espied from steady-state expression. Without methods to quantify the temporal dynamics of protein networks, we lack a basic starting point from which to identify protein pathways targeted by proteostasis disruptions. Our goal is to better understand the proteostatic processes of the cardiac proteome and how they are regulated in health and disease.

Figure: Proteostatic changes under acute oxidative stress in the heart.