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Principal Investigator: Maggie Lam
Organization: UNIVERSITY OF COLORADO DENVER
Fiscal Year: 2024
Award: $388,750
Funding agency: National Heart Lung and Blood Institute
PROJECT SUMMARY
Cardiac hypertrophy and failure involve a rewiring of gene expression through alternative splicing, but it remains
unclear which splicing changes are relevant to disease development, and how splice variants affect protein
function. Although many alternative transcript isoforms have been discovered, not all are translated into
proteins and instead may be degraded via non-sense mediated decay or co-translational protein quality control.
Proteomics methods that can identify and quantitate splice variant proteins empirically and on a large scale
provide essential tools to study how alternative splicing regulates cardiac gene expression. We and others
showed that tissue-specific splice variant proteins may be identified using a combined RNA sequencing and
mass spectrometry approach. Accordingly, our goal here is to examine the mechanisms by which alternative
splicing regulates the genetic program in hypertrophic and failing hearts, by identifying the proteins and
pathways that are coordinately regulated by splicing, the resulting complement of protein isoform species
(`proteoforms') in the heart, and the consequences of proteoform sequences on protein structure and function.
Specifically, we plan to: (1) apply a quantitative RNA-guided proteomics framework to identify key isoform
switches at the transcript and the protein level, with emphasis on the changes in splice factors and RNA-binding
proteins in mouse models of systolic and diastolic dysfunction; (2) combine RNA-guided proteomics and
proteome-wide biophysics approaches, we will interrogate the impact of splice variants on protein structure
and thermal stability, and discover significant isoforms through alternative splicing, intrinsically disordered, and
regulatory post-translational modification modules. We anticipate the successful completion of these aims will
generate new conceptual insights into how alternative splicing regulatory networks reprogram the cardiac
proteome in pathological remodeling and heart failure, and more generally, contribute to methods and concepts
to elucidate the regulation and function of alternative splicing in the heart.
Terms: <Address><Affect><Aging><Alternate Splicing><Alternative RNA Splicing><Alternative Splicing><Architecture><Area><Assay><Bioassay><Biological Assay><Biological Function><Biological Process><Biophysics><Body Tissues><Cardiac><Cardiac Diseases><Cardiac Disorders><Causality><Complement><Complement Proteins><Computing Methodologies><Custom><Data><Development><Disease><Disorder><Dysfunction><Engineering / Architecture><Etiology><Exons><Failure><Functional disorder><Gene Expression><Genes><Genetic><Goals><Guide RNA><Half-Life><Heart><Heart Diseases><Heart Hypertrophy><Heart failure><Intervening Sequences><Introns><Isoforms><Knowledge><Large-Scale Sequencing><Mass Photometry/Spectrum Analysis><Mass Spectrometry><Mass Spectroscopy><Mass Spectrum><Mass Spectrum Analyses><Mass Spectrum Analysis><Mediating><Metabolic><Methods><Mice><Mice Mammals><Modeling><Molecular><Murine><Mus><Non-sense Mediated Decay><Nonsense-Mediated Decay><Pathologic><Pathway interactions><Pattern><Phenotype><Physiopathology><Post-Translational Modification Protein/Amino Acid Biochemistry><Post-Translational Modifications><Post-Translational Protein Modification><Post-Translational Protein Processing><Posttranslational Modifications><Posttranslational Protein Processing><Protein Databases><Protein Isoforms><Protein Modification><Proteins><Proteome><Proteomics><Quality Control><RNA Seq><RNA Splicing><RNA sequencing><RNA-Binding Proteins><RNAseq><Regulation><Role><Solubility><Splicing><Stable Isotope Labeling><Structure><System><Tissue-Specific Splicing><Tissues><Transcript><Translating><Variant><Variation><Ventricle Remodeling><Ventricular Cardiac Remodeling><Ventricular Myocardial Remodeling><Ventricular Remodeling><biophysical approaches><biophysical foundation><biophysical methodology><biophysical methods><biophysical principles><biophysical sciences><biophysical techniques><cardiac failure><cardiac hypertrophy><causation><complementation><computational methodology><computational methods><computer based method><computer methods><computing method><customs><deep learning><deep learning method><deep learning strategy><detection assay><developmental><disease causation><experiment><experimental research><experimental study><experiments><gRNA><gene regulatory network><heart disorder><in vivo><insight><mouse model><multiomics><multiple omics><murine model><myocardial remodeling><panomics><pathophysiology><pathway><prediction algorithm><programs><protein folding><protein function><protein structure><protein structures><proteins structure><response><social role><tool><transcriptome sequencing><transcriptomic sequencing>