PSI-QPI metrics improved prediction of TTN-TV disease penetrance and expressivity in cardiomyopathy patients.

Background: Truncating variants in the titin (TTN) gene (TTN-TV) are the most common genetic cause of dilated cardiomyopathy (DCM) and confer a significant risk of progression to advanced heart failure (AHF). Disease penetrance of TTN-TV has been linked to the level of expression of the exon containing the TTN-TV, quantified using the percent spliced in (PSI). We hypothesized that recalculating PSI using long-read RNA sequencing and including all 15 TTN isoforms would provide more accurate predictions of cardiomyopathy (penetrance) and advanced heart failure [AHF] (expressivity) in patients with TTN cardiomyopathy. Additionally, transcript and protein abundance can be discordant due to post-translational regulation in myocardium which motivated us to compare PSI values to exon-specific TTN peptide abundance. Methods: We performed long-read RNA sequencing on cardiac tissue from 10 unused organ donors and 15 DCM patients and identified all TTN isoforms. We also performed mass spectrometry-based peptide mapping specific for each TTN isoform. Exon abundance was quantified using: 1) PSI-DCM-LR-15, a novel PSI metric calculated from long-read RNA sequencing which includes all 15 TTN isoforms and 2) quantile peptide intensity (QPI), a novel quantitative metric reflecting exon-specific peptide abundance. We then assessed the ability of PSI-DCM-LR-15 and QPI to predict AHF in two cohorts of patients with cardiomyopathy due to TTN-TV. Results: Multiple TTN transcript isoforms are expressed in myocardium. PSI-DCM-LR-15 values differed from the original PSI values, especially for the I-band. Proteomic profiling revealed discordance between mRNA and protein-level exon abundance across multiple domains, also highest for the I-band. A hybrid metric, PSI-QPI, combining transcriptional and proteomic exon abundance improved prediction of TTN-TV disease penetrance and expressivity. Conclusions: A novel hybrid proteogenomic metric, PSI-QPI, that incorporates both transcript and protein abundance more accurately predicts cardiomyopathy (penetrance) and AHF (expressivity) in patients with TTN-TV. This updated tool has direct clinical implications for patient management and suggests that combined proteogenomic strategies may enhance risk stratification for other genetic cardiomyopathies.