Multi-omic, histopathologic, and clinicopathologic effects of once-weekly oral rapamycin in a naturally occurring feline model of hypertrophic cardiomyopathy: A pilot study
Cite this dataset
Rivas, Victor; Stern, Joshua (2023). Multi-omic, histopathologic, and clinicopathologic effects of once-weekly oral rapamycin in a naturally occurring feline model of hypertrophic cardiomyopathy: A pilot study [Dataset]. Dryad. https://doi.org/10.25338/B82P9D
Abstract
Hypertrophic cardiomyopathy (HCM) remains the single most common cardiomyopathy in cats, with a staggering prevalence as high as 15%. To date, little to no direct therapeutical intervention for HCM exists for veterinary patients. A previous study aimed to evaluate the effects of delayed-release (DR) rapamycin dosing in a client-owned population of subclinical, non-obstructive, HCM-affected cats and reported that the drug was well tolerated and resulted in beneficial LV remodeling. However, the precise effects of rapamycin in the hypertrophied myocardium remain unknown. Using a feline research colony with naturally occurring hereditary HCM (n = 9), we embarked on the first-ever pilot study to examine the tissue-, urine-, and plasma-level proteomic and tissue-level transcriptomic effects of an intermittent low dose (0.15 mg/kg) and high dose (0.30 mg/kg) of DR oral rapamycin once weekly. Rapamycin remained safe and well tolerated in cats receiving both doses for eight weeks. Following repeated weekly dosing, transcriptomic differences between the low- and high-dose groups support dose-responsive suppressive effects on myocardial hypertrophy and stimulatory effects on autophagy. Differences in the myocardial proteome between treated and control cats suggest potential anti-coagulant/-thrombotic, cellular remodeling, and metabolic effects of the drug. The results of this study closely recapitulate what is observed in the human literature, and the use of rapamycin in the clinical setting as the first therapeutic agent with disease-modifying effects on HCM remains promising. The results of this study establish the need for future validation efforts that investigate the fine-scale relationship between rapamycin treatment and the most compelling gene expression and protein abundance differences reported here.
README: Multi-omic, histopathologic, and clinicopathologic effects of once-weekly oral rapamycin in a naturally occurring feline model of hypertrophic cardiomyopathy: A pilot study
https://doi.org/10.25338/B82P9D
Description of the data and file structure
Project overview:
Raw tissue transcriptomics (LV & IVS) and proteomics (LV, IVS, plasma, and urine) samples are provided. Nine colony cats affected with hypertrophic cardiomyopathy (HCM) were included in this study: three cats did not receive treatment, whereas, six cats were equally randomized and subject to either low- (0.15mg/kg) or high-dose (0.30mg/kg) rapamycin (sirolimus) treatment. Pre- and post-treatment plasma and urine proteomic files are provided for rapamycin-treated cats. A supporting table decoding raw proteomic file names is provided as ProteomicsFileNameKey.xlsx. Refer to publication for expanded study outlines and methods.
Transcriptomic methods:
Tissues of the LV posterior wall and IVS were collected for RNA extraction. Mature RNA transcripts were selected using the polyA selection method. High-quality mature RNA (RNA integrity number [RIN] = 7–10) was converted to cDNA and NEBNext Ultra II stranded library preparations were made. Samples were later used for paired-end 150 bp RNA-seq on the Illumina HiSeq platform with a targeted read depth of 50 million reads per sample (Azenta Life Sciences, South Plainfield, NJ, USA). The resulting raw RNA-sequencing files are provided here.
Proteomic methods:
LV and IVS tissues were cut into 0.30 cm pieces and placed in 1 mL of solubilization buffer (5% SDS, 50 mM triethyl ammonium bicarbonate, complete protease inhibitor cocktail [Roche], pH 7.5) inside MagNA Lyser tubes containing ceramic beads (Roche) and were later homogenized with a MagNA Lyser instrument (Roche) to achieve full mechanical disruption. Tissue homogenates, plasma, and precipitated urine protein samples were subjected to proteolysis by using suspension-trap (ProtiFi) devices. All operations of reduction, alkylation, tryptic digestion, and peptide clean-up were carried out within these devices. The eluted tryptic peptides were dried in a vacuum centrifuge and re-constituted in 0.1% trifluoroacetic acid. Peptides were injected into an LCMS system, where they were first trapped on a Thermo PepMap trap for desalting and separated on PepSep 100 μm × 25 cm analytical columns. Chromatography was performed with a Dionex Ultimate 3000 nUPLC at 600 nL/min. Peptides were eluted directly into a Tribrid Lumos Mass Spectrometer (ThermoFisher, Waltham, MA, USA) using a gradient mix of 0.1% formic acid in water and 0.1% formic acid in acetonitrile over a 60 min period. The samples were run in data-independent analysis (DIA) mode; mass spectra were acquired using a collision energy of 35, M1 resolution of 120 k, and MS2 of 30 k, using overlapped isolation windows of 47 Da in a 360–1080 m/z range and 3 s cycle time. The resulting raw LCMS files are provided here.
HCM-affected low-dose group:
5183-Sarabi
5232-Mikey
5189-Cow
HCM-affected high-dose group:
5148-Sokka
5194-Buttercup
5272-Sam
HCM-affected untreated:
479-Juan
482-Rockstar
717-Dali
Methods
See publication
Funding
National Heart Lung and Blood Institute, Award: T32 HL086350
National Center for Advancing Translational Sciences, Award: TL1 TR001861
TriviumVet