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RNA sequencing of the left ventricle from non-failing donors and heart failure samples from the MAGNet consortium

ABSTRACT: The Myocardial Applied Genomics Network (MAGNet; www.med.upenn.edu/magnet), collects and banks human cardiac tissue for genomic research. All subjects or next of kin provided written informed consent for tissue donation and analyses and all study protocols were approved by relevant institutional review boards. Left ventricular free-wall tissue was harvested at the time of cardiac surgery from subjects with heart failure undergoing transplantation and from unused donor hearts with apparently normal function. The heart was perfused with cold cardioplegia prior to cardiectomy to arrest contraction and prevent ischemic damage, and tissue specimens were frozen in liquid nitrogen.

ORGANISM(S): Homo sapiens

PROVIDER: GSE141910 | GEO | 2019/12/13

REPOSITORIES: GEO

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Project description:Cardiac amyloidosis is a severe clinical condition leading to restrictive cardiomyopathy and heart failure. With increasing options for specific treatment of different cardiac amyloid diseases, correct amyloid subtyping is essential for clinical outcome. Mass spectrometry-based methods for cardiac amyloid subtyping have become important diagnostic tools but are currently used only in a few reference laboratories. Such methods typically include laser-capture microdissection to ensure the specific analysis of amyloid deposits. While this strategy effectively reduces background signals, it is a labor-intensive and costly procedure hampering the implementation of these methods into a wider group of laboratories. Here we introduce a more direct proteomics-based method for subtyping of cardiac amyloids. Endomyocardial biopsies were retrospectively analyzed from fresh frozen material of 78 patients with cardiac amyloidosis and from 12 biopsies of unused donor heart explants. Cryostat sections were directly digested with trypsin and analyzed with the nano-liquid chromatography (nLC-MS/MS), and the data were evaluated by a proteomic software. With a diagnostic threshold set to 70% for each of the four most common amyloid proteins affecting the heart (LC k, LC l, TTR and SAA), 65 of the cases (87%) could be diagnosed, and of these, 61 cases (94%) were in concordance with the original diagnoses. The specimens were also analyzed for the summed intensities of the amyloid signature proteins (ApoE, ApoA-IV and SAP). The summed intensities were significantly higher (p<0.001) for all assigned amyloid cases, whereas unassigned cases were not significantly different from controls and had lower signals than the assigned cases (p<0.001), suggesting that signature proteins can serve as in situ quality markers of cardiac amyloid deposits. We argue that this efficient workflow can be useful for disseminating proteomics for cardiac amyloid subtyping into accredited clinical laboratories.

Dataset Information

RNA sequencing of the left ventricle from non-failing donors and heart failure samples from the MAGNet consortium

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