Repeatome Analysis of Plasma Circulating DNA in Patients with Cardiovascular Disease: Variation with Cell-Free DNA Integrity/Length and Clinical Parameters

first_pagesettingsOrder Article Reprints Open AccessArticle Repeatome Analysis of Plasma Circulating DNA in Patients with Cardiovascular Disease: Variation with Cell-Free DNA Integrity/Length and Clinical Parameters by Stefania Fumarola 1,†ORCID,Monia Cecati 2,†,Francesca Marchegiani 3ORCID,Emanuele Francini 3,Rosanna Maniscalco 1,Jacopo Sabbatinelli 3,4ORCID,Massimiliano Gasparrini 5,*ORCID,Fabrizia Lattanzio 6ORCID,Fabiola Olivieri 1,4ORCID andMaurizio Cardelli 1,*ORCID 1 Advanced Technology Center for Aging Research, IRCCS INRCA, 60121 Ancona, Italy 2 Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, 00166 Rome, Italy 3 Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy 4 Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy 5 Department of Agriculture, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy 6 Scientific Direction, IRCCS INRCA, 60124 Ancona, Italy * Authors to whom correspondence should be addressed. † These authors contributed equally to this work. Int. J. Mol. Sci. 2025, 26(14), 6657; https://doi.org/10.3390/ijms26146657 Submission received: 22 May 2025 / Revised: 30 June 2025 / Accepted: 8 July 2025 / Published: 11 July 2025 (This article belongs to the Section Molecular Genetics and Genomics) Downloadkeyboard_arrow_down Browse Figures Review Reports Versions Notes Abstract Repetitive DNA represents over 50% of the human genome and is an abundant component of circulating cell-free DNA (cfDNA). We previously showed that cfDNA levels and integrity can predict survival in elderly patients with cardiovascular disease. Here, we aimed to clarify whether a low-pass next-generation sequencing (NGS) approach can characterize the repeat content of cfDNA. Considering the bimodal distribution of cfDNA fragment lengths, we examined the occurrence of repetitive DNA subfamilies separately in dinucleosomal (>250 bp) and mononucleosomal (≤250 bp) cfDNA sequences from 24 patients admitted for heart failure. An increase in the relative abundance of Alu repetitive elements was observed in the longer fraction, while alpha satellites were enriched in the mononucleosomal fraction. The relative abundance of Alu, ALR, and L1HS DNA in the dinucleosomal fraction correlated with different prognostic biomarkers, and Alu DNA was negatively associated with the presence of chronic kidney disease comorbidity. These results, together with the observed inverse correlation between Alu DNA abundance and cfDNA integrity, suggest that the composition of plasma cfDNA could be determined by multiple mechanisms in different physio-pathological conditions. In conclusion, low-pass NGS is an inexpensive method to analyze the cfDNA repeat landscape and identify new cardiovascular disease biomarkers.