{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T01:28:27Z","timestamp":1792114107298,"version":"4.4.0"},"posted":{"date-parts":[[2023,1,25]]},"group-title":"Genomics","reference-count":34,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,1,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Patient monitoring is a cornerstone in clinical practice to define disease phenotypes and guide clinical management. Unfortunately, this is often reliant on invasive and\/or less sensitive methods that do not provide deep phenotype assessments of disease state to guide treatment. This paper examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) to define molecular gene sets in physiological and heart transplant patients taking immunosuppression medications. We show cfChIP-seq reliably detect gene signals that correlate with gene expression. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of the relevant immune and non-immune molecular pathways that were predominantly downregulated in immunosuppressed heart transplant patients compared to healthy controls. cfChIP-seq also identified tissue sources of cfDNA, detecting greater cell-free DNA from cardiac, hematopoietic, and other non-hematopoietic tissues such as the pulmonary, digestive, and neurological tissues in transplant patients than healthy controls. cfChIP-seq gene signals were reproducible between patient populations and blood collection methods. cfChIP-seq may therefore be a reliable approach to provide dynamic assessments of molecular pathways and tissue injury associated to disease.<\/jats:p>","DOI":"10.1101\/2023.01.24.525414","type":"posted-content","created":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:40:13Z","timestamp":1674646813000},"source":"Crossref","is-referenced-by-count":2,"title":["Cell-free Chromatin Immunoprecipitation to detect molecular pathways in Physiological and Disease States"],"prefix":"10.64898","author":[{"given":"Moon K.","family":"Jang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tovah E.","family":"Markowitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Temesgen E.","family":"Andargie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zainab","family":"Apalara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Skyler","family":"Kuhn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"Agbor-Enoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2023012707050516000_2023.01.24.525414v1.1","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1016\/j.healun.2017.05.026","article-title":"Applying rigor and reproducibility standards to assay donor-derived cell-free DNA as a non-invasive method for detection of acute rejection and graft injury after heart transplantation","volume":"36","year":"2017","journal-title":"The Journal of Heart and Lung Transplantation"},{"key":"2023012707050516000_2023.01.24.525414v1.2","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/j.ebiom.2018.12.029","article-title":"Donor-derived cell-free DNA predicts allograft failure and mortality after lung transplantation","volume":"40","year":"2019","journal-title":"EBioMedicine"},{"key":"2023012707050516000_2023.01.24.525414v1.3","doi-asserted-by":"crossref","unstructured":"Andargie TE , Tsuji N , Seifuddin F , Jang MK , Yuen PST , Kong H , Tunc I , Singh K , Charya A , Wilkins K . 2021. 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