{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:34:28Z","timestamp":1787027668339,"version":"build-2736575974"},"reference-count":35,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T00:00:00Z","timestamp":1736121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ENDOLIFE","award":["1819"],"award-info":[{"award-number":["1819"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Endometriosis is a chronic, estrogen-dependent disorder associated with the presence of endometrial cells mainly in the pelvic cavity, causing systemic immune inflammation, infertility, epigenetic dysregulation of differential DNA methylation, coelomic metaplasia, and pain. It affects approximately 10\u201312% of women. Despite decades of research, full pathophysiology, a diagnostic roadmap, and clinical management strategies for endometriosis are not yet fully elucidated. Cell-free DNA (Cf-DNA) in the peripheral blood of diseased and healthy individuals was discovered in the 1950s. Quantifying peripheral Cf-DNA and the specific differential methylation of a group of genes have been proposed as potential non-invasive diagnostic biomarkers for somatic and constitutional genetics and for various other pathological disorders. In this study, we investigated the Cf-DNA levels of 78 young women, 38 of whom had endometriosis confirmed via laparoscopy and 40 of whom were healthy. We found a significant difference between the two groups when Cf-DNA was quantified, with 3.9 times more Cf-DNA in the serum of women with endometriosis. We also identified nine target genes potentially involved in the pathogenesis of endometriosis, with a different methylation profile between the two groups. Our data suggest that the combination of cell-free DNA quantification and the assessment of the epigenetic signature of differential methylation of nine genes can be proposed as a non-invasive predictive and diagnostic test for endometriosis.<\/jats:p>","DOI":"10.3390\/biom15010069","type":"journal-article","created":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T09:17:02Z","timestamp":1736155022000},"page":"69","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Quantification of Free Circulating DNA and Differential Methylation Profiling of Selected Genes as Novel Non-Invasive Biomarkers for Endometriosis Diagnosis"],"prefix":"10.3390","volume":"15","author":[{"given":"Moncef","family":"Benkhalifa","sequence":"first","affiliation":[{"name":"IVF & Reproductive Genetics and PeRiTox Laboratory, University Hospital & School of Medicine, Picardy University Jules Verne, 80000 Amiens, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre Alain","family":"Menoud","sequence":"additional","affiliation":[{"name":"Unilabs, Molecular Diagnostic Laboratory\u2014Lausanne, CH-1011 Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5870-4276","authenticated-orcid":false,"given":"David","family":"Piquemal","sequence":"additional","affiliation":[{"name":"ACOBIOM, Biopole Eurom\u00e9decine II Montpellier, 1682 Rue de la Valsi\u00e8re, 34790 Grabels, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jack Y.","family":"Hazout","sequence":"additional","affiliation":[{"name":"ENDOLIFE, 28 Rue de Courcelles, 75008 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sami","family":"Mahjoub","sequence":"additional","affiliation":[{"name":"Alyssa Fertility Group (AFG), Clinique Alyssa, Tunis 1053, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed","family":"Zarquaoui","sequence":"additional","affiliation":[{"name":"IRIFIV Center, Les IRIS Clinic, Casablanca 20000, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noureddine","family":"Louanjli","sequence":"additional","affiliation":[{"name":"IRIFIV Center, Les IRIS Clinic, Casablanca 20000, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosalie","family":"Cabry","sequence":"additional","affiliation":[{"name":"IVF & Reproductive Genetics and PeRiTox Laboratory, University Hospital & School of Medicine, Picardy University Jules Verne, 80000 Amiens, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0829-3143","authenticated-orcid":false,"given":"Andre","family":"Hazout","sequence":"additional","affiliation":[{"name":"ENDOLIFE, 28 Rue de Courcelles, 75008 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1093\/humrep\/11.suppl_3.53","article-title":"Theories on the pathogenesis of endometriosis","volume":"11","year":"1996","journal-title":"Hum. Reprod."},{"key":"ref_2","first-page":"1161","article-title":"M\u00fcllerianosis","volume":"22","author":"Batt","year":"2007","journal-title":"Histol. Histopathol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1756-9966-28-49","article-title":"Ectopic endometrium in human foetuses is a common event and sustains the theory of m\u00fcllerianosis in the pathogenesis of endometriosis, a disease that predisposes to cancer","volume":"28","author":"Signorile","year":"2009","journal-title":"J. Exp. Clin. Cancer Res."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Lagana, A.S., Garzon, S., Gotte, M., Vigano, P., Franchi, M., Ghezzi, F., and Martin, D.C. (2019). The pathogenesis of endometriosis: Molecular and cell biology insights. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20225615"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1210\/er.2018-00242","article-title":"Endometriosis","volume":"40","author":"Bulun","year":"2019","journal-title":"Endocr. Rev."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1016\/j.fertnstert.2004.08.025","article-title":"Endometriosis in premenarcheal girls who do not have an associated obstructive anomaly","volume":"83","author":"Marsh","year":"2005","journal-title":"Fertil. Steril."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"hoae045","DOI":"10.1093\/hropen\/hoae045","article-title":"Is retrograde menstruation a universal, recurrent, physiological phenomenon? A systematic review of the evidence in humans and non-human primates","volume":"2024","author":"Vigano","year":"2024","journal-title":"Hum. Reprod. Open"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s40001-015-0137-1","article-title":"Hepatic endometriosis: A rare case and review of the literature","volume":"20","author":"Liu","year":"2015","journal-title":"Eur. J. Med. Res."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Smolarz, B., Szy\u0142\u0142o, K., and Romanowicz, H. (2021). Endometriosis: Epidemiology, Classification, Pathogenesis, Treatment, and Genetics (Review of Literature). Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms221910554"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1093\/humrep\/dev051","article-title":"Functional evaluation of genetic variants associated with endometriosis nearGREB1","volume":"30","author":"Fung","year":"2015","journal-title":"Hum. Reprod."},{"key":"ref_11","first-page":"803","article-title":"Uterine Stem Cells and Begnin Gynecological Disorders Role in Pathology and Therapeutic Implications","volume":"17","author":"Afrin","year":"2020","journal-title":"Stem Cell Rev. Rep."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1177\/1933719116687661","article-title":"Stem cell trafficking during endometriosis: May epigenetics play a pivotal role?","volume":"25","author":"Lagana","year":"2017","journal-title":"Reprod. Sci."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Abramiuk, M., Gryvalska, E., Malkowska, P., Sierawska, O., Hrynkiewicz, R., and Niedzwiedzka-Rystwej, P. (2022). The Role of the Immune System in the Development of Endometriosis. Cells, 11.","DOI":"10.3390\/cells11132028"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1093\/eurpub\/ckad216","article-title":"Prevalence, diagnostic delay and economic burden of endometriosis and its impact on quality of life: Results from an Eastern Mediterranean population","volume":"34","author":"Swift","year":"2023","journal-title":"Eur. J. Public Health"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"11","DOI":"10.31128\/AJGP\/04-23-6805","article-title":"Endometriosis: A review recent evidence and guidelines","volume":"53","author":"Crump","year":"2024","journal-title":"Aust. J. Gen. Pract."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"hoac009","DOI":"10.1093\/hropen\/hoac009","article-title":"ESHRE guideline: Endometriosis","volume":"2022","author":"Becker","year":"2022","journal-title":"Hum. Reprod. Open"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1906","DOI":"10.1093\/humrep\/deu161","article-title":"DNA methylation of HOXA10 in eutopic and ectopic endometrium","volume":"29","author":"Andersson","year":"2014","journal-title":"Hum. Reprod."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2296","DOI":"10.1093\/humrep\/dead216","article-title":"The role of small extracellular vesicle-miRNAs in endometriosis","volume":"38","author":"Nazri","year":"2023","journal-title":"Hum. Reprod."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/s41416-022-01776-9","article-title":"Integrating circulating-free DNA (cfDNA) analysis into clinical practice: Opportunities and challenges","volume":"127","author":"Makarem","year":"2022","journal-title":"Br. J. Cancer"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"788","DOI":"10.1016\/j.rbmo.2021.08.004","article-title":"Comparison of methods for isolation and quantification of circulating cell-free DNA from patients with endometriosis","volume":"43","author":"Huebner","year":"2021","journal-title":"Reprod. Biomed. Online"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/S1472-6483(10)60100-9","article-title":"Circulating cell-free DNA as a potential biomarker for minimal and mild endometriosis","volume":"18","author":"Zachariah","year":"2009","journal-title":"Reprod. Biomed. Online"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Bendifallah, S., Dabi, Y., Suisse, S., Jornea, L., Bouteiller, D., Touboul, C., Puchar, A., and Dara\u00ef, E. (2022). A Bioinformatics Approach to MicroRNA-Sequencing Analysis Based on Human Saliva Samples of Patients with Endometriosis. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23148045"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Casteleiro Alves, M.M., Oliani, L., Almeida, M., Jose Cardoso, H., Oliani, A.H., Breitenfeld, L., and Ramalhinho, A.C. (2023). Cell-Free DNA as a New Biomarker of IVF Success, Independent of Any Infertility Factor, Including Endometriosis. Diagnostics, 13.","DOI":"10.3390\/diagnostics13020208"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.cca.2007.09.001","article-title":"Characterization of Circulating DNA in Healthy Human Plasma","volume":"387","author":"Suzuki","year":"2008","journal-title":"Clin. Chim. Acta"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/S0009-8981(01)00665-9","article-title":"About the possible origin and mechanism of circulating DNA Apoptosis and active DNA release","volume":"313","author":"Stroun","year":"2001","journal-title":"Clin. Chim. Acta"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1016\/j.rbmo.2021.11.006","article-title":"Comparison of total and endometrial circulating cell-free DNA in women with and without endometriosis","volume":"44","author":"Alonso","year":"2022","journal-title":"Reprod. Biomed. Online"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2560","DOI":"10.1093\/humrep\/deac198","article-title":"Circulating cell-free endometrial DNA level is unaltered during menstruation and in endometriosis","volume":"37","author":"Yuwono","year":"2022","journal-title":"Hum. Reprod."},{"key":"ref_28","first-page":"e59288","article-title":"Role of Molecular Biomarkers in Endometriosis-Related Infertility: A Narrative Review of the Literature","volume":"16","author":"Koutalia","year":"2024","journal-title":"Cureus"},{"key":"ref_29","first-page":"854","article-title":"Proteomics approach to discovering non-invasive diagnostic biomarkers and understanding the pathogenesis of endometriosis: A systematic review and meta-analysis","volume":"110","author":"Azeze","year":"2024","journal-title":"Biol. Reprod."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1186\/s12905-023-02668-7","article-title":"Signatures of necroptosis-related genes as diagnostic markers of endometriosis and their correlation with immune infiltration","volume":"23","author":"Wang","year":"2023","journal-title":"BMC Womens Health"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"6871","DOI":"10.2174\/0109298673283426231220100011","article-title":"Development and Validation of the Diagnostic Model of 7 Gene in Endometriosis","volume":"31","author":"Zhu","year":"2024","journal-title":"Curr. Med. Chem."},{"key":"ref_32","first-page":"685","article-title":"The pathogenesis of endometriosis and adenomyosis: Insights from single-cell RNA sequencing","volume":"22","author":"Li","year":"2024","journal-title":"J. Transl. Med."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.ejogrb.2023.10.015","article-title":"New class of RNA biomarker for endometriosis diagnosis: The potential of salivary piRNA expression","volume":"291","author":"Dabi","year":"2023","journal-title":"Eur. J. Obstet. Gynecol. Reprod. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Bronkhorst, A.J., Ungerer, V., Oberhofer, A., Gabriel, S., Polatoglou, E., Randeu, H., Uhlig, C., Pfister, H., Mayer, Z., and Holdenrieder, S. (2022). New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics, 12.","DOI":"10.3390\/diagnostics12092147"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1007\/s10815-020-02038-4","article-title":"Cell-free DNA discoveries in human reproductive medicine providing a new tool for biomarker genetic assays in ART","volume":"38","author":"Qasemi","year":"2021","journal-title":"J. Assist. Reprod. Genet."}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/15\/1\/69\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T10:23:27Z","timestamp":1759919007000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/15\/1\/69"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,6]]},"references-count":35,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,1]]}},"alternative-id":["biom15010069"],"URL":"https:\/\/doi.org\/10.3390\/biom15010069","relation":{},"ISSN":["2218-273X"],"issn-type":[{"value":"2218-273X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,6]]}}}