Boos CJ, Balakrishnan B, Blann AD, Lip GY. The relationship of circulating endothelial cells to plasma indices of endothelial damage/dysfunction and apoptosis in acute coronary syndromes: implications for prognosis. J Thromb Haemost. 2008;6(11):1841–50. https://doi.org/10.1111/j.1538-7836.2008.03148.x.

Article  CAS  PubMed  Google Scholar 

Sultan SM. The assessment and importance of disease activity versus disease damage in patients with inflammatory myopathy. Curr Rheumatol Rep. 2003;5(6):445–50. https://doi.org/10.1007/s11926-003-0055-z.

Article  PubMed  Google Scholar 

Foell D, Wittkowski H, Roth J. Monitoring disease activity by stool analyses: from occult blood to molecular markers of intestinal inflammation and damage. Gut. 2009;58(6):859–68. https://doi.org/10.1136/gut.2008.170019.

Article  CAS  PubMed  Google Scholar 

Roh D, Park S. Brain multimodality monitoring: updated perspectives. Curr Neurol Neurosci. 2016;16(6):56. https://doi.org/10.1007/s11910-016-0659-0.

Article  Google Scholar 

Garnero P, Landewe R, Chapurlat RD. The role of biochemical markers of joint tissue remodelling to predict progression and treatment efficacy in inflammatory rheumatic diseases. Rheumatology. 2020;59(6):1207–17. https://doi.org/10.1093/rheumatology/kez647.

Article  CAS  PubMed  Google Scholar 

Frantz TL, Steenburg SD, Gaski GE, Zarzaur BL, Bell TM, McCarroll T, et al. Tissue damage volume predicts organ dysfunction and inflammation after injury. J Surg Res. 2016;202(1):188–95. https://doi.org/10.1016/j.jss.2015.12.043.

Article  PubMed  Google Scholar 

Chong AS, Alegre ML. The impact of infection and tissue damage in solid-organ transplantation. Nat Rev Immunol. 2012;12(6):459–71. https://doi.org/10.1038/nri3215.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee S, Cho HW, Kim B, Lee JK, Kim T. The effectiveness of anti-apoptotic agents to preserve primordial follicles and prevent tissue damage during ovarian tissue cryopreservation and xenotransplantation. Int J Mol Sci. 2021;22(5):2534. https://doi.org/10.3390/ijms22052534.

Article  CAS  PubMed  PubMed Central  Google Scholar 

den Bakker MA. Is histopathology still the gold standard? Ned Tijdschr Geneeskd. 2017;160:D981.

Google Scholar 

Zhu JK. Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet. 2009;43:143–66. https://doi.org/10.1146/annurev-genet-102108-134205.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu SC, Zhang Y. Active DNA demethylation: many roads lead to rome. Nat Rev Mol Cell Biol. 2010;11(9):607–20. https://doi.org/10.1038/nrm2950.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol. 2010;28(10):1057–68. https://doi.org/10.1038/nbt.1685.

Article  CAS  PubMed  Google Scholar 

Vardimon L, Neumann R, Kuhlmann I, Sutter D, Doerfler W. DNA methylation and viral gene expression in adenovirus-transformed and -infected cells. Nucleic Acids Res. 1980;8(11):2461–73. https://doi.org/10.1093/nar/8.11.2461.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lo Y, Han D, Jiang P, Chiu R. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science. 2021;372(6538):eaaw6616. https://doi.org/10.1126/science.aaw3616.

Article  CAS  Google Scholar 

Shen Y, Wang D, Yuan T, Fang H, Zhu C, Qin J, et al. Novel DNA methylation biomarkers in stool and blood for early detection of colorectal cancer and precancerous lesions. Clin Epigenet. 2023;15(1):26. https://doi.org/10.1186/s13148-023-01443-7.

Article  CAS  Google Scholar 

Cortes-Ciriano I, Steele CD, Piculell K, Al-Ibraheemi A, Eulo V, Bui MM, et al. Genomic patterns of malignant peripheral nerve sheath tumor (MPNST) evolution correlate with clinical outcome and are detectable in cell-free DNA. Cancer Discov. 2023;13(3):654–71. https://doi.org/10.1158/2159-8290.CD-22-0786.

Article  PubMed  PubMed Central  Google Scholar 

Deng L, Chao H, Deng H, Yu Z, Zhao R, Huang L, et al. A novel and sensitive DNA methylation marker for the urine-based liquid biopsies to detect bladder cancer. BMC Cancer. 2022;22(1):510. https://doi.org/10.1186/s12885-022-09616-y.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Snyder TM, Khush KK, Valantine HA, Quake SR. Universal noninvasive detection of solid organ transplant rejection. Proc Natl Acad Sci USA. 2011;108(15):6229–34. https://doi.org/10.1073/pnas.1013924108.

Article  PubMed  PubMed Central  Google Scholar 

Sigdel TK, Vitalone MJ, Tran TQ, Dai H, Hsieh SC, Salvatierra O, et al. A rapid noninvasive assay for the detection of renal transplant injury. Transplantation. 2013;96(1):97–101. https://doi.org/10.1097/TP.0b013e318295ee5a.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luo H, Wei W, Ye Z, Zheng J, Xu RH. Liquid biopsy of methylation biomarkers in cell-free DNA. Trends Mol Med. 2021;27(5):482–500. https://doi.org/10.1016/j.molmed.2020.12.011.

Article  CAS  PubMed  Google Scholar 

Nikanjam M, Kato S, Kurzrock R. Liquid biopsy: current technology and clinical applications. J Hematol Oncol. 2022;15(1):131. https://doi.org/10.1186/s13045-022-01351-y.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pos O, Biro O, Szemes T, Nagy B. Circulating cell-free nucleic acids: characteristics and applications. Eur J Hum Genet. 2018;26(7):937–45. https://doi.org/10.1038/s41431-018-0132-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guo S, Diep D, Plongthongkum N, Fung HL, Zhang K, Zhang K. Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA. Nat Genet. 2017;49(4):635–42. https://doi.org/10.1038/ng.3805.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moiso E, Farahani A, Marble HD, Hendricks A, Mildrum S, Levine S, et al. Developmental deconvolution for classification of cancer origin. Cancer Discov. 2022;12(11):2566–85. https://doi.org/10.1158/2159-8290.CD-21-1443.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keukeleire P, Makrodimitris S, Reinders M. Cell type deconvolution of methylated cell-free DNA at the resolution of individual reads. Nar Genom Bioinform. 2023;5(2):Iqad048. https://doi.org/10.1093/nargab/lqad048.

Article  CAS  Google Scholar 

Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, et al. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol. 2022;40(4):585–97. https://doi.org/10.1038/s41587-022-01222-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lubotzky A, Zemmour H, Neiman D, Gotkine M, Loyfer N, Piyanzin S, et al. Liquid biopsy reveals collateral tissue damage in cancer. JCI Insight. 2022. https://doi.org/10.1172/jci.insight.153559.

Article  PubMed  PubMed Central  Google Scholar 

Peixoto P, Cartron PF, Serandour AA, Hervouet E. From 1957 to nowadays: a brief history of epigenetics. Int J Mol Sci. 2020;21(20):7571. https://doi.org/10.3390/ijms21207571.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li Y. Modern epigenetics methods in biological research. Methods. 2021;187:104–13. https://doi.org/10.1016/j.ymeth.2020.06.022.

Article  CAS  PubMed  Google Scholar 

Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317–30. https://doi.org/10.1038/nature14248.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gardiner-Garden M, Frommer M. Cpg islands in vertebrate genomes. J Mol Biol. 1987;196(2):261–82. https://doi.org/10.1016/0022-2836(87)90689-9.

Article  CAS  PubMed  Google Scholar 

Singal R, Ginder GD. DNA methylation. Blood. 1999;93(12):4059–70.

Article  CAS  PubMed  Google Scholar 

Lo R, Weksberg R. Biological and biochemical modulation of DNA methylation. Epigenomics UK. 2014;6(6):593–602. https://doi.org/10.2217/epi.14.49.

Article  CAS  Google Scholar