{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T09:24:41Z","timestamp":1780392281871,"version":"3.54.1"},"reference-count":103,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T00:00:00Z","timestamp":1676419200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ISCIII from Spain.","award":["PI19\/01154"],"award-info":[{"award-number":["PI19\/01154"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The process and evolution of an organ transplant procedure has evolved in terms of the prevention of immunological rejection with the improvement in the determination of immune response genes. These techniques include considering more important genes, more polymorphism detection, more refinement of the response motifs, as well as the analysis of epitopes and eplets, its capacity to fix complement, the PIRCHE algorithm and post-transplant monitoring with promising new biomarkers that surpass the classic serum markers such as creatine and other similar parameters of renal function. Among these new biomarkers, we analyze new serological, urine, cellular, genomic and transcriptomic biomarkers and computational prediction, with particular attention to the analysis of donor free circulating DNA as an optimal marker of kidney damage.<\/jats:p>","DOI":"10.3390\/ijms24043908","type":"journal-article","created":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T05:12:26Z","timestamp":1676437946000},"page":"3908","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Monitoring of Serological, Cellular and Genomic Biomarkers in Transplantation, Computational Prediction Models and Role of Cell-Free DNA in Transplant Outcome"],"prefix":"10.3390","volume":"24","author":[{"given":"V\u00edctor","family":"Jimenez-Coll","sequence":"first","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4933-8243","authenticated-orcid":false,"given":"Santiago","family":"Llorente","sequence":"additional","affiliation":[{"name":"Nephrology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3926-7920","authenticated-orcid":false,"given":"Francisco","family":"Boix","sequence":"additional","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"Alfaro","sequence":"additional","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Antonio","family":"Gali\u00e1n","sequence":"additional","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helios","family":"Martinez-Banaclocha","sequence":"additional","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmen","family":"Botella","sequence":"additional","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda R.","family":"Moya-Quiles","sequence":"additional","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel","family":"Muro-P\u00e9rez","sequence":"additional","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2472-5893","authenticated-orcid":false,"given":"Alfredo","family":"Minguela","sequence":"additional","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1140-4313","authenticated-orcid":false,"given":"Isabel","family":"Legaz","sequence":"additional","affiliation":[{"name":"Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence \u201cCampus Mare Nostrum\u201d, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9987-0994","authenticated-orcid":false,"given":"Manuel","family":"Muro","sequence":"additional","affiliation":[{"name":"Immunology Service, Instituto Murciano de Investigaci\u00f3n Biosanitaria (IMIB), Hospital Cl\u00ednico Universitario Virgen de la Arrixaca (HCUVA), 30120 Murcia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,2,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Aldea, P.L., Rachisan, A.L., Stanciu, B.I., Picos, A., Picos, A.M., Delean, D.I., Stroescu, R., Starcea, M.I., Borzan, C.M., and Elec, F.I. (2022). The Perspectives of Biomarkers in Predicting the Survival of the Renal Graft. Front. Pediatr., 10.","DOI":"10.3389\/fped.2022.869628"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fgene.2022.1031894","article-title":"Donor-derived cell-free DNA as a diagnostic tool in transplantation","volume":"13","author":"Oellerich","year":"2022","journal-title":"Front. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"100629","DOI":"10.1016\/j.trre.2021.100629","article-title":"Emerging biomarkers of delayed graft function in kidney transplantation","volume":"35","author":"Mezzolla","year":"2021","journal-title":"Transplant. Rev."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1007\/978-1-60327-118-9_30","article-title":"HistoCheck. Evaluating structural and functional MHC similarities","volume":"409","author":"DeLuca","year":"2007","journal-title":"Methods Mol. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"469","DOI":"10.3389\/fimmu.2016.00469","article-title":"Reflections on HLA epitope-based matching for transplantation","volume":"7","author":"Duquesnoy","year":"2016","journal-title":"Front. Immunol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/j.jceh.2017.10.003","article-title":"Acute and Chronic Rejection After Liver Transplantation: What A Clinician Needs to Know","volume":"7","author":"Choudhary","year":"2017","journal-title":"J. Clin. Exp. Hepatol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fimmu.2020.01454","article-title":"The Role of Natural Killer Cells in the Immune Response in Kidney Transplantation","volume":"11","author":"Pontrelli","year":"2020","journal-title":"Front. Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Lemieux, W., Fleischer, D., Yang, A.Y., Niemann, M., Oualkacha, K., Klement, W., Richard, L., Polychronakos, C., Liwski, R., and Claas, F. (2022). Dissecting the impact of molecular T-cell HLA mismatches in kidney transplant failure: A retrospective cohort study. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.1067075"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.2174\/1389203719666180730164542","article-title":"Cell-Mediated Immunity (CMI) as the Instrument to Assess the Response Against the Allograft: Present and Future","volume":"19","author":"Boix","year":"2018","journal-title":"Curr. Protein Pept. Sci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1490","DOI":"10.1111\/ajt.14142","article-title":"Renal Operational Tolerance Is Associated with a Defect of Blood Tfh Cells That Exhibit Impaired B Cell Help","volume":"17","author":"Chenouard","year":"2017","journal-title":"Am. J. Transplant."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1111\/ajt.14987","article-title":"Longitudinal profile of circulating T follicular helper lymphocytes parallels anti-HLA sensitization in renal transplant recipients","volume":"19","author":"Lora","year":"2019","journal-title":"Am. J. Transplant."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1097\/MOT.0000000000000775","article-title":"Artificial intelligence and organ transplantation: Challenges and expectations","volume":"25","year":"2020","journal-title":"Curr. Opin. Organ Transplant."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1111\/imr.13040","article-title":"Imaging reveals novel innate immune responses in lung, liver, and beyond","volume":"306","author":"Neupane","year":"2022","journal-title":"Immunol. Rev."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2816","DOI":"10.1111\/ajt.13909","article-title":"2016 comprehensive update of the Banff working group on liver allograft pathology: Introduction of antibody-mediated rejection","volume":"16","author":"Demetris","year":"2016","journal-title":"Am. J. Transplant."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"7771","DOI":"10.3748\/wjg.v27.i45.7771","article-title":"Chronic rejection after liver transplantation: Opening the Pandora\u2019s box","volume":"27","author":"Angelico","year":"2021","journal-title":"World J. Gastroenterol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1111\/ajt.12721","article-title":"Kidney Transplant Recipients Treated with Belatacept Exhibit Increased Na\u00efve and Transitional B Cells","volume":"14","author":"Leibler","year":"2014","journal-title":"Am. J. Transplant."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Jaikaransingh, V., and Kadambi, P.V. (2021). Donor-derived cell-free DNA (ddcf-DNA) and acute antibody-mediated rejection in kidney transplantation. Medicina, 57.","DOI":"10.3390\/medicina57050436"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.nephro.2020.10.003","article-title":"The role of donor-derived cell-free DNA in the detection of renal allograft injury","volume":"17","author":"Zhou","year":"2021","journal-title":"Nephrol. Ther."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2400","DOI":"10.1016\/j.transproceed.2015.08.035","article-title":"Donor-Derived Cell-Free DNA Is a Novel Universal Biomarker for Allograft Rejection in Solid Organ Transplantation","volume":"47","author":"Beck","year":"2015","journal-title":"Transplant. Proc."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/s41581-021-00428-0","article-title":"Liquid biopsies: Donor-derived cell-free DNA for the detection of kidney allograft injury","volume":"17","author":"Oellerich","year":"2021","journal-title":"Nat. Rev. Nephrol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"E785","DOI":"10.1097\/TXD.0000000000001247","article-title":"CXCL13 Is an Indicator of Germinal Center Activity and Alloantibody Formation Following Transplantation","volume":"7","author":"Crichton","year":"2021","journal-title":"Transplant. Direct"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"G\u0103man, M.A., Cozma, M.A., Dobric\u0103, E.C., Cre\u021boiu, S.M., G\u0103man, A.M., and Diaconu, C.C. (2021). Liquid biopsy and potential liquid biopsy-based biomarkers in philadelphia-negative classical myeloproliferative neoplasms: A systematic review. Life, 11.","DOI":"10.3390\/life11070677"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/j.imbio.2016.01.008","article-title":"High expression of CD38, CD69, CD95 and CD154 biomarkers in cultured peripheral T lymphocytes correlates with an increased risk of acute rejection in liver allograft recipients","volume":"221","author":"Boix","year":"2016","journal-title":"Immunobiology"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1111\/cei.13533","article-title":"Identification of peripheral CD154+ T cells and HLA-DRB1 as biomarkers of acute cellular rejection in adult liver transplant recipients","volume":"203","author":"Boix","year":"2021","journal-title":"Clin. Exp. Immunol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.trim.2017.04.001","article-title":"CD28 biomarker quantification and expression level profiles in CD4+ T-lymphocytes in solid organ transplantation","volume":"42","author":"Boix","year":"2017","journal-title":"Transpl. Immunol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Alfaro, R., Legaz, I., Gonz\u00e1lez-Mart\u00ednez, G., Jimenez-Coll, V., Mart\u00ednez-Banaclocha, H., Gali\u00e1n, J.A., Botella, C., de la Pe\u00f1a-Moral, J., Moya-Quiles, M.R., and Campillo, J.A. (2021). Monitoring of b cell in kidney transplantation: Development of a novel clusters analysis and role of transitional b cells in transplant outcome. Diagnostics, 11.","DOI":"10.3390\/diagnostics11040641"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1093\/intimm\/dxv048","article-title":"High frequency of central memory regulatory T cells allows detection of liver recipients at risk of early acute rejection within the first month after transplantation","volume":"28","author":"Millan","year":"2016","journal-title":"Int. Immunol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Seiler, L.K., Phung, N.L., Nikolin, C., Immenschuh, S., Erck, C., Kaufeld, J., Haller, H., Falk, C.S., Jonczyk, R., and Lindner, P. (2022). An Antibody-Aptamer-Hybrid Lateral Flow Assay for Detection of CXCL9 in Antibody-Mediated Rejection after Kidney Transplantation. Diagnostics, 12.","DOI":"10.3390\/diagnostics12020308"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"S54","DOI":"10.1097\/TP.0b013e3181af7d84","article-title":"HLA-C matching and liver transplants: Donor-recipient genotypes influence early outcome and CD8+KIR2D+ T-cells recuperation","volume":"88","author":"Minguela","year":"2009","journal-title":"Transplantation"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1097\/TP.0b013e31824fd892","article-title":"Urinary neutrophil gelatinase-associated lipocalin accurately detects acute allograft rejection among other causes of acute kidney injury in renal allograft recipients","volume":"93","author":"Heyne","year":"2012","journal-title":"Transplantation"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1016\/j.immuni.2013.09.007","article-title":"Circulating Precursor CCR7loPD-1hi CXCR5+ CD4+ T Cells Indicate Tfh Cell Activity and Promote Antibody Responses upon Antigen Reexposure","volume":"39","author":"He","year":"2013","journal-title":"Immunity"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"745","DOI":"10.2174\/1389203722666210706163149","article-title":"Evaluation of Antibodies Directed Against Two GPCRs, Anti-AT1R and Anti-ETAR, on Kidney Transplant Outcome","volume":"22","author":"Llorente","year":"2021","journal-title":"Curr. Protein Pept. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1089\/omi.2021.0099","article-title":"Personalized Medicine for Kidney Transplantation: Association of Graft Survival and Acute Transplant Rejection with Genetic Variation in B Cell Activating Factor System Signaling","volume":"25","author":"Alfaro","year":"2021","journal-title":"OMICS A J. Integr. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Alfaro, R., Legaz, I., Jimenez-Coll, V., El Kaaoui El Band, J., Mart\u00ednez-Banaclocha, H., Gali\u00e1n, J.A., Parrado, A., Mrowiec, A., Botella, C., and Moya-Quiles, M.R. (2021). MicroRNA Expression Changes in Kidney Transplant: Diagnostic Efficacy of miR-150-5p as Potential Rejection Biomarker, Pilot Study. J. Clin. Med., 10.","DOI":"10.3390\/jcm10132748"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"13336","DOI":"10.1073\/pnas.1517494112","article-title":"Noninvasive monitoring of infection and rejection after lung transplantation","volume":"112","author":"Martin","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e14295","DOI":"10.1111\/ctr.14295","article-title":"Identification of cell-free DNA methylation patterns unique to the human left ventricle as a potential indicator of acute cellular rejection","volume":"35","author":"Pattar","year":"2021","journal-title":"Clin. Transplant."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13148-022-01241-7","article-title":"The applications of DNA methylation as a biomarker in kidney transplantation: A systematic review","volume":"14","author":"Cristoferi","year":"2022","journal-title":"Clin. Epigenetics"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e1489","DOI":"10.1002\/wsbm.1489","article-title":"Molecular networks in Network Medicine: Development and applications","volume":"12","author":"Silverman","year":"2020","journal-title":"Wiley Interdiscip. Rev. Syst. Biol. Med."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2840","DOI":"10.1681\/ASN.2014080797","article-title":"Urinary C-X-C Motif Chemokine 10 Independently Improves the Noninvasive Diagnosis of Antibody\u2013Mediated Kidney Allograft Rejection","volume":"26","author":"Rabant","year":"2015","journal-title":"J. Am. Soc. Nephrol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1111\/tri.13584","article-title":"Longitudinal assessment of the CXCL10 blood and urine concentration in kidney transplant recipients with BK polyomavirus replication\u2014a retrospective study","volume":"33","author":"Weseslindtner","year":"2020","journal-title":"Transpl. Int."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2390","DOI":"10.1111\/j.1523-1755.2004.00663.x","article-title":"Noninvasive detection of renal allograft inflammation by measurements of mRNA for IP-10 and CXCR3 in urine","volume":"65","author":"Tatapudi","year":"2004","journal-title":"Kidney Int."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1097\/01.TP.0000160759.85080.2E","article-title":"High CXCL10 expression in rejected kidneys and predictive role of pretransplant serum CXCL10 for acute rejection and chronic allograft nephropathy","volume":"79","author":"Lazzeri","year":"2005","journal-title":"Transplantation"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2228","DOI":"10.1111\/j.1600-6143.2011.03680.x","article-title":"Urinary Chemokines CXCL9 and CXCL10 Are Noninvasive Markers of Renal Allograft Rejection and BK Viral Infection","volume":"11","author":"Jackson","year":"2011","journal-title":"Am. J. Transplant."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"251","DOI":"10.5500\/wjt.v5.i4.251","article-title":"Role for urinary biomarkers in diagnosis of acute rejection in the transplanted kidney","volume":"5","author":"Merhi","year":"2015","journal-title":"World J. Transplant."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1080\/10408360490504934","article-title":"Biochemistry and Clinical Role of Human Cystatin C","volume":"41","author":"Mussap","year":"2008","journal-title":"Crit. Rev. Clin. Lab. Sci."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Jensen, D., Kierulf-Lassen, C., Kristensen, M.L.V., N\u00f8rregaard, R., Weyer, K., Nielsen, R., Christensen, E.I., and Birn, H. (2017). Megalin dependent urinary cystatin C excretion in ischemic kidney injury in rats. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0178796"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"377","DOI":"10.4155\/bio-2017-0228","article-title":"Novel automated immune turbidimetric assay for routine urinary cystatin-C determinations","volume":"10","author":"Szirmay","year":"2018","journal-title":"Bioanalysis"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1053\/j.ajkd.2012.06.002","article-title":"Serum Cystatin C\u2013 Versus Creatinine-Based Definitions of Acute Kidney Injury Following Cardiac Surgery: A Prospective Cohort Study","volume":"60","author":"Spahillari","year":"2012","journal-title":"Am. J. Kidney Dis."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"11","DOI":"10.15171\/jrip.2018.03","article-title":"Serum cystatin C versus creatinine in the assessment of allograft function in early periods of kidney transplantation","volume":"7","author":"Alizadeh","year":"2017","journal-title":"J. Ren. Inj. Prev."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2877","DOI":"10.2169\/internalmedicine.54.4749","article-title":"The Potential Role of Inflammation Associated with Interaction between Osteopontin and CD44 in a Case of Pulmonary Tumor Thrombotic Microangiopathy Caused by Breast Cancer","volume":"54","author":"Higashi","year":"2015","journal-title":"Intern. Med."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.clim.2014.07.007","article-title":"Should IFN-\u03b3, IL-17 and IL-2 be considered predictive biomarkers of acute rejection in liver and kidney transplant? Results of a multicentric study","volume":"154","author":"Boix","year":"2014","journal-title":"Clin. Immunol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1016\/j.jpeds.2012.02.007","article-title":"Urine Biomarkers Predict Acute Kidney Injury in Newborns","volume":"161","author":"Askenazi","year":"2012","journal-title":"J. Pediatr."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Castello, L.M., Raineri, D., Salmi, L., Clemente, N., Vaschetto, R., Quaglia, M., Garzaro, M., Gentilli, S., Navalesi, P., and Cantaluppi, V. (2017). Osteopontin at the Crossroads of Inflammation and Tumor Progression. Mediators Inflamm., 2017.","DOI":"10.1155\/2017\/4049098"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1111\/j.1523-1755.2005.00153.x","article-title":"Osteopontin expression in acute renal allograft rejection","volume":"67","author":"Alchi","year":"2005","journal-title":"Kidney Int."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.jss.2012.08.006","article-title":"Osteopontin level correlates with acute cellular renal allograft rejection","volume":"182","author":"Wang","year":"2013","journal-title":"J. Surg. Res."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1152\/ajprenal.00399.2009","article-title":"Loss of clusterin expression worsens renal ischemia-reperfusion injury","volume":"298","author":"Zhou","year":"2010","journal-title":"Am. J. Physiol.-Ren. Physiol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"98","DOI":"10.15171\/jrip.2016.21","article-title":"Role of plasma neutrophil gelatinase-associated lipocalin as an emerging biomarker of acute renal failure following kidney transplantation and its correlation with plasma creatinine","volume":"5","author":"Pezeshgi","year":"2016","journal-title":"J. Ren. Inj. Prev."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1007\/s00467-018-3924-4","article-title":"Urinary clusterin\u2014A novel urinary biomarker associated with pediatric lupus renal histopathologic features and renal survival","volume":"33","author":"Wu","year":"2018","journal-title":"Pediatr. Nephrol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Musia\u0142, K., Augustynowicz, M., Mi\u015bkiewicz-Migo\u0144, I., Ka\u0142wak, K., Ussowicz, M., and Zwoli\u0144ska, D. (2020). Clusterin as a New Marker of Kidney Injury in Children Undergoing Allogeneic Hematopoietic Stem Cell Transplantation\u2014A Pilot Study. J. Clin. Med., 9.","DOI":"10.3390\/jcm9082599"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1097\/TP.0000000000000256","article-title":"Clusterin in kidney transplantation: Novel biomarkers versus serum creatinine for early prediction of delayed graft function","volume":"99","author":"Pianta","year":"2015","journal-title":"Transplantation"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1097\/TP.0000000000000202","article-title":"High proportion of pretransplantation activated regulatory T cells (CD4+ CD25highCD62L+ CD45RO+) predicts acute rejection in kidney transplantation: Results of a multicenter study","volume":"98","author":"Boix","year":"2014","journal-title":"Transplantation"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1016\/j.humimm.2011.06.004","article-title":"CD28 and KIR2D receptors as sensors of the immune status in heart and liver transplantation","volume":"72","author":"Garrido","year":"2011","journal-title":"Hum. Immunol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1016\/j.kint.2020.02.039","article-title":"Imbalance favoring follicular helper T cells over IL10+ regulatory B cells is detrimental for the kidney allograft","volume":"98","year":"2020","journal-title":"Kidney Int."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.jaci.2016.09.042","article-title":"Human regulatory B cells control the TFH cell response","volume":"140","author":"Achour","year":"2017","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.drugpo.2017.05.017","article-title":"The extent of and factors associated with self-reported overdose and self-reported receipt of naloxone among people who inject drugs (PWID) in England, Wales and Northern Ireland","volume":"46","author":"Cullen","year":"2017","journal-title":"Int. Jounal Drug Policy"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.21037\/tau-22-266","article-title":"Identification of a novel peripheral blood signature diagnosing subclinical acute rejection after renal transplantation","volume":"11","author":"Xu","year":"2022","journal-title":"Transl. Androl. Urol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Halloran, P.F., Reeve, J., Madill-Thomsen, K.S., Kaur, N., Ahmed, E., Cantos, C., Al Haj Baddar, N., Demko, Z., Liang, N., and Swenerton, R.K. (2022). Combining Donor-derived Cell-free DNA Fraction and Quantity to Detect Kidney Transplant Rejection Using Molecular Diagnoses and Histology as Confirmation. Transplantation, 106.","DOI":"10.1097\/TP.0000000000004212"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Benincasa, G., Viglietti, M., Coscioni, E., and Napoli, C. (2022). \u201cTransplantomics\u201d for predicting allograft rejection: Real-life applications and new strategies from Network Medicine. Hum. Immunol.","DOI":"10.1016\/j.humimm.2022.11.004"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1007\/s12551-020-00713-5","article-title":"Understanding and using AlloSure donor derived cell-free DNA","volume":"12","author":"Seeto","year":"2020","journal-title":"Biophys. Rev."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"8440","DOI":"10.18632\/aging.202654","article-title":"Donor plasma mitochondrial DNA is associated with antibody-mediated rejection in renal allograft recipients","volume":"13","author":"Han","year":"2021","journal-title":"Aging (Albany NY)"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1161\/CIRCULATIONAHA.116.022907","article-title":"Gene expression profiling for the identification and classification of antibody-mediated heart rejection","volume":"135","author":"Loupy","year":"2017","journal-title":"Circulation"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Warmuzi\u0144ska, N., \u0141uczykowski, K., and Bojko, B. (2022). A Review of Current and Emerging Trends in Donor Graft-Quality Assessment Techniques. J. Clin. Med., 11.","DOI":"10.3390\/jcm11030487"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"2851","DOI":"10.1111\/ajt.14329","article-title":"Real Time Central Assessment of Kidney Transplant Indication Biopsies by Microarrays: The INTERCOMEX Study","volume":"17","author":"Halloran","year":"2017","journal-title":"Am. J. Transplant."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Eller, K., B\u00f6hmig, G.A., Banas, M.C., and Viklicky, O. (2022). Editorial: Advances in the diagnosis and treatment in kidney transplantation. Front. Med., 9.","DOI":"10.3389\/fmed.2022.967749"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1111\/ajt.12465","article-title":"Microarray Diagnosis of Antibody-Mediated Rejection in Kidney Transplant Biopsies: An International Prospective Study (INTERCOM)","volume":"13","author":"Halloran","year":"2013","journal-title":"Am. J. Transplant."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"5330","DOI":"10.1073\/pnas.0813121106","article-title":"MicroRNA expression profiles predictive of human renal allograft status","volume":"106","author":"Anglicheau","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1097\/TP.0b013e3182751efd","article-title":"MicroRNA Sequence Profiles of Human Kidney Allografts With or Without Tubulointerstitial Fibrosis","volume":"94","author":"Muthukumar","year":"2012","journal-title":"Transplantation"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-60327-118-9_1","article-title":"Immunoinformatics and the in silico prediction of immunogenicity. An introduction","volume":"409","author":"Flower","year":"2007","journal-title":"Methods Mol. Biol."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Burlacu, A., Iftene, A., Jugrin, D., Popa, I.V., Lupu, P.M., Vlad, C., and Covic, A. (2020). Using Artificial Intelligence Resources in Dialysis and Kidney Transplant Patients: A Literature Review. Biomed Res. Int., 2020.","DOI":"10.1155\/2020\/9867872"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.dss.2017.12.004","article-title":"Predicting graft survival among kidney transplant recipients: A Bayesian decision support model","volume":"106","author":"Topuz","year":"2018","journal-title":"Decis. Support Syst."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/j.bspc.2017.01.012","article-title":"Decision tree and random forest models for outcome prediction in antibody incompatible kidney transplantation","volume":"52","author":"Shaikhina","year":"2019","journal-title":"Biomed. Signal Process. Control"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"1883","DOI":"10.1001\/jama.293.15.1883","article-title":"Kidney Paired Donation and Optimizing the Use of Live Donor Organs","volume":"293","author":"Segev","year":"2005","journal-title":"JAMA"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.pbiomolbio.2016.08.007","article-title":"A framework to establish credibility of computational models in biology","volume":"129","author":"Patterson","year":"2017","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"106407","DOI":"10.1016\/j.compbiomed.2022.106407","article-title":"UncertainSCI: Uncertainty quantification for computational models in biomedicine and bioengineering","volume":"152","author":"Narayan","year":"2023","journal-title":"Comput. Biol. Med."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"5418","DOI":"10.3389\/fimmu.2021.800968","article-title":"Computational Prediction of Biomarkers, Pathways, and New Target Drugs in the Pathogenesis of Immune-Based Diseases Regarding Kidney Transplantation Rejection","volume":"12","author":"Alfaro","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Agapito, G., and Cannataro, M. (2022, January 9\u201311). A parallel software pipeline to select relevant genes for pathway enrichment. Proceedings of the 2022 30th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP), Valladolid, Spain.","DOI":"10.1109\/PDP55904.2022.00041"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1038\/s41467-021-21146-y","article-title":"Individualized interactomes for network-based precision medicine in hypertrophic cardiomyopathy with implications for other clinical pathophenotypes","volume":"12","author":"Maron","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2390","DOI":"10.3389\/fimmu.2020.583702","article-title":"Kidney Failure Associates with T Cell Exhaustion and Imbalanced Follicular Helper T Cells","volume":"11","author":"Hartzell","year":"2020","journal-title":"Front. Immunol."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Wang, L.J., Ma, X.B., Xia, H.Y., Sun, X., Yu, L., Yang, Q., Hu, Z.Q., Zhao, Y.H., Hu, W., and Ran, J.H. (2021). Identification of Biomarkers for Predicting Allograft Rejection following Kidney Transplantation Based on the Weighted Gene Coexpression Network Analysis. Biomed Res. Int., 2021.","DOI":"10.1155\/2021\/9933136"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"846695","DOI":"10.3389\/fimmu.2022.846695","article-title":"SLAMF8 Participates in Acute Renal Transplant Rejection via TLR4 Pathway on Pro-Inflammatory Macrophages","volume":"13","author":"Teng","year":"2022","journal-title":"Front. Immunol."},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Benincasa, G., Maron, B.A., Affinito, O., D\u2019Alto, M., Franzese, M., Argiento, P., Schiano, C., Romeo, E., Bontempo, P., and Golino, P. (2022). Association Between Circulating CD4+ T Cell Methylation Signatures of Network-Oriented SOCS3 Gene and Hemodynamics in Patients Suffering Pulmonary Arterial Hypertension. J. Cardiovasc. Transl. Res., 1\u201314.","DOI":"10.1007\/s12265-022-10294-1"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"547849","DOI":"10.3389\/fmed.2021.547849","article-title":"PCR Array Technology in Biopsy Samples Identifies Up-Regulated mTOR Pathway Genes as Potential Rejection Biomarkers After Kidney Transplantation","volume":"8","author":"Legaz","year":"2021","journal-title":"Front. Med."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"6229","DOI":"10.1073\/pnas.1013924108","article-title":"Universal noninvasive detection of solid organ transplant rejection","volume":"108","author":"Snyder","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_94","unstructured":"(2020, March 31). STRING: Functional Protein Association Networks. Available online: https:\/\/string-db.org\/."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.1016\/0140-6736(92)91840-5","article-title":"Cell migration, chimerism, and graft acceptance","volume":"339","author":"Starzl","year":"1992","journal-title":"Lancet"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1016\/S0140-6736(05)79055-3","article-title":"Presence of donor-specific DNA in plasma of kidney and liver-transplant recipients","volume":"351","author":"Lo","year":"1998","journal-title":"Lancet"},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Liu, Z., Zhao, J., Wang, W., Zhu, H., Qian, J., Wang, S., Que, S., Zhang, F., Yin, S., and Zhou, L. (2021). Integrative Network Analysis Revealed Genetic Impact of Pyruvate Kinase L\/R on Hepatocyte Proliferation and Graft Survival after Liver Transplantation. Oxid. Med. Cell. Longev., 2021.","DOI":"10.1155\/2021\/7182914"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1373\/clinchem.2005.058974","article-title":"Soluble Donor DNA Concentrations in Recipient Serum Correlate with Pancreas-Kidney Rejection","volume":"52","author":"Gadi","year":"2006","journal-title":"Clin. Chem."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"e568","DOI":"10.1097\/TXD.0000000000001019","article-title":"Donor-derived Cell-free DNA in Infections in Kidney Transplant Recipients: Case Series","volume":"6","author":"Goussous","year":"2020","journal-title":"Transplant. Direct"},{"key":"ref_100","doi-asserted-by":"crossref","unstructured":"Kant, S., Bromberg, J., Haas, M., and Brennan, D. (2020). Donor-derived Cell-free DNA and the Prediction of BK Virus-associated Nephropathy. Transplant. Direct, 6.","DOI":"10.1097\/TXD.0000000000001061"},{"key":"ref_101","doi-asserted-by":"crossref","unstructured":"Sigdel, T.K., Archila, F.A., Constantin, T., Prins, S.A., Liberto, J., Damm, I., Towfighi, P., Navarro, S., Kirkizlar, E., and Demko, Z.P. (2018). Optimizing Detection of Kidney Transplant Injury by Assessment of Donor-Derived Cell-Free DNA via Massively Multiplex PCR. J. Clin. Med., 8.","DOI":"10.3390\/jcm8010019"},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Jordan, S.C., Bunnapradist, S., Bromberg, J.S., Langone, A.J., Hiller, D., Yee, J.P., Sninsky, J.J., Woodward, R.N., and Matas, A.J. (2018). Donor-derived Cell-free DNA Identifies Antibody-mediated Rejection in Donor Specific Antibody Positive Kidney Transplant Recipients. Transplant. Direct, 4.","DOI":"10.1097\/TXD.0000000000000821"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.1111\/ajt.15289","article-title":"Early clinical experience using donor-derived cell-free DNA to detect rejection in kidney transplant recipients","volume":"19","author":"Huang","year":"2019","journal-title":"Am. J. Transplant."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/4\/3908\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:36:19Z","timestamp":1760121379000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/4\/3908"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,15]]},"references-count":103,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2023,2]]}},"alternative-id":["ijms24043908"],"URL":"https:\/\/doi.org\/10.3390\/ijms24043908","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,15]]}}}