{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:43:49Z","timestamp":1760147029934,"version":"build-2065373602"},"reference-count":34,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2023,1,3]],"date-time":"2023-01-03T00:00:00Z","timestamp":1672704000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008385","name":"Italian Cystic Fibrosis Research Foundation","doi-asserted-by":"publisher","award":["28.2018"],"award-info":[{"award-number":["28.2018"]}],"id":[{"id":"10.13039\/501100008385","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Chronic rejection (CR) is the main culprit for reduced survival and quality of life in patients undergoing lung transplantation (Ltx). High-throughput approaches have been used to unveil the molecular pathways of CR, mainly in the blood and\/or in bronchoalveolar lavage. We hypothesized that a distinct molecular signature characterizes the biopsies of recipients with clinically confirmed histological signs of CR. Eighteen cystic fibrosis patients were included in the study and RNA sequencing was performed in 35 scheduled transbronchial biopsies (TBBs): 5 with acute cellular rejection, 9 with CR, and 13 without any sign of post-LTx complication at the time of biopsy; 8 donor lung samples were used as controls. Three networks with 33, 26, and 36 differentially expressed genes (DEGs) were found in TBBs with CR. Among these, seven genes were common to the identified pathways and possibly linked to CR and five of them (LCN2, CCL11, CX3CL1, CXCL12, MUC4) were confirmed by real-time PCR. Immunohistochemistry was significant for LCN2 and MUC4. This study identified a typical gene expression pattern in TBBs with histological signs of CR and the LCN2 gene appeared to play a central role. Thus, it could be crucial in CR pathophysiology.<\/jats:p>","DOI":"10.3390\/biom13010097","type":"journal-article","created":{"date-parts":[[2023,1,4]],"date-time":"2023-01-04T05:02:30Z","timestamp":1672808550000},"page":"97","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Molecular Profiling of Tissue Samples with Chronic Rejection from Patients with Chronic Lung Allograft Dysfunction: A Pilot Study in Cystic Fibrosis Patients"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5792-4683","authenticated-orcid":false,"given":"Francesca","family":"Lunardi","sequence":"first","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniela Isabel","family":"Abbrescia","sequence":"additional","affiliation":[{"name":"Schena Foundation, University Hospital of Bari, 70124 Bari, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4847-2333","authenticated-orcid":false,"given":"Luca","family":"Vedovelli","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8023-3108","authenticated-orcid":false,"given":"Federica","family":"Pezzuto","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8954-5888","authenticated-orcid":false,"given":"Francesco","family":"Fortarezza","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giovanni Maria","family":"Comacchio","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincenza","family":"Guzzardo","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pia","family":"Ferrigno","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monica","family":"Loy","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0924-5883","authenticated-orcid":false,"given":"Chiara","family":"Giraudo","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna Sara","family":"Fraia","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eleonora","family":"Faccioli","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7197-9821","authenticated-orcid":false,"given":"Fausto","family":"Braccioni","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emanuele","family":"Cozzi","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7906-0580","authenticated-orcid":false,"given":"Dario","family":"Gregori","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geert M.","family":"Verleden","sequence":"additional","affiliation":[{"name":"Department of Respiratory Diseases, University Hospitals Leuven, 3000 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fiorella","family":"Calabrese","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7927-5207","authenticated-orcid":false,"given":"Francesco Paolo","family":"Schena","sequence":"additional","affiliation":[{"name":"Schena Foundation, University Hospital of Bari, 70124 Bari, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Federico","family":"Rea","sequence":"additional","affiliation":[{"name":"Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1016\/j.healun.2019.08.004","article-title":"The International Thoracic Organ Transplant Registry of the International Society for Heart and Lung Transplantation: Thirty-sixth adult lung and heart-lung transplantation Report-2019; Focus theme: Donor and recipient size match","volume":"38","author":"Khush","year":"2019","journal-title":"J. Heart Lung Trans."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1016\/j.healun.2019.03.009","article-title":"Chronic lung allograft dysfunction: Definition, diagnostic criteria, and approaches to treatment\u2015A consensus report from the Pulmonary Council of the ISHLT","volume":"38","author":"Verleden","year":"2019","journal-title":"J. Heart Lung Trans."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"417","DOI":"10.21037\/atm.2020.01.05","article-title":"An update on chronic lung allograft dysfunction","volume":"8","author":"Kotecha","year":"2020","journal-title":"Ann. Trans. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1016\/j.healun.2019.03.008","article-title":"Chronic lung allograft dysfunction: Definition and update of restrictive allograft syndrome\u2015A consensus report from the Pulmonary Council of the ISHLT","volume":"38","author":"Glanville","year":"2019","journal-title":"J. Heart Lung Trans."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1164\/rccm.200302-165OC","article-title":"Association of minimal rejection in lung transplant recipients with obliterative bronchiolitis","volume":"170","author":"Hopkins","year":"2004","journal-title":"Am. J. Res. Crit. Care Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1111\/j.1600-6143.2004.00650.x","article-title":"HLA-specific antibodies are risk factors for lymphocytic bronchiolitis and chronic lung allograft dysfunction","volume":"5","author":"Girnita","year":"2005","journal-title":"Am. J. Trans."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3178","DOI":"10.1016\/j.ajpath.2015.08.016","article-title":"Molecular profiling in lung biopsies of human pulmonary allografts to predict chronic lung allograft dysfunction","volume":"185","author":"Jonigk","year":"2015","journal-title":"Am. J. Pathol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1016\/j.healun.2019.01.1317","article-title":"Molecular assessment of rejection and injury in lung transplant biopsies","volume":"38","author":"Halloran","year":"2019","journal-title":"J. Heart Lung Trans."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Sacreas, A., Yang, J., Vanaudenaerde, B.M., Sigdel, T.K., Liberto, J.M., Damm, I., Verleden, G.M., Vos, R., Verleden, S.E., and Sarwal, M.M. (2018). The common rejection module in chronic rejection post lung transplantation. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0205107"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1111\/ajt.16895","article-title":"Transcripts associated with chronic lung allograft dysfunction in transbronchial biopsies of lung transplants","volume":"22","author":"Parkes","year":"2022","journal-title":"Am. J. Trans."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e13515","DOI":"10.1111\/ctr.13515","article-title":"Gene signatures common to allograft rejection are associated with lymphocytic bronchitis","volume":"33","author":"Greenland","year":"2019","journal-title":"Clin. Trans."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1111\/ajt.16293","article-title":"Chronic lung allograft dysfunction small airways reveal a lymphocytic inflammation gene signature","volume":"21","author":"Dugger","year":"2021","journal-title":"Am. J. Trans."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1111\/j.1432-2277.2005.00089.x","article-title":"Bronchoscopy in the diagnosis and surveillance of respiratory infections in lung and heart-lung transplant recipients","volume":"18","author":"Lehto","year":"2005","journal-title":"Trans. Int."},{"key":"ref_14","unstructured":"(2022, May 20). Available online: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1089\/cmb.2017.0096","article-title":"cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing","volume":"24","author":"Kechin","year":"2017","journal-title":"J. Comput. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: Ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_17","unstructured":"(2022, May 20). Available online: https:\/\/www.gencodegenes.org\/."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_19","unstructured":"(2022, May 20). Available online: Rsubread\/Subread%20Users%20Guide.%20Rsubread%20v2.6.2\/Subread%20v2.0.2."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Geno. Biol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Soneson, C., and Delorenzi, M. (2013). A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-91"},{"key":"ref_22","unstructured":"(2022, May 20). ENCODE Guidelines and Best Practices for RNA-Seq. Available online: https:\/\/www.encodeproject.org\/documents\/cede0cbe-d324-4ce7-ace4-f0c3eddf5972\/@@download\/attachment\/ENCODE%20Best%20Practices%20for%20RNA_v2.pdf."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1006\/geno.1997.4896","article-title":"Molecular characterization and pattern of tissue expression of the gene for neutrophil gelatinase-associated lipocalin from humans","volume":"45","author":"Cowland","year":"1997","journal-title":"Genomics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"6799","DOI":"10.1038\/s41598-021-85949-1","article-title":"Potential novel biomarkers for chronic lung allograft dysfunction and azithromycin responsive allograft dysfunction","volume":"11","author":"Veraar","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/s41385-020-00343-w","article-title":"MUC4 is overexpressed in idiopathic pulmonary fibrosis and collaborates with transforming growth factor \u03b2 inducing fibrotic responses","volume":"14","author":"Milara","year":"2021","journal-title":"Mucosal. Immunol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1002\/jcp.20277","article-title":"Presence of MUC4 in human milk and at the luminal surfaces of blood vessels","volume":"204","author":"Zhang","year":"2005","journal-title":"J. Cell Physiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1080\/02713680601052155","article-title":"Muc4 expression during blood vessel formation in damaged rat cornea","volume":"31","author":"Zhang","year":"2006","journal-title":"Curr. Eye Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1681\/ASN.2014070679","article-title":"Markers of Endothelial-to-Mesenchymal Transition: Evidence for Antibody-Endothelium Interaction during Antibody-Mediated Rejection in Kidney Recipients","volume":"27","author":"Peltier","year":"2016","journal-title":"J. Am. Soc. Nephrol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1158\/1078-0432.CCR-13-2174","article-title":"MUC4-Mediated Regulation of Acute Phase Protein Lipocalin 2 through HER2\/AKT\/NF-\u03baB Signaling in Pancreatic Cancer","volume":"20","author":"Kaur","year":"2014","journal-title":"Clin. Cancer Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/s13019-017-0673-6","article-title":"The role of epithelial-mesenchymal transition in the post-lung transplantation bronchiolitis obliterans","volume":"12","author":"Zhang","year":"2017","journal-title":"J. Cardiothorac. Surg."},{"key":"ref_31","unstructured":"(2022, May 20). Available online: https:\/\/string-db.org\/."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1146\/annurev.immunol.18.1.593","article-title":"The Role of Chemokine Receptors in Primary, Effector, and Memory Immune Responses","volume":"18","author":"Sallusto","year":"2000","journal-title":"Annu. Rev. Immunol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/S1074-7613(01)00118-2","article-title":"Chemokines, Chemokine Receptors, and Allograft Rejection","volume":"14","author":"Nelson","year":"2001","journal-title":"Immunity"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Santiago-S\u00e1nchez, G.S., Pita-Grisanti, V., Qui\u00f1ones-D\u00edaz, B., Gumpper, K., Cruz-Monserrate, Z., and Vivas-Mej\u00eda, P.E. (2020). Biological Functions and Therapeutic Potential of Lipocalin 2 in Cancer. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21124365"}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/13\/1\/97\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T17:57:44Z","timestamp":1760119064000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/13\/1\/97"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,3]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,1]]}},"alternative-id":["biom13010097"],"URL":"https:\/\/doi.org\/10.3390\/biom13010097","relation":{},"ISSN":["2218-273X"],"issn-type":[{"type":"electronic","value":"2218-273X"}],"subject":[],"published":{"date-parts":[[2023,1,3]]}}}