{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T11:15:48Z","timestamp":1768562148058,"version":"3.49.0"},"posted":{"date-parts":[[2023,4,3]]},"group-title":"Transplantation","reference-count":46,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Long term outcomes of allograft recipients are compromised by the development of chronic lung allograft dysfunction (CLAD) promoting bronchiolitis obliterans syndrome (BOS). We established baseline transcriptomic profiles of both the large and small airway epithelial cells (referred as LAEC and SAEC, respectively) to identify regional differences irrespective of initiating disease.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We obtained matched primary LAEC and SAEC from lung allograft recipients (n=4, 42.5 \u00b1 4.2 years) and established primary cultures. Bulk RNA sequencing was performed to determine differentially expressed genes.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    We observed differences in the transcriptional program between LAEC and SAEC Transcription factors (TF) were ranked within the top ten differentially regulated genes. The most abundant TF families included C2H2-ZF, homeobox and bHLH. Upstream regulator analyses identified homeobox genes being significantly in LAEC. Protein-protein interaction network analysis emphasised the role of TFs (\n                    <jats:italic>ISL1, MSX1, HOXA1, GATA6, ZNF423<\/jats:italic>\n                    ) in airway modulation. Additionally, functional enrichment analysis revealed the activation of chemotaxis, metalloendipeptidase\/metallopeptidase activity and pro-inflammatory signatures (IL17 signalling and RAGE), in LAEC, while SAEC were characterised by elevated expression of surfactant metabolism related genes. Moreover, alveolar and club cells-related genes were expressed in SAEC, suggesting a lower airway-specific signature.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Our analysis shows robust transcriptional differences between LAEC and SAEC. We suggest a potential role for homeobox TF family as well as the activation of the immune system in the biology of LAEC. Conversely, we observed an alveoli-like transcriptional signature in SAEC, including gas-exchange signals and surfactant metabolism; pathways involved in lung homeostasis.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2023.04.03.23288063","type":"posted-content","created":{"date-parts":[[2023,4,4]],"date-time":"2023-04-04T00:50:28Z","timestamp":1680569428000},"source":"Crossref","is-referenced-by-count":0,"title":["Transcriptomic analyses reveal regional signatures in lung allograft recipients"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3703-4111","authenticated-orcid":false,"given":"Patricia","family":"Agudelo-Romero","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7743-3179","authenticated-orcid":false,"given":"Kak-Ming","family":"Ling","sequence":"additional","affiliation":[]},{"given":"Melanie A.","family":"Lavender","sequence":"additional","affiliation":[]},{"given":"Jeremy P.","family":"Wrobel","sequence":"additional","affiliation":[]},{"given":"Michael","family":"Musk","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5386-8482","authenticated-orcid":false,"given":"Stephen M","family":"Stick","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0008-9733","authenticated-orcid":false,"given":"Anthony","family":"Kicic","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2023040603350561000_2023.04.03.23288063v1.1","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.ccm.2022.10.011","article-title":"Acute Rejection and Chronic Lung Allograft Dysfunction: Obstructive and Restrictive Allograft Dysfunction","volume":"44","year":"2023","journal-title":"Clin Chest Med"},{"key":"2023040603350561000_2023.04.03.23288063v1.2","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1164\/rccm.201707-1368OC","article-title":"Depletion of Airway Submucosal Glands and TP63 + KRT5 + Basal Cells in Obliterative Bronchiolitis","volume":"197","year":"2018","journal-title":"Am J Respir Crit Care Med"},{"key":"2023040603350561000_2023.04.03.23288063v1.3","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1097\/TP.0000000000000892","article-title":"Obliterative Bronchiolitis","volume":"100","year":"2016","journal-title":"Transplantation"},{"key":"2023040603350561000_2023.04.03.23288063v1.4","doi-asserted-by":"publisher","DOI":"10.1186\/1465-9921-10-99"},{"key":"2023040603350561000_2023.04.03.23288063v1.5","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"2023040603350561000_2023.04.03.23288063v1.6","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"2023040603350561000_2023.04.03.23288063v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu638"},{"key":"2023040603350561000_2023.04.03.23288063v1.8","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw354"},{"key":"2023040603350561000_2023.04.03.23288063v1.9","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp616"},{"key":"2023040603350561000_2023.04.03.23288063v1.10","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007"},{"key":"2023040603350561000_2023.04.03.23288063v1.11","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl117"},{"key":"2023040603350561000_2023.04.03.23288063v1.12","doi-asserted-by":"crossref","unstructured":"Benjamini Y , Hochberg Y. 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