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Our previous work showed that NPCCs regress to a transitional-like state immediately after isolation and undergo dynamic transcriptional changes during short-term in vitro culture. The present study aimed to further delineate the molecular cues underlying these changes during porcine pancreatic tissue isolation and cultivation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Method<\/jats:title>\n                    <jats:p>Transcriptomic and proteomic analysis were performed to compare Neonatal Porcine Pancreata (NPP), freshly isolated NPCCs (NPCCs-0D) and 3-day in vitro cultured NPCCs (NPCCs-3D). Using an in-house analysis pipeline, molecular differences between groups were identified.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>NPCCs\u20110D showed lower molecular abundance compared with NPP and NPCCs\u20113D groups under the tested conditions. Gene Sets Enrichment Analysis (GSEA) revealed that pathways related to receptor signaling and cell\u2013microenvironment interactions were enriched in NPP and NPCCs\u20113D, highlighting the importance of external regulation in maintaining pancreatic tissue architecture. In contrast. organelle- and catalysis-associated gene sets were enriched in NPCCs\u20110D, suggesting a transcriptionally active and adaptive state.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Collectively, these findings indicate that molecular differences among NPP, NPCCs-0D, and NPCCs-3D reflect changes in tissue organization, cellular composition, and adaptation to isolation and culture conditions, rather than a linear differentiation process.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s11033-026-12376-8","type":"journal-article","created":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T10:29:44Z","timestamp":1784802584000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated transcriptomic and proteomic analysis reveals isolation and culture associated molecular changes in neonatal porcine pancreatic cell clusters"],"prefix":"10.1007","volume":"53","author":[{"given":"Chang-Yi","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen-Ling","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen-Wei","family":"Kao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen-Yi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wan-Wen","family":"Hung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ching-Wen","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jyuhn-Huarng","family":"Juang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0481-4215","authenticated-orcid":false,"given":"Wan-Chun","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,23]]},"reference":[{"key":"12376_CR1","doi-asserted-by":"publisher","first-page":"14565","DOI":"10.3389\/ti.2025.14565","volume":"38","author":"L Piemonti","year":"2025","unstructured":"Piemonti L (2025) The Last Mile in Beta-Cell Replacement Therapy for Type 1 Diabetes: Time to Grow Up. 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