{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T14:52:21Z","timestamp":1774536741347,"version":"3.50.1"},"reference-count":39,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T00:00:00Z","timestamp":1774483200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation of China Grants\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t              https:\/\/ror.org\/01h0zpd94","award":["82373017"],"award-info":[{"award-number":["82373017"]}]},{"name":"National Natural Science Foundation of China Grants\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t              https:\/\/ror.org\/01h0zpd94","award":["82373827"],"award-info":[{"award-number":["82373827"]}]},{"name":"National Key R&D Program \u201cStrategic Scientific and Technological Innovation Cooperation\u201d Key Project","award":["2022YFE0203600"],"award-info":[{"award-number":["2022YFE0203600"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Metabolites"],"abstract":"<jats:p>Background\/Objectives: Malignant transformation of hepatocellular adenoma (HCA) represents a clinically significant yet incompletely understood process. Although the pathological and clinical characteristics of HCA have been extensively described, its spatial molecular heterogeneity and spatially organized molecular variation at the tissue level remain insufficiently characterized. This study aimed to establish a spatially integrated multi-omics workflow and to delineate spatially organized molecular variation across histologically defined regions from adenoma to carcinoma. Methods: A sequential dual-layer matrix-assisted laser desorption\/ionization mass spectrometry imaging (MALDI-MSI) workflow was developed to acquire small-molecule metabolomic and N-glycan spatial data from the same formalin-fixed paraffin-embedded (FFPE) tissue section. Four rare HCA specimens containing focal carcinoma transformation were included in this study. Pixel-level clustering, region-based co-localization analysis, and diffusion pseudotime modeling were applied to characterize spatial metabolic and N-glycan patterns across normal liver tissue (NL), hepatocellular adenoma (HCA), and carcinoma-transformed regions within adenoma (HCA-HCC). Results: Small-molecule MSI revealed spatial metabolic stratification within HCA, with variation observed in nucleotide-related, lipid-related, sulfur-related, and sugar nucleotide\u2013associated metabolites. Pseudotime analysis revealed a spatial ordering of samples across NL, HCA, and HCA-HCC regions, showing differences in antioxidant-associated metabolites, lipid-related features, and bile acid-related metabolites across regions. N-glycan MSI identified independent glycosylation niches, with increasing structural complexity and enrichment of highly branched glycans in carcinoma-transformed regions. Integration of metabolomic and glycomic data suggested spatially associated patterns between metabolite features and glycan structures across regions. Conclusions: This study provides spatially resolved evidence of spatially organized patterns of molecular variation across histologically defined regions of HCA. The identified metabolic and N-glycan gradients provide insights into spatial molecular organization during malignant transformation of hepatocellular adenoma.<\/jats:p>","DOI":"10.3390\/metabo16040217","type":"journal-article","created":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T13:50:15Z","timestamp":1774533015000},"page":"217","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Single-Section Sequential MALDI-MSI Reveals Metabolic and N-Glycan Remodeling During Malignant Transformation in Hepatocellular Adenoma"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3973-3431","authenticated-orcid":false,"given":"Jianfeng","family":"Xu","sequence":"first","affiliation":[{"name":"Hepatobiliary Surgery, Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China"},{"name":"Cancer Metastasis Institute, Fudan University, Shanghai 200040, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Sui","sequence":"additional","affiliation":[{"name":"Shanghai Zenith Bio Co., Ltd., Shanghai 201203, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Da","family":"Xu","sequence":"additional","affiliation":[{"name":"Hepatobiliary Surgery, Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China"},{"name":"Cancer Metastasis Institute, Fudan University, Shanghai 200040, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoxue","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China"},{"name":"University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Youhong","family":"Hu","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China"},{"name":"University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China"},{"name":"Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Yuan","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8167-9750","authenticated-orcid":false,"given":"Jia","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China"},{"name":"Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"},{"name":"China-Serbia \u201cBelt and Road\u201d Joint Laboratory for Natural Products and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lu","family":"Lu","sequence":"additional","affiliation":[{"name":"Hepatobiliary Surgery, Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China"},{"name":"Cancer Metastasis Institute, Fudan University, Shanghai 200040, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1001\/jama.1979.03300070040020","article-title":"Epidemiology of hepatocellular adenoma. 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