Imaging mass cytometry reveals novel cellular neighbourhoods predicting prognosis of non-alcoholic fatty liver disease-associated hepatocellular carcinoma

Imaging mass cytometry reveals novel cellular neighbourhoods predicting prognosis of non-alcoholic fatty liver disease-associated hepatocellular carcinoma | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Imaging mass cytometry reveals novel cellular neighbourhoods predicting prognosis of non-alcoholic fatty liver disease-associated hepatocellular carcinoma Wen Wen, Xianming Wang, Bowen Xu, Xin Geng, Wendi Bi, Qinyi Jia, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4919292/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Objective Nonalcoholic fatty liver disease (NAFLD) is increasingly implicated in hepatocellular carcinoma (HCC) pathogenesis. We aimed to examine panoramic cellular composition and spatial structure of NAFLD-HCC clinical samples, assess the role of tumor micro-environment (TME) in the process of liver fibrosis and oncogenesis, and find potential clinical intervention measures. Methods Imaging mass cytometry (IMC) technology was used to reveal the expression and spatial distribution of biomarkers in samples from 56 patients with NAFLD-HCC and 6 patients with focal nodular hyperplasia as control. 37 different metal coupling biomarkers were designed to label the tumor, border and adjacent regions of the tissues to generate 367 highly multiplexed histology images at single-cell resolution. By integrating the expression levels of biomarkers with the relative positional relationships between cells, we defined functional units as tightly interacting cellular neighborhoods (CNs). The relationship between CNs and patients’ prognosis was then accessed to identify potential clinical targets of NAFLD-HCC. Results Cells were dimensionally reduced to access the cellular phenotype and 18 clusters of cells and 9 CNs were defined. Heterogeneity in TME and CN composition was observed not only across various regions within the same individual but also among comparable regions in different patients. The combined analysis of the overall survival data revealed that patients with a high enrichment of T & NK cell associated CN exhibited a more favorable clinical prognosis. In contrast, those with a high enrichment of myofibroblast associated CN and a YAP+ cancer cell associated CN exhibited a poor clinical prognosis. Conclusion Our study provided a landscape of NAFLD-HCC and its TME characteristics from the topological perspective. The findings indicated that changing the low immune cell infiltration status of NAFLD-HCC through the augmentation of active T and NK cells and hepatic antifibrotic therapy may benefit the long-term prognosis of patients with NAFLD-HCC. Key words: imaging mass cytometry, NAFLD-HCC, cellular neighborhoods, prognosis, tumor micro-environment Health sciences/Diseases/Cancer/Cancer imaging Biological sciences/Cancer/Cancer microenvironment imaging mass cytometry NAFLD-HCC cellular neighborhoods prognosis tumor micro-environment Full Text Additional Declarations There is NO Competing Interest. Supplementary Files S1.pdf S2.pdf S3.pdf Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4919292","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":344163266,"identity":"46d8137d-899f-4e19-993b-723c4d84a2e0","order_by":0,"name":"Wen 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micro-environment","lastPublishedDoi":"10.21203/rs.3.rs-4919292/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4919292/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eObjective\u003c/strong\u003e Nonalcoholic fatty liver disease (NAFLD) is increasingly implicated in hepatocellular carcinoma (HCC) pathogenesis. We aimed to examine panoramic cellular composition and spatial structure of NAFLD-HCC clinical samples, assess the role of tumor micro-environment (TME) in the process of liver fibrosis and oncogenesis, and find potential clinical intervention measures.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods\u003c/strong\u003e Imaging mass cytometry (IMC) technology was used to reveal the expression and spatial distribution of biomarkers in samples from 56 patients with NAFLD-HCC and 6 patients with focal nodular hyperplasia as control. 37 different metal coupling biomarkers were designed to label the tumor, border and adjacent regions of the tissues to generate 367 highly multiplexed histology images at single-cell resolution. By integrating the expression levels of biomarkers with the relative positional relationships between cells, we defined functional units as tightly interacting cellular neighborhoods (CNs). The relationship between CNs and patients’ prognosis was then accessed to identify potential clinical targets of NAFLD-HCC.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e Cells were dimensionally reduced to access the cellular phenotype and 18 clusters of cells and 9 CNs were defined. Heterogeneity in TME and CN composition was observed not only across various regions within the same individual but also among comparable regions in different patients. The combined analysis of the overall survival data revealed that patients with a high enrichment of T \u0026amp; NK cell associated CN exhibited a more favorable clinical prognosis. In contrast, those with a high enrichment of myofibroblast associated CN and a YAP+ cancer cell associated CN exhibited a poor clinical prognosis.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion\u003c/strong\u003e Our study provided a landscape of NAFLD-HCC and its TME characteristics from the topological perspective. The findings indicated that changing the low immune cell infiltration status of NAFLD-HCC through the augmentation of active T and NK cells and hepatic antifibrotic therapy may benefit the long-term prognosis of patients with NAFLD-HCC. 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