Z02: High-resolution multi-parametric cell and tissue analysis

Project Z02 provides cutting-edge expertise for analyses of high-resolution single-cell level histology, mass cytometry and spatial transcriptomics for the members of the consortium. In addition to various support offers such as a slide consultation service by an expert pathologist, histology staining and guidance from conceptualization to analysis of mass cytometry experiments, incl. method and data analysis training, this project will further develop spatial single-cell level multiomics methods. Specifically, Z02, in close collaboration with Z03, will work towards a spatially resolved multiomics cell atlas of the HBV infected liver by integrating multiple spatial omics approaches such as spatial proteomics, spatial transcriptomics and spatial metabolomics.

Prof. Dr. Dr. Bertram Bengsch

Prof. Dr. Carolin Mogler

Winkler F, Hipp AV, Ramirez C, Martin B, Villa M, Neuwirt E, Gorka O, Aerssens J, Johansson SE, Rana N, Llewellyn-Lacey S, Price DA, Panning M, Gross O, Pearce EL, Herrmann CM, Schumann K, Hannibal L, Neumann-Haefelin C, Boettler T, Knolle P, Hofmann M, Wohlleber D, Thimme R, Bengsch B. (2023) Enolase represents a metabolic checkpoint controlling the differential exhaustion programs of hepatitis virus-specific CD8+ T cells. Gut. 72(10):1971-1984. doi: 10.1136/gutjnl-2022-328734.

Pallett LJ, Swadling L, Diniz M, Maini AA, Schwabenland M, Gasull AD, Davies J, Kucykowicz S, Skelton JK, Thomas N, Schmidt NM, Amin OE, Gill US, Stegmann KA, Burton AR, Stephenson E, Reynolds G, Whelan M, Sanchez J, de Maeyer R, Thakker C, Suveizdyte K, Uddin I, Ortega-Prieto AM, Grant C, Froghi F, Fusai G, Lens S, Pérez-Del-Pulgar S, Al-Akkad W, Mazza G, Noursadeghi M, Akbar A, Kennedy PTF, Davidson BR, Prinz M, Chain BM, Haniffa M, Gilroy DW, Dorner M, Bengsch B, Schurich A, Maini MK. (2023) Tissue CD14+CD8+ T cells reprogrammed by myeloid cells and modulated by LPS. Nature. 614(7947):334-342. doi: 10.1038/s41586-022-05645-6.

Su J, Brunner L, Ates Oz E, Sacherl J, Frank G, Kerth HA, Thiele F, Wiegand M, Mogler C, Aguilar JC, Knolle PA, Collin N, Kosinska AD, Protzer U. (2023) Activation of CD4 T cells during prime immunization determines the success of a therapeutic hepatitis B vaccine in HBV-carrier mouse models. J Hepatol. 78(4):717-730. doi: 10.1016/j.jhep.2022.12.013.

Boettler T, Csernalabics B, Salié H, Luxenburger H, Wischer L, Salimi Alizei E, Zoldan K, Krimmel L, Bronsert P, Schwabenland M, Prinz M, Mogler C, Neumann-Haefelin C, Thimme R, Hofmann M, Bengsch B. (2022) SARS-CoV-2 vaccination can elicit a CD8 T-cell dominant hepatitis. J Hepatol. 77(3):653-659. doi: 10.1016/j.jhep.2022.03.040.

Tulessin M, Sarker RSJ, Griger J, Leibing T, Geraud C, Weichert W, Steiger K, Mogler C. (2022) Vascular Remodeling Is a Crucial Event in the Early Phase of Hepatocarcinogenesis in Rodent Models for Liver Tumorigenesis. Cells. 11(14):2129. doi: 10.3390/cells11142129.

Schwabenland M, Salié H, Tanevski J, Killmer S, Lago MS, Schlaak AE, Mayer L, Matschke J, Püschel K, Fitzek A, Ondruschka B, Mei HE, Boettler T, Neumann-Haefelin C, Hofmann M, Breithaupt A, Genc N, Stadelmann C, Saez-Rodriguez J, Bronsert P, Knobeloch KP, Blank T, Thimme R, Glatzel M, Prinz M, Bengsch B. (2021) Deep spatial profiling of human COVID-19 brains reveals neuroinflammation with distinct microanatomical microglia-T-cell interactions. Immunity. 13;54(7):1594-1610.e11. doi: 10.1016/j.immuni.2021.06.002.

Michler T, Kosinska AD, Festag J, Bunse T, Su J, Ringelhan M, Imhof H, Grimm D, Steiger K, Mogler C, Heikenwalder M, Michel ML, Guzman CA, Milstein S, Sepp-Lorenzino L, Knolle P, Protzer U. (2020) Knockdown of Virus Antigen Expression Increases Therapeutic Vaccine Efficacy in High-Titer Hepatitis B Virus Carrier Mice. Gastroenterology. 158(6):1762-1775.e9. doi: 10.1053/j.gastro.2020.01.032.

Schulien I, Kemming J, Oberhardt V, Wild K, Seidel LM, Killmer S, Sagar, Daul F, Salvat Lago M, Decker A, Luxenburger H, Binder B, Bettinger D, Sogukpinar O, Rieg S, Panning M, Huzly D, Schwemmle M, Kochs G, Waller CF, Nieters A, Duerschmied D, Emmerich F, Mei HE, Schulz AR, Llewellyn-Lacey S, Price DA, Boettler T, Bengsch B, Thimme R, Hofmann M, Neumann-Haefelin C. (2021) Characterization of pre-existing and induced SARS-CoV-2-specific CD8+ T cells. Nat Med. 27(1):78-85. doi: 10.1038/s41591-020-01143-2.

Papaioannou S, See JX, Jeong M, De La Torre C, Ast V, Reiners-Koch PS, Sati A, Mogler C, Platten M, Cerwenka A, Stojanovic A. (2023) Liver sinusoidal endothelial cells orchestrate NK cell recruitment and activation in acute inflammatory liver injury. Cell Rep. 29;42(8):112836. doi: 10.1016/j.celrep.2023.112836.

Bengsch B, Ohtani T, Khan O, Setty M, Manne S, O'Brien S, Gherardini PF, Herati RS, Huang AC, Chang KM, Newell EW, Bovenschen N, Pe'er D, Albelda SM, Wherry EJ. (2018) Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells. Immunity. 15;48(5):1029-1045.e5. doi: 10.1016/j.immuni.2018.04.026.

Project in detail +

In this funding period we will be continuing the service for TRR179 projects and - in addition - be generating a multiomics cell atlas of the HBV infected liver that serves as an important resource of information related to the spatial positioning of hepatic immune cells and their activation and exhaustion status in the infected liver. The service project focuses on tissue services (human and rodent) to address the growing need for high-resolution spatial profiling. This will be addressed by offering basic histology, immunohistochemistry, RNA scope and slide consultation service for rodent and human liver tissue as well as access to large cohorts of human liver tissue with or without chronic viral hepatitis (available as resection specimen, whole fine needle biopsies or tissue microarrays). In addition, CyTOF and Imaging mass cytometry is provided to support the members ranging from experiment planning and staining advice up to analyzing samples.
Furthermore, we will address the lack of information regarding the micro-anatomic localization of hepatic immune cells and their activation and exhaustion status during HBV infection. The pathology and mass-based imaging expertise by Mogler and Bengsch, respectively, is being combined to generate a spatially resolved multiomics cell atlas of the HBV-infected liver comprising a comprehensive spatial characterization of various cell populations residing within the HBV infected liver, also in relation to infected vs non-infected cells, and the functional status of parenchymal and immune cells. To reach this goal we use several state-of-the-art spatial -omics techniques (including 10x Visium, 10x Xenium, Akoya Phenocycler, Vizgen Merscope) in close collaboration with Z03 (Herrmann/Rippe) that strongly supports the integration of the complex data sets. This spatial analysis of the HBV-infected liver allows the identification of distinct microenvironments using single-cell segmentation, clustering and neighborhood prediction algorithms as well as HBV-related virological and immunological niches. This analysis helps to elucidate how HBV escapes immune control (e.g. by spatial segregation) and inform the projects within TRR179 working on related topics. A major asset is the use of a virologically and histopathologically well-defined set of patient samples that include existing samples across distinct HBeAg-positive and HBeAg-negative chronic HBV infection cohorts as well as HBV/HDV co-infection patients. Results arising from this HBV-infected liver cell atlas are being to and shared with all members of the TRR179, in line with a data management concept, and once completed also with the scientific community, thus providing a valuable resource for future virological and immunological studies.