Populationsstruktur myeloider Zellen in gesundem und erkrankten humanen Lungengewebe.
Zusammenfassung der Projektergebnisse
In the current project, we performed an extensive profiling of end-stage diseased and control (tumor-free, non-end stage) lung tissues in different compartments, i.e. parenchyma, lymph node (LN) and trachea. In our analyses, we simultaneously applied classical immunological techniques such as immunophenotyping along with high throughput unbiased single cell transcriptomic (scRNA Seq.) approaches. Due to logistical and technical reasons, we processed parenchyma and LN tissues using the two approaches, while trachea was analyzed only by immunophenotyping due to limited cell numbers in this special compartment. The sc RNA sequencing technique “Seq-Well” is unbiased and cost-effective and allowed us to cover the majority of myeloid, lymphoid and even non-immune cell compartments, e.g. alveolar epithelial cells. In addition, for each parenchyma tissue, we collected formaldehyde-fixed paraffin blocks enabling further insights into the morphological location of specific immune cell subsets by multicolor immunohistochemistry. As the field of scRNA sequencing is highly competitive, more than 15 studies with an overlapping scope have been published in high ranking peer-reviewed journals during the funding period. Furthermore, the dataset will be used to start multiple follow up projects and is provided to the scientific community in form of a resource within a currently planned human lung cell atlas (a collaborative effort with the European DiscovAIR project with Prof. J.L. Schultze as member). Furthermore, we expanded our initial aims by selecting different end-stage diseases which allows us to directly compare these lung diseases by using exactly the same workflows, analyses of several paired tissue compartments i.e. parenchyma and LN, parallel coverage of a broad list of immune cell types, and the application of multiple complementary methods, i.e. multicolor flow cytometry, scRNA sequencing, immunohistochemistry, ex-vivo assays for the analyses of the same tissue material. In further work, we focus on the lung parenchyma T cell compartment, to understand the origin of the donor T cells which exhibit a peculiar phenotype that we also found in perfusion solutions as well as in peripheral recipient blood of lung transplant patients (LTx). Such chimerism with donor T cells might be protective from the development of chronic allograft dysfunction after LTx. By studying the lung T cell compartment with scRNA-seq and immunophenotyping we identified TRM-like cell subsets with similar characteristics as the aforementioned donor T cells which may comprise a mobile TRM compartment participating in the chimerism with recipient immune cells. We also focus on the characterization of a broad spectrum of immune cells found in various lung compartments, i.e. parenchyma vs. LN, and identified immune subsets that were either affected or appeared denovo in the different end-stage lung diseases that were included in our study. This project is also serves as a starting point for follow up projects, as we will move towards single cell multiomics analysis combining mRNA expression profiling with TCR/BCR sequencing and proteomics (CITE-Seq). Our data contributed to the multi-center meta-study to identify mRNA expression profile of protein genes ACE-2, TMPRSS2 and CTSL involved in entry of SARS-CoV-2 throughout all tissues of the body. Taken together, our project provides data and insights to the understanding of end-stage diseased human lung immune compartments revealing new biomarker candidates and potentially novel therapy targets and eventually may contribute to improved therapeutic options.
Projektbezogene Publikationen (Auswahl)
- Back signaling of HLA class I molecules and T/NK cell receptor ligands in epithelial cells reflects the rejection-specific microenvironment in renal allograft biopsies. Am J Transplant. PubMed PMID:31062482. 2019
Egelkamp, J., Chichelnitskiy, E., Kühne, J.F., Wandrer, F., Daemen, K., Keil, J., Bräsen, J.H., Schmitz, J., Bellmàs-Sanz, R., Iordanidis, S., Katsirntaki, K., Hake, K., Akhdar, A. ,Neudörfl, C., Haller, H., Blume, C., Falk CS
(Siehe online unter https://doi.org/10.1111/ajt.15417) - “Single-cell RNA sequencing reveals macrophage and epithelial cell heterogeneity in healthy and fibrotic human lung tissue”, Life Time Opening Conference, 6th -7 th May 2019
Kapellos TS, Chichelnitskiy E, Falk C, Schultze JL
- Alveolar macrophage transcriptomic profiling in COPD shows major lipid metabolism changes. ERJ Open Res. 2021 Sep 13;7(3):00915-2020
Fujii W, Kapellos TS, Baßler K, Händler K, Holsten L, Knoll R, Warnat-Herresthal S, Oestreich M, Hinkley ER, Hasenauer J, Pizarro C, Thiele C, Aschenbrenner AC, Ulas T, Skowasch D, Schultze JL
(Siehe online unter https://doi.org/10.1183/23120541.00915-2020) - Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis. Circulation. 142(7):708-710. 2020
Tucker NR, Chaffin M, Bedi KC Jr, Papangeli I, Akkad AD, Arduini A, Hayat S, Eraslan G, Muus C, Bhattacharyya RP, Stegmann CM; Human Cell Atlas Lung Biological Network, Margulies KB, Ellinor PT; Human Cell Atlas Lung Biological Network Consortium Members
(Siehe online unter https://doi.org/10.1161/circulationaha.120.047911) - SARS-CoV- 2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Cell. 181(5):1016-1035.e19. 2020
Ziegler CGK, ... Ordovas-Montanes J; HCA Lung Biological Network
(Siehe online unter https://doi.org/10.1016/j.cell.2020.04.035) - SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat Med.; 26(5):681-687. PMID: 32327758. 2020
Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL; HCA Lung Biological Network
(Siehe online unter https://doi.org/10.1038/s41591-020-0868-6) - Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med. 2021 Jan 13;13(1):7
Aschenbrenner AC, Mouktaroudi M, Krämer B, Oestreich M, Antonakos N, Nuesch-Germano M, Gkizeli K, Bonaguro L, Reusch N, Baßler K, Saridaki M, Knoll R, Pecht T, Kapellos TS, Doulou S, Kröger C, Herbert M, Holsten L, Horne A, Gemünd ID, Rovina N, Agrawal S, Dahm K, van Uelft M, Drews A, Lenkeit L, Bruse N, Gerretsen J, Gierlich J, Becker M, Händler K, Kraut M, Theis H, Mengiste S, De Domenico E, Schulte-Schrepping J, Seep L, Raabe J, Hoffmeister C, ToVinh M, Keitel V, Rieke G, Talevi V, Skowasch D, Aziz NA, Pickkers P, van de Veerdonk FL, Netea MG, Schultze JL, Kox M, Breteler MMB, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T; German COVID-19 Omics Initiative (DeCOI)
(Siehe online unter https://doi.org/10.1186/s13073-020-00823-5) - Identification of distinct secretory patterns and their regulatory networks of ischemia versus reperfusion phases in clinical heart transplantation. Cytokine. 2021 Oct 11;149:155744
Ledwoch N, Wiegmann B, Chichelnitskiy E, Wandrer F, Kühne JF, Beushausen K, Keil J, Radomsky L, Sommer W, Knöfel AK, Rojas SV, Ius F, Haverich A, Warnecke G, Falk CS
(Siehe online unter https://doi.org/10.1016/j.cyto.2021.155744) - Single-cell metaanalysis of SARS-CoV-2 entry genes across tissues and demographics. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med. 2021 Mar;27(3):546-559
Muus C, ... Ziegler CGK; NHLBI LungMap Consortium; Human Cell Atlas Lung Biological Network
(Siehe online unter https://doi.org/10.1038/s41591-020-01227-z)
