Publications – Core Facility for Integrated Technology Development

Beumer N, Imbusch CD, Kaufmann T, Schmidleithner L, Gütter K, Stüve P, Marchel H, Weichenhan D, Bähr M, Ruhland B, Marini F, Sanderink L, Ritter U, Simon M, Braband KL, Voss MM, Helbich SS, Mihoc DM, Hotz-Wagenblatt A, Nassabi H, Eigenberger A, Prantl L, Gebhard C, Rehli M, Strieder N, Singh K, Schmidl C, Plass C, Huehn J, Hehlgans T, Polansky JK, Brors B, Delacher M, Feuerer M. DNA hypomethylation traits define human regulatory T cells in cutaneous tissue and identify their blood recirculating counterparts. Nat Immunol. 2025 Aug;26(8):1315-1328. doi: 10.1038/s41590-025-02210-x. Epub 2025 Jul 16. PMID: 40670618

In this publication, we isolated immune cells from human skin and fat tissue as well as human blood, and FACS sorted T cell subsets of interest for whole genome bisulfite sequencing (WGBS). We further analysed RNA-seq data and scATAC-seq data from a previous study, identifying differential expression or differential peaks, respectively. We then integrated this data with our WGBS data to define and analyse DMR-gene-peak links. Transposable elements were further analysed regarding methylation and chromatin accessibility. We also used scRNA/TCR-seq data from a previous study to perform TCR clonotype-based analyses.

Simon M, Stüve P, Schmidleithner L, Bittner S, Beumer N, Strieder N, Schmidl C, Pant A, Gebhard C, Eigenberger A, Rehli M, Prantl L, Hehlgans T, Brors B, Imbusch CD, Delacher M, Feuerer M. Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells. Immunity. 2024 Aug 13;57(8):1975-1993.e10. doi: 10.1016/j.immuni.2024.06.015. Epub 2024 Jul 23. PMID: 39047731

In this publication, we isolated immune cells from murine fat, skin, colon and spleen as well as from human skin, fat and blood for FACS sorting and scATAC-seq. scATAC-seq data was annotated, differentially accessible genes and transposable elements were analysed, and trajectory- and motif enrichment analyses were performed.

Delacher M, Schmidleithner L, Simon M, Stüve P, Sanderink L, Hotz-Wagenblatt A, Wuttke M, Schambeck K, Ruhland B, Hofmann V, Bittner S, Ritter U, Pant A, Helbich SS, Voss M, Lemmermann NA, Bessiri-Schake L, Bohn T, Eigenberger A, Menevse AN, Gebhard C, Strieder N, Abken H, Rehli M, Huehn J, Beckhove P, Hehlgans T, Junger H, Geissler EK, Prantl L, Werner JM, Schmidl C, Brors B, Imbusch CD, Feuerer M. The effector program of human CD8 T cells supports tissue remodeling. J Exp Med. 2024 Feb 5;221(2):e20230488. doi: 10.1084/jem.20230488. Epub 2024 Jan 16. PMID: 38226976

In this publication, we isolated immune cells and fibroblasts from human skin, fat, blood, healthy liver tissue and liver tumor tissue. We FACS sorted cell types of interest for in vitro assays, bulk RNA-seq and scRNA/TCR-seq. scRNA/TCR-seq data was used to identify clonal relationships of our cell types of interest.

Braband KL, Nedwed AS, Helbich SS, Simon M, Beumer N, Brors B, Marini F, Delacher M. Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues. Front Immunol. 2023 Oct 16;14:1232511. doi: 10.3389/fimmu.2023.1232511. PMID: 37908367

In this methods article, we describe the whole value chain needed to perform a successful scATAC-sequencing experiment: from immune cell isolation from tissues, via FACS sorting and sample preparation for sequencing, to a complete bioinformatic analysis workflow. We discuss quality control steps and pitfalls along the process.

Nedwed AS, Helbich SS, Braband KL, Volkmar M, Delacher M, Marini F. Using combined single-cell gene expression, TCR sequencing and cell surface protein barcoding to characterize and track CD4+ T cell clones from murine tissues. Front Immunol. 2023 Oct 12;14:1241283. doi: 10.3389/fimmu.2023.1241283. PMID: 37901204

In this methods article, we describe the whole value chain needed to perform a successful scRNA/TCR-sequencing experiment with cell surface protein barcoding: from immune cell isolation from tissues, via FACS sorting and sample preparation for sequencing, to a complete bioinformatic analysis workflow. We discuss quality control steps and pitfalls along the process.

Delacher M, Simon M, Sanderink L, Hotz-Wagenblatt A, Wuttke M, Schambeck K, Schmidleithner L, Bittner S, Pant A, Ritter U, Hehlgans T, Riegel D, Schneider V, Groeber-Becker FK, Eigenberger A, Gebhard C, Strieder N, Fischer A, Rehli M, Hoffmann P, Edinger M, Strowig T, Huehn J, Schmidl C, Werner JM, Prantl L, Brors B, Imbusch CD, Feuerer M. Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells. Immunity. 2021 Apr 13;54(4):702-720.e17. doi: 10.1016/j.immuni.2021.03.007. Epub 2021 Mar 30. PMID: 33789089

In this publication, we isolated immune cells from murine fat, skin, lung, colon, spleen, and tumor, as well as human skin, fat, blood, liver, and liver tumor tissue. We FACS sorted cells of interest for scATAC-seq and created signatures for our cell types of interest. We further analysed scATAC-seq data in detail, including transcription factor activity estimation, differential chromatin accessibility analysis, transcription factor analysis and trajectory analysis. We also generated and analysed bulk RNA-seq and scRNA/TCR-seq data.

Delacher M, Imbusch CD, Hotz-Wagenblatt A, Mallm JP, Bauer K, Simon M, Riegel D, Rendeiro AF, Bittner S, Sanderink L, Pant A, Schmidleithner L, Braband KL, Echtenachter B, Fischer A, Giunchiglia V, Hoffmann P, Edinger M, Bock C, Rehli M, Brors B, Schmidl C, Feuerer M. Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF. Immunity. 2020 Feb 18;52(2):295-312.e11. doi: 10.1016/j.immuni.2019.12.002. Epub 2020 Jan 7. PMID: 31924477

In this publication, we isolated immune cells from murine fat, skin, liver, lung, colon, blood, bone marrow, spleen and lymph nodes and FACS sorted our cell types of interest for bulk ATAC-seq, bulk RNA-seq, scRNA/TCR-seq and in vitro assays. ATAC-seq data and RNA-seq data was integrated and analysed to characterise our cell type of interest, and TCR sequences were used to analyse clonal diversity.