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Articles by Malte Simon
Single-cell chromatin landscape and DNA methylation patterns reveal shared molecular programs in human tumor and non-tumor tissue CCR8+ Treg cells
Abstract Regulatory T (Treg) cells, a subset of CD4+ T cells, play a crucial role in immunoregulation. Notably, CCR8-expressing Treg cells in tissues also contribute to organ homeostasis and repair. To determine whether these tissue-regenerative programs are active in the tumor microenvironment, we employed single-cell chromatin accessibility and genome-wide DNA methylation analyses to investigate CCR8+ tissue Treg cells isolated from human tumor and adjacent tumor-free tissues.
Identifying similar populations across independent single cell studies without data integration
Abstract Supervised and unsupervised methods have emerged to address the complexity of single cell data analysis in the context of large pools of independent studies. Here, we present ClusterFoldSimilarity (CFS), a novel statistical method design to quantify the similarity between cell groups acroos any number of independent datasets, without the need for data correction or integration.
Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells
Highlights • Generation of a scATAC-seq dataset of tissue-resident mouse and human immune cells • Tissue adaptation shows organ-specific and conserved features across immune cells • The tissue Treg cell adaptation program was conserved in AREG-producing Th17 cells • Families of accessible transposable elements are associated with tissue adaptation Summary Tissue adaptation is required for regulatory T (Treg) cell function within organs.
Multiple myeloma long-term survivors display sustained immune alterations decades after first line therapy
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Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating CD8+ T cells
To investigate the chromatin landscape of human TILs, we first adapted a published plate-based single-cell assay for transposase-accessible chromatin (ATAC)-seq. 22 Chen X. Miragaia R.J. Natarajan K.N. Teichmann S.A. A rapid and robust method for single cell chromatin accessibility profiling. We optimized published buffer conditions 23 Corces M.R. Trevino A.E. Hamilton E.G. Greenside P.G. Sinnott-Armstrong N.A. Vesuna S. Satpathy A.T. Rubin A.J. Montine K.S. Wu B. et al.
Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells
Highlights • Comparison of chromatin accessibility between murine und human tissue Treg cells • TCR tracking revealed clonal relationship between tissue and blood BATF+CCR8+ Tregs • Treg cells from healthy tissues were similar to CCR8+ Treg cells from tumors • Tfh-like differentiation program induces tissue Treg cell repair characteristics Summary Murine regulatory T (Treg) cells in tissues promote tissue homeostasis and regeneration.
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