A5002129125- Single-cell and spatial transcriptomics
- Immune Cell Function and Interaction
- IL-33, ST2, and ILC Pathways
- Cancer Immunotherapy and Biomarkers
- T-cell and B-cell Immunology
- Immunotherapy and Immune Responses
- Cell Image Analysis Techniques
- Gene Regulatory Network Analysis
- Cancer Genomics and Diagnostics
- CAR-T cell therapy research
- Eosinophilic Esophagitis
- Immune cells in cancer
- Cancer, Stress, Anesthesia, and Immune Response
- Hematopoietic Stem Cell Transplantation
- Liver physiology and pathology
- RNA Interference and Gene Delivery
- Cancer Cells and Metastasis
- Acute Myeloid Leukemia Research
- Systemic Lupus Erythematosus Research
- Atherosclerosis and Cardiovascular Diseases
- Pregnancy and preeclampsia studies
- Invertebrate Immune Response Mechanisms
- Reproductive System and Pregnancy
- Asthma and respiratory diseases
- Liver Disease Diagnosis and Treatment
Cancer Research UK
2022-2024
Queen Mary University of London
2021-2024
Wellcome Sanger Institute
2018-2021
Innsbruck Medical University
2012-2021
Universität Innsbruck
2016-2021
Institute of Bioinformatics
2021
St. Jude Children's Research Hospital
2019
Institute for Molecular Medicine
2019
University Medical Center of the Johannes Gutenberg University Mainz
2019
Johannes Gutenberg University Mainz
2019
The Cancer Genome Atlas revealed the genomic landscapes of human cancers. In parallel, immunotherapy is transforming treatment advanced Unfortunately, majority patients do not respond to immunotherapy, making identification predictive markers and mechanisms resistance an area intense research. To increase our understanding tumor-immune cell interactions, we characterized intratumoral immune cancer antigenomes from 20 solid cancers created Immunome (https://tcia.at/). Cellular...
Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis therapy. Specifically, whole-exome using next-generation (NGS) is gaining popularity the human genetics community due moderate costs, manageable data amounts straightforward interpretation of analysis results. While and, near future, whole-genome are becoming commodities, still poses significant challenges led...
The skin confers biophysical and immunological protection through a complex cellular network established early in embryonic development. We profiled the transcriptomes of more than 500,000 single cells from developing human fetal skin, healthy adult with atopic dermatitis psoriasis. leveraged these datasets to compare cell states across development, homeostasis, disease. Our analysis revealed an enrichment innate immune during first trimester clonal expansion disease-associated lymphocytes...
Immune landscape of the human kidney Single-cell RNA sequencing has begun to shed light on full cellular diversity specific organs. However, these studies rarely examine organ-specific immune cells. Stewart et al. sequenced healthy adult and fetal samples at a single-cell level define heterogeneity in epithelial, myeloid, lymphoid From this dataset, they identified zonation cells, with relevance disease varied perturbations that occur different tumor settings. This profiling generates...
SUMMARY The Cancer Genome Atlas revealed the genomic landscapes of common human cancers. In parallel, immunotherapy with checkpoint blockers is transforming treatment advanced As only a minority patients responsive to blockers, identification predictive markers and mechanisms resistance subject intense research. To facilitate understanding tumor-immune cell interactions, we characterized intratumoral immune cancer antigenomes from 20 solid cancers, created Immunome ( http://tcia.at )....
Abstract The cancer immunoediting hypothesis postulates a dual role of the immune system: protecting host by eliminating tumor cells, and shaping editing its genome. Here, we elucidate impact evolutionary immune-related forces on in mouse model for hypermutated microsatellite-instable colorectal cancer. Analyses wild-type immunodeficient RAG1 knockout mice transplanted with MC38 cells reveal that upregulation checkpoint molecules infiltration Tregs are major escape mechanisms. Our results...
Here, using single-cell RNA sequencing, we examine the stromal compartment in murine melanoma and draining lymph nodes (LNs) at points across tumor development, providing data http://www.teichlab.org/data/. Naive lymphocytes from LNs undergo activation clonal expansion within tumor, before PD1 Lag3 expression, while tumor-associated myeloid cells promote formation of a suppressive niche. We identify three temporally distinct populations displaying unique functional signatures, conserved...
Psoriatic arthritis (PsA) is a debilitating immune-mediated inflammatory of unknown pathogenesis commonly affecting patients with skin psoriasis. Here we use complementary single-cell approaches to study leukocytes from PsA joints. Mass cytometry demonstrates 3-fold expansion memory CD8 T cells in the joints compared peripheral blood. Meanwhile, droplet-based and plate-based RNA sequencing paired cell receptor alpha beta chain sequences show pronounced clonal expansions within Transcriptome...
Teasing apart the mosquito immune system Hemocytes are key cells of insects, playing a major role in how vector species transmit disease. Raddi et al. collected and sequenced RNA more than 8000 individual hemocytes from disease-carrying mosquitoes Anopheles gambiae Aedes aegypti . These data were then analyzed to determine hemocyte differentiation lineages population changes response noninfected Plasmodium -infected blood meals. From these data, researchers identified new type, megacyte,...
Abstract Cell-cell communication mediated by receptor-ligand complexes is crucial for coordinating diverse biological processes, such as development, differentiation and responses to infection. In order understand how the context-dependent crosstalk of different cell types enables physiological processes proceed, we developed CellPhoneDB, a novel repository ligands, receptors their interactions 1 . Our takes into account subunit architecture both ligands receptors, representing heteromeric...
Analyzing mouse tumor models in vivo, human T cells ex and lung cancer samples, we provide direct evidence that NR2F6 acts as an immune checkpoint. Genetic ablation of Nr2f6, particularly combination with established checkpoint blockade, efficiently delays progression improves survival experimental models. The target genes deregulated intratumoral lymphocytes upon genetic Nr2f6 alone or together PD-L1 blockade reveal multiple advantageous transcriptional alterations. Acute silencing both...
Multimodal data is rapidly growing in many fields of science and engineering, including single-cell biology. We introduce MultiMAP, a novel algorithm for dimensionality reduction integration. MultiMAP can integrate any number datasets, leverages features not present all restricted to linear mapping, allows the user specify influence each dataset, extremely scalable large datasets. apply transcriptomics, chromatin accessibility, methylation, spatial show that it outperforms current...
Single cell data integration methods aim to integrate cells across batches and modalities, tasks can be categorized into horizontal, vertical, diagonal, mosaic integration, where is the most general challenging case with few developed. We propose scMoMaT, a method that able single multi-omics under scenario using matrix tri-factorization. During scMoMaT also uncover cluster specific bio-markers modalities. These multi-modal are used interpret annotate clusters types. Moreover, unequal type...
Atrial fibrillation (AF) is the most common sustained arrhythmia and carries an increased risk of stroke heart failure. Here we investigated how immune infiltrate human epicardial adipose tissue (EAT), which directly overlies myocardium, contributes to AF. Flow cytometry analysis revealed enrichment tissue-resident memory T (T
Background Immunotherapy with checkpoint inhibitors has shown impressive results in patients melanoma, but still many do not benefit from this line of treatment. A lack tumor-infiltrating T cells is a common reason for therapy failure also loss intratumoral dendritic (DCs) been described. Methods We used the transgenic tg(Grm1)EPv melanoma mouse strain that develops spontaneous, slow-growing tumors to perform immunological analysis during tumor progression. With flow cytometry, frequencies...
The transcription factor Rora has been shown to be important for the development of ILC2 and regulation ILC3, macrophages Treg cells. Here we investigate role across CD4+ T cells in general, but with an emphasis on Th2 cells, both vitro as well context several vivo type 2 infection models. We dissect function using overexpression a CD4-conditional Rora-knockout mouse, RORA-reporter mouse. establish importance controlling lung inflammation induced by Nippostrongylus brasiliensis infection,...