A5058154063- Single-cell and spatial transcriptomics
- Extracellular vesicles in disease
- Cancer Immunotherapy and Biomarkers
- Breast Cancer Treatment Studies
- CAR-T cell therapy research
- Brain Metastases and Treatment
- Immune Cell Function and Interaction
- Immunotherapy and Immune Responses
- Lung Cancer Treatments and Mutations
- Immune cells in cancer
- Lung Cancer Research Studies
- Cell Image Analysis Techniques
- Cancer Diagnosis and Treatment
- MicroRNA in disease regulation
- Metastasis and carcinoma case studies
- Global Cancer Incidence and Screening
- HER2/EGFR in Cancer Research
- Cancer and Skin Lesions
- Cancer Genomics and Diagnostics
University of Lausanne
2019-2024
SIB Swiss Institute of Bioinformatics
2019-2024
Ludwig Cancer Research
2019-2024
Swiss Cancer Center Léman
2024
Centre de Recherche Inria Bordeaux - Sud-Ouest
2018
Institut de Mathématiques de Bordeaux
2018
Ottawa Hospital
2010
University of Ottawa
2010
Westmead Hospital
1986
Fully functional, tumor-specific, SLAMF7-expressing cytotoxic CD4 T cells directly mediate immunity against human cancer.
Recent studies have proposed that tumor-specific tumor-infiltrating CD8+ T lymphocytes (CD8 TIL) can be classified into two main groups: "exhausted" TILs, characterized by high expression of the inhibitory receptors PD-1 and TIM-3 lack transcription factor 1 (Tcf1); "memory-like" with self-renewal capacity co-expressing Tcf1 PD-1. However, a comprehensive definition heterogeneity existing within CD8 TILs has yet to clearly established. To investigate this at transcriptomic level, we...
Single-cell RNA sequencing (scRNA-seq) technologies offer unique opportunities for exploring heterogeneous cell populations. However, in-depth single-cell transcriptomic characterization of complex tissues often requires profiling tens to hundreds thousands cells. Such large numbers cells represent an important hurdle downstream analyses, interpretation and visualization.
Abstract Brain metastases (BMs) are associated with poor prognosis in non-small cell lung cancer (NSCLC), but only visible when large enough. Therapeutic decisions such as whole brain radiation therapy would benefit from patient-specific predictions of radiologically undetectable BMs. Here, we propose a mathematical modeling approach and use it to analyze clinical data BM NSCLC. Primary tumor growth was best described by gompertzian model for the pre-diagnosis history, followed inhibition...
Abstract The advent of high-throughput single-cell genomics technologies has fundamentally transformed biological sciences. Currently, millions cells from complex tissues can be phenotypically profiled across multiple modalities. scaling computational methods to analyze such data is a constant challenge and tools need regularly updated, if not redesigned, cope with ever-growing numbers cells. Over the last few years, metacells have been introduced reduce size complexity while preserving...
Three patients are described in whom primary gastric carcinoma of the linitis plastica type was initially diagnosed. All three had been treated for breast carcinoma; two disease bilateral, and tumour first manifestation relapse that patient's carcinoma. The cases examples a pattern spread particularly likely to occur infiltrating lobular breast. importance recognizing this is paramount if appropriate therapy be given. One has an excellent remission on Tamoxifen, another may showing some...
Abstract Brain metastases (BMs) are associated with poor prognosis in non-small cell lung cancer (NSCLC), but only visible when large enough. Therapeutic decisions such as whole brain radiation therapy would benefit from patient-specific predictions of radiologically undetectable BMs. Here, we propose a mathematical modeling approach and use it to analyze clinical data BM NSCLC. Primary tumor growth was best described by gompertzian model for the pre-diagnosis history, followed inhibition...
Background and purpose: To critically appraise the assertion that an interval beyond 8 weeks between breast-conserving surgery (BCS) adjuvant radiotherapy (RT) in early-breast cancer increases risk of local recurrence absence chemotherapy.Methods: A full review recent literature, including results single multiple institutional clinical databases, randomized trials on sequencing RT, administrative a critical appraisal main meta-analysis 1 topic were undertaken.Results: The one wait time has...
<h3>Background</h3> CD4 T cells have been implicated in cancer immunity for their helper functions. However, direct cytotoxic potential remains elusive patients. Here, we aimed at assessing the presence, rate and function of tumor-specific Th-CTX directly <h3>Methods</h3> We capitalized on published single cell transcriptomic analyses patient samples, integrated with phenotypic functional characterization clonal, populations, using peptide-MHC class II multimers a novel high-throughput...
Abstract The exponential scaling of scRNA-seq data represents an important hurdle for downstream analyses. Here we develop a coarse-graining framework where highly similar cells are merged into metacells. We demonstrate that metacells not only preserve but often improve the results analyses including visualization, clustering, differential expression, cell type annotation, gene correlation, imputation, RNA velocity and integration. By capitalizing on redundancy inherent to data,...
ABSTRACT Recent studies have proposed that tumor-specific tumor-infiltrating CD8 + T lymphocytes (CD8 TIL) can be classified into two main groups: “exhausted” TILs, characterized by high expression of the inhibitory receptors PD-1 and TIM-3 lack transcription factor 1 (Tcf1); “memory-like” with self-renewal capacity co-expressing Tcf1 PD-1. However, a comprehensive definition heterogeneity existing within both total TILs has yet to clearly established. To investigate this at transcriptomic...