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Varrone, M.

Publications and source records attributed to Varrone, M..

2 recordsLinked to original sources

Patient-derived lymphomoids preserve the tumor architecture and allow to assess response to therapies in lymphoma

The efficacy of anti-cancer therapies depends on the genomic composition of the tumor, its microenvironment, spatial organization, and intra-tumor heterogeneity. B cell lymphomas are a heterogeneous group of tumors emerging from B cells at different stages of differentiation and exhibiting tumor-specific interactions with the tumor microenvironment. Thus, to measure response to therapy in lymphoma, it is critical to preserve the tumor composition and functional interactions among immune cells. Here, we developed a platform to maintain small fragments of human lymphoma tissue in culture for several days and use them to test response to therapies. We collected 25 patient samples representative of different lymphoma subtypes and established ex vivo tissue fragments that retained histological, cellular, and molecular characteristics of the original tissue, here referred to as lymphomoids. Using lymphomoids, we tested sensitivity to several clinically approved small molecule inhibitors in parallel and examined tissue remodeling upon treatment. Importantly, when this information was available, we showed that sensitivity to therapy observed in lymphomoids was consistent with patients response in the clinic. Lymphomoids are an innovative tool to assess treatment efficacy in clinically relevant contexts and could be used to uncover novel aspects of lymphoma biology.

cancer biology↗

CellCharter: a scalable framework to chart and compare cell niches across multiple samples and spatial -omics technologies.

Tissues are organized in cellular niches, the composition and interactions of which can be investigated using spatial omics technologies. However, systematic analyses of tissue composition are challenged by the scale and diversity of the data. Here we present CellCharter, an algorithmic framework to identify, characterize, and compare cellular niches in spatially resolved datasets. CellCharter outperformed existing approaches and effectively identified cellular niches across datasets generated using different technologies, and comprising hundreds of samples and millions of cells. In multiple human lung cancer cohorts, CellCharter uncovered a cellular niche composed of tumor-associated neutrophils and cancer cells expressing markers of hypoxia and cell migration. This cancer cell state was spatially segregated from more proliferative tumor cell clusters and was associated with tumor-associated neutrophil infiltration and poor prognosis in independent patient cohorts. Overall, CellCharter enables systematic analyses across data types and technologies to decode the link between spatial tissue architectures and cell plasticity.

bioinformatics↗