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bioRxiv2022

Single-cell Spatial Explorer: Easy exploration of spatial and multimodal transcriptomics

The development of single cell technologies yields large datasets of informations as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called spatial transcriptomics. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 6 human and murine tissues datasets.

bioinformatics↗

bioRxiv2021

An Agent-Based Model of monocyte differentiation into Tumour-Associated Macrophages in Chronic Lymphocytic Leukemia

Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumors, recent studies have uncovered complex macrophage populations, including tumor-associated macrophages, which support tumorigenesis through cancer hallmarks such as immunosuppression, angiogenesis or matrix remodeling. In the case of chronic lymphocytic leukemia, these macrophages are known as nurse-like cells and they protect leukemic cells from spontaneous apoptosis contributing to their chemoresistance. We propose an agent-based model of monocyte differentiation into nurse-like cells upon contact with leukemic B cells in vitro. We performed patient-specific model calibrations using cultures of peripheral blood mononuclear cells from patients. Using our model, we were able to reproduce temporal survival dynamics of cancer cells in a patient-specific manner and to identify patient groups related to distinct macrophage phenotypes. Our results show a potentially important role of phagocytosis in the polarization process of nurse-like cells and in promoting cancer cells enhanced survival.

systems biology↗