Contributors:Giorgio Cattoretti, Maddalena M Bolognesi, Francesca M Bosisio, Mario Faretta, Francesco Mascadri et al
Background: Antibody validation for tissue staining is required for reproducibility and criteria to ensure validity have been published recently. The majority of these recommendations imply the use of routinely processed tissue (FFPE).
Materials & Methods: We applied to lightly fixed frozen sections a panel of 126 antibodies validated for FFPE with extended criteria.
Results: Less than 30% performed conservatively with all fixations, 35% preferred one fixation over another, 13% gave non-specific staining, 23% did not stain at all.
Conclusions: Individual antibody variability of the paratope fitness for the fixed antigen may be the cause. Re-validation of established antibody panels is required when applied to sections whose fixation and processing is different from the tissue where they have been initially validated.
These are supplementary Data to the manuscript. In addition Tabel 1 and Supplementary Table 1 are provided in Excel format.
Contributors:Marco Manzoni, Maddalena Bolognesi, Asier Antoranz, Mario Faretta, Francesca M Bosisio et al
Personalized immune intervention to release and redirect the T cells against a tumor has shown substantial progress in aggressive tumors such as melanoma and lung cancer, despite the fact that predictors of sustained response are still unclear. Data on less common histotypes are scanty. Among soft tissue sarcomas, uterine leiomyosarcomas (ULMS) have a dire prognosis, yet therapeutic advances are needed in order to improve the actual treatment. Immune checkpoint inhibitor therapy has been applied to exceptionally few cases, of which the immune cell composition was not examined in detail. We analyzed in situ the inflammatory infiltrate of 21 untreated ULMS in high-dimensional, single cell phenotyping on routinely processed tissue, directed at the characterization of lymphoid cells and macrophages. T-lymphoid cells displayed a composite phenotype common to all tumors, suggestive of antigen-exposure; in about half of the cases containing sufficient lymphocytes, we found evidence of exhaustion and a CD8+ TCF7+ phenotype, this latter associated with T-cell reactivation. To the contrary, myelomonocytic cells had case-specific individual combinations of phenotypes and subsets. We identified five distinct monocyte-macrophage cell types: histiocytes, phagocytes, tumor-associated macrophages, inflammatory monocytes and myelomonocytic cells of undefined phenotype. Immunosuppressive molecules (TIM3, B7H3, VISTA, PD1, PDL1) were heterogeneously expressed in inflammatory and endothelial cells. The heterogeneity and phenotype of the monocyte-macrophage population may represents a challenge for which we provide an initial understanding.
Contributors:Giacomo Guidali, Alberto Pisoni, Nadia Bolognini, Costanza Papagno
Dataset and materials for the rTMS study "Keeping order in the brains: the supramarginal gyrus and serial order in short-term memory". In the "Experiment folders" there are the E-Prime script of the tasks and the stimuli used. In the "Database and all anlysis" folder, there is the anonymus excel database of all 4 experiments and the Statistica workbook with all the analyses conducted and reported in the paper.
Pipelines for CellProfiler mask generation, creation of heatmaps with R from Phenograph .csv data, .csv data exported from HistoCAT after segmentation and analysis.
Refers to The landscape of S100B+ and HLA-DR+ dendritic cell subsets in tonsils at the single cell level via high-parameter mapping. by Bolognesi MM et al.