S. Santagata

Highly Multiplexed 3D Profiling of Cell States and Immune Niches in Human Tumours

This paper introduces 3D CyCIF, a method for high-plex 3D profiling of cell states and immune niches in human tumors, revealing detailed spatial interactions and cytokine niches previously unattainable in thin sections.

2D and 3D multiplexed subcellular profiling of nuclear instability in human cancer

The paper shows nuclear rupture is common in cancer, especially glioblastoma, and links it to lamin proteins and immune signaling.

Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter

This paper introduces CyLinter, a quality control tool that removes imaging artefacts from high-plex spatial profiling data, improving single-cell analysis of archival tumor specimens.

Multi-modal digital pathology for colorectal cancer diagnosis by high-plex immunofluorescence imaging and traditional histology of the same tissue section

The paper develops a multi-modal imaging platform combining H&E and high-plex immunofluorescence for colorectal cancer diagnosis, showing improved predictive models for progression-free survival.

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

The paper maps lymphocyte interactions in lung adenocarcinoma using spatial analysis and machine learning, revealing dynamic lymphocyte networks that support anti-tumor immune responses.

Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data

Visinity analyzes spatial cell interactions in multiplexed tissue images to identify biological processes and immune-tumor interactions.

Single Cell Spatial Analysis Reveals the Topology of Immunomodulatory Purinergic Signaling in Glioblastoma

The paper uses spatial single-cell analysis to show that CD73 and CD39 expression in glioblastoma correlates with poor clinical outcomes and immunosuppressive signaling.

The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution

The paper uses spatial techniques to study immune evasion and immunoediting in primary melanoma, finding localized immunosuppressive environments and coexistence of invasion and regression.

Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer

This study uses multiplexed 3D imaging and machine learning to analyze colorectal cancer morphology and immune interactions, revealing molecular gradients and cell state transitions.

Micro-region transcriptomics of fixed human tissue using Pick-Seq

Pick-Seq enables deep spatial transcriptomic profiling of fixed human tissue, revealing transcriptional differences in tumor invasion, proliferation, and immuno-editing.

Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung

The paper uses multiplexed proteomics and imaging to compare inflammatory and thrombotic responses in resolving SARS-CoV-2 infection in rhesus macaques and lethal COVID-19 in humans.

Online narrative guides for illuminating tissue atlas data and digital pathology images

The paper discusses the need for interactive guides to help interpret complex tissue atlas data and digital pathology images, using Minerva software as an example.

Systemic immune response profiling with SYLARAS implicates a role for CD45R/B220+ CD8+ T cells in glioblastoma immunology

The paper introduces SYLARAS, a tool for immune response profiling, and shows CD45R/B220+ CD8+ T cells are depleted in circulation and accumulate in glioblastoma tumors in mice, with similar cells found in human GBM.

Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer

The paper describes a dataset of multiplexed immunofluorescence images and single-cell immune marker data from human tonsil and lung cancer tissues, along with analysis methods and tools.

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

This paper introduces t-CyCIF, a method for highly multiplexed immunofluorescence imaging of FFPE tissues using conventional microscopes, and demonstrates its application in analyzing tumor antigens and immune markers.

Inhibition of mitochondrial ferredoxin 1 (FDX1) prevents adaptation to proteotoxic stress

This study identifies FDX1 inhibition as a strategy to prevent proteasome inhibitor resistance in cancer by targeting mitochondrial Fe-S cluster biosynthesis.