Sandro Santagata

Perinatal Elimination of Genetically Aberrant Neurons from Human Cerebral Cortex

The paper investigates somatic copy number variants (CNVs) in human neurons across development, finding that perinatal elimination of neurons with aberrant genomes reduces CNV prevalence and targets dosage-sensitive genes.

Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Tumour, Stroma, and Immune Structures in Human FFPE Tissue

The paper introduces v-CyCIF, a method for 3D spatial profiling of human FFPE tissue, enabling detailed analysis of tumor, stroma, and immune structures.

Reconstruction of epithelial transcriptional trajectories reveals heterogeneous progression and early therapy-resistance programs in high-grade serous carcinomaprecursors

This study reconstructs transcriptional trajectories of Fallopian-tube epithelium to show STICs occupy diverse positions along a progression continuum and exhibit variable PARPi resistance signatures.

Immunogenic tumor mass dormancy as a driver of persistent residual lesions in immunotherapy-treated melanoma

This study shows that immunogenic tumor mass dormancy, not cell-level quiescence, persists in residual melanoma lesions after immunotherapy, with active tumor cells and immune interactions.

Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis

This study uses 3D reconstruction and optimal transport modeling to analyze TLS development in TB-infected lungs, revealing distinct maturation trajectories and spatial dynamics.

Compositional and interpretable representation of histology using AI foundation models and sparse autoencoders

This paper introduces a human-in-the-loop framework using AI foundation models and sparse autoencoders to interpret H&E histology images and integrate them with molecular spatial profiling.

Epigenetic dysregulation of metabolic programs mediates liposarcoma cell plasticity

This study identifies epigenetic dysregulation of metabolic programs in liposarcoma, linking IGF1 loss and PPARG2 deficiency to dedifferentiation and proposing IGF1R-targeted therapy.

In vivo evidence for bleb-induced survival signaling in metastatic melanoma

This paper shows that bleb-induced septin signaling supports survival of metastatic melanoma cells in vivo, and disrupting this pathway reduces metastasis.

Integrative single-cell and spatial mapping of oxidative stress response uncovers GCLC+ mesenchymal tumor cell state linked with favorable outcomes in triple negative breast cancer

The paper maps oxidative stress response in TNBC using single-cell and spatial data, identifying GCLC+ mesenchymal tumor cells linked to better patient outcomes.

Morphology-Aware Profiling of Highly Multiplexed Tissue Images using Variational Autoencoders

This paper introduces a method that combines autoencoders with segmentation to improve single-cell analysis of multiplexed tissue images by capturing morphology and reducing signal spillover.

Spatial determinants of tumor cell dedifferentiation and plasticity in primary cutaneous melanoma

The paper maps spatial patterns of tumor cell dedifferentiation and plasticity in melanoma by analyzing RNA and protein expression across 300 histological domains.

Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement

The paper describes how the Human Tumor Atlas Network shares data through standards, infrastructure, and community engagement, making datasets accessible via multiple platforms.

Multiomic analysis identifies suppressive myeloid cell populations in human TB granulomas.

This study identifies suppressive myeloid cell populations in human TB granulomas using spatial transcriptomics and single-cell immunophenotyping, revealing IDO1+ dendritic cells as key regulators of immune suppression.

ZNFX1 is a Novel Master Regulator in Epigenetically-induced Pathogen Mimicry and Inflammasome Signaling in Cancer

This study identifies ZNFX1 as a master regulator of epigenetically-induced pathogen mimicry and inflammasome signaling in ovarian cancer, linking its expression to disease progression and survival.

Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma

This study uses spatial profiling to show immune suppression and microenvironment changes in fallopian tube precursors of high-grade serous ovarian cancer.

Integrating spatial profiles and cancer genomics to identify immune-infiltrated mismatch repair proficient colorectal cancers

The paper identifies a subset of mismatch repair proficient colorectal cancers with high immune infiltration that may benefit from immune checkpoint inhibitors, using spatial profiling and genomics.

Spatial Profiling of Metals through Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging

This paper introduces a MALDI MSI method to spatially profile metals in tissues, applying it to study embryogenesis, genetic disorders, and chemotherapy delivery.

Cell Spotter (CSPOT): A machine-learning approach to automated cell spotting and quantification of highly multiplexed tissue images

Cell Spotter (CSPOT) uses supervised machine learning to automate cell spotting and quantification in highly multiplexed tissue images, improving speed, accuracy, and reproducibility.

3D multiplexed tissue imaging reconstruction and optimized region-of-interest (ROI) selection through deep learning model of channels embedding

The paper proposes deep learning methods to reconstruct 3D CyCIF images and select optimal ROIs from histology and MTI data for tumor representation.

UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues

The paper introduces two methods to improve tissue segmentation in highly multiplexed images using real augmentations and nuclear envelope imaging, resulting in more accurate models.

Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR

ASHLAR is a Python tool that stitches and registers highly multiplexed whole slide images to generate accurate mosaics, outperforming existing software.

Temporal and spatial topography of cell proliferation in cancer

This study quantifies cell proliferation in tumors using multiplexed imaging and identifies spatial and temporal patterns of cell cycle regulation.

MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging

MCMICRO processes multiplexed tissue images into single-cell data, demonstrating its versatility across different tissues and imaging platforms.