Peter Karl Sorger

Genomic classification and immune profiling define mucosal melanoma

This study identifies genomic subtypes and immune features of mucosal melanoma, linking CD163+ macrophages to immune resistance and suggesting TIM-3 blockade as a therapeutic target.

Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights

A free Meta Quest virtual reality app harmonizes CODEX, Visium, Xenium, volumetric immunofluorescence and electron microscopy data from 5 organs into 4 scale levels using the Human Reference Atlas.

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.

Restraint of melanoma progression by cells in the local skin environment

The paper shows that keratinocyte EMT-like transformation in melanoma reduces tumor invasion and improves survival through altered cell-cell interactions.

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.

Polypharmacology is an enduring and nearly universal property of kinase inhibitors

This paper shows that kinase inhibitors commonly target multiple kinases, independent of approval status, and highlights the need for better understanding of their polypharmacology.

Single-cell spatial atlas of high-grade serous ovarian cancer unveils MHC class II as a key driver of spatial tumor ecosystems and clinical outcomes

Cyclic immunofluorescence of 265 high-grade serous ovarian carcinomas and random-forest feature ranking identify cancer-cell MHC-II as an adjusted predictor of longer survival marking immune-activated tumor-stroma hotspots.

Harnessing Inflammatory Monocytes to Overcome Resistance to Anti-PD-1 Immunotherapy

This study shows CD40 agonist therapy reduces tumor growth in antigen presentation-deficient tumors by reprogramming monocytes and requiring IFN-gamma and CD8+ T cells for efficacy.

Ribosome-associated quality control of aberrant protein production during amino acid limitation

The paper investigates how amino acid limitation affects translation by analyzing ribosome stalling and the role of RQC pathways and RNF14 in response to arginine depletion.

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.

SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data

SEAL integrates spatial imaging context with dimensionality reduction embeddings to improve interpretation of complex datasets through interactive visualization and feature importance analysis.

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.

Universal consensus 3D segmentation of cells from 2D segmented stacks

The paper introduces u-Segment3D, a tool that converts 2D cell segmentations into 3D consensus segmentations without training data, demonstrating effectiveness across diverse datasets.

The initial melanoma T cell infiltrate is defined by tissue-resident programs restrained by regulatory T cells

The paper identifies regulatory T cells suppressing tissue-resident CD8+ T cell programs in early melanoma, revealing a mechanism of immune evasion.

Craters on the melanoma surface facilitate tumor-immune interactions and demonstrate pathologic response to checkpoint blockade in humans

The paper identifies crater-shaped structures in melanoma that enhance immune response to checkpoint blockade therapy in humans and zebrafish.

Dynamic Modeling of Cell Cycle Arrest Through Integrated Single-Cell and Mathematical Modelling Approaches

The paper develops a framework to integrate multiplexed immunofluorescence data with mathematical models to study cell cycle dynamics and arrest, validated on MCF-10A cells exposed to arresting agents.

Multiomic profiling of a unique in-transit melanoma cohort identifies melanoma differentiation as predictor of tumor progression and therapy response

The paper identifies melanoma differentiation and immune exhaustion as predictors of tumor progression and therapy response in in-transit melanoma patients through multiomic profiling.

Spatial statistics for identifying and scoring immune clusters in high-plex profiles of primary prostate cancer

The paper introduces statistical tools to analyze immune cluster patterns in prostate cancer and finds high-grade tumors show more immune infiltration and active immune features.

Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours

This study distinguishes tissue-resident memory (TRM) and exhausted T (TEX) cells in tumors by analyzing their antigen reactivity, clonality, and functional 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.

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.

Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer

This study shows chemotherapy causes myeloid-driven spatial T-cell exhaustion in ovarian cancer by altering immune cell states and interactions, suggesting new immunotherapy approaches.

An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer

This study identifies an estrogen receptor signaling program in HR+ breast cancer that suppresses immune responses by reducing T cell infiltration and HLA expression, suggesting therapeutic targets to enhance immunogenicity.

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.

PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation

This study shows PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation, with reduced 5hmC levels correlating with PRAME upregulation.