P. K. Sorger

psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring

psudo is an interactive system that optimizes pseudocolor palettes for multichannel biomedical images to enhance perceptual distinction and reduce color confusion in overlapping channels.

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.

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.

ASCT2 is the primary serine transporter in cancer cells

This study identifies ASCT2 as the primary serine transporter in cancer cells and shows its role in purine biosynthesis and therapeutic targeting.

Resident memory T cell development is associated with AP-1 transcription factor upregulation across anatomical niches.

This study identifies AP-1 transcription factors as key regulators of TRM development across tissues using scRNA-seq and ATAC-seq, revealing a novel mechanism for TRM reactivation.

Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers

This study creates a multimodal tumor atlas to analyze how metastatic HR+ breast cancers adapt to CDK4/6 inhibitors, revealing mechanisms like mTORC1 activation and immune microenvironment changes.

Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence

This study compares CyCIF and IHC for immune profiling in ICI-induced dAEs, finding CyCIF provides more detailed single-cell characterization of immune infiltrates.

A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments

This study uses a CRISPRi/a screening platform to identify nutrient transporters critical for cancer cell proliferation in diverse microenvironments and reveals their functional roles.

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.

Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes

This study integrates multi-omics data to identify DUB functions and therapeutic targets, revealing key enzymes like USP14, UCHL5, and USP7 with potential in cancer therapy.

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.

Cancer patient survival can be accurately parameterized, revealing time-dependent therapeutic effects and doubling the precision of small trials

The paper imputes survival data from oncology trials and shows that using Weibull distributions improves trial precision and reveals time-dependent therapeutic effects in immune checkpoint inhibitor trials.

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.

Proteomic profiling of breast cancer cell lines and models

The paper performs proteomic profiling of 61 breast cancer cell lines, identifies molecular subtypes, and makes datasets publicly available for drug response prediction and therapeutic marker discovery.

Channel Embedding for Informative Protein Identification from Highly Multiplexed Images

This paper introduces a channel embedding method for interpreting highly multiplexed biomedical images, demonstrating its effectiveness on synthetic data and breast cancer cell images.

Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2

This paper identifies an ancestral recombination event in the RBD of SARS-CoV and SARS-CoV-2 that increased hACE2 binding affinity, suggesting SARS-like viruses may have pandemic potential.

Biomarker-guided treatment strategies for ovarian cancer identified from a heterogeneous panel of patient-derived tumor xenografts

This study identifies biomarker-guided treatment strategies for ovarian cancer using patient-derived tumor xenografts, finding that nearly 90% of PDXs responded to at least one targeted therapy.

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.

Sporadic ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cells

The paper shows that sporadic ERK pulses in BRAFV600E melanoma cells drive non-genetic resistance to RAF/MEK inhibitors.

Opposing immune and genetic forces shape oncogenic programs in synovial sarcoma

The paper profiles synovial sarcoma tumors to show that the SS18-SSX fusion drives oncogenic programs, which are repressed by immune cells and can be targeted with HDAC and CDK4/6 inhibitors.

A curative combination therapy for lymphomas achieves high fractional cell killing through low cross-resistance and drug additivity but not synergy

This study analyzes the R-CHOP combination therapy for lymphomas, finding low cross-resistance and drug additivity rather than synergy contribute to its effectiveness.

Combined inhibition of mTOR and PIKKs exploits replicative and checkpoint vulnerabilities to induce death of PI3K-activated triple-negative breast cancer cells

The paper shows that combining mTOR and PIKK inhibitors kills triple-negative breast cancer cells by exploiting replication and checkpoint vulnerabilities.

Adaptation of human iPSC-derived cardiomyocytes to tyrosine kinase inhibitors reduces acute cardiotoxicity via metabolic reprogramming

Time resolved quantitative phosphoproteomics reveals distinct patterns of SHP2 dependence in EGFR signaling

The paper uses time-resolved phosphoproteomics to analyze SHP2's role in EGFR signaling, identifying distinct phosphotyrosine response patterns upon SHP099 treatment.