G. Coukos

Myeloid cell networks determine reinstatement of original immune environments in recurrent ovarian cancer

The paper identifies immune phenotypes and myeloid cell networks in recurrent ovarian cancer that influence prognosis and immune environment reinstatement.

Acidity-induced dysfunction of CD8+ T cells is characterized by impaired IL-2 responsiveness and perturbations to mTORC1 signaling and c-Myc levels

This study shows that low pH impairs CD8+ T cell function by reducing IL-2 responsiveness, disrupting mTORC1 signaling, and altering c-Myc levels and amino acid metabolism.

Dissection and reconstruction of the colorectal cancer tumor microenvironment

This study reconstructs the colorectal cancer tumor microenvironment using patient-derived organoids and co-cultures, revealing how stromal cells influence cancer behavior and immune evasion.

Tumor-reactive clonotype dynamics underlying clinical response to TIL therapy in melanoma

This study tracks tumor-reactive TIL clonotypes in melanoma patients before and after TIL-ACT to identify factors associated with clinical response.

Combination of NY-ESO-1-TCR-T-cells coengineered to secrete SiRPalpha decoys with anti-tumor antibodies to augment macrophage phagocytosis

This study combines NY-ESO-1 TCR-T cells secreting SiRPalpha decoys with anti-tumor antibodies to enhance macrophage phagocytosis and improve tumor control.

TCRpcDist: Estimating TCR physico-chemical similarity to analyze repertoires and predict specificities

TCRpcDist clusters TCR repertoires based on physico-chemical properties to predict antigen specificity and identify TCR groups likely to bind similar epitopes.

Tumor Microenvironment Cellular Crosstalk Predicts Response to Adoptive TIL Therapy in Melanoma

This study identifies CD8+ TIL-myeloid cell networks as predictors of response to adoptive TIL therapy in melanoma using single-cell RNA-seq and spatial proteomic analyses.

Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes

The paper predicts MHC-II epitope specificities using machine learning, revealing a reverse binding mode in ligands across multiple species.

Orthogonal Gene Engineering Enables CD8+ T Cells to Control Tumors through a Novel PD-1+ TOX-indifferent Synthetic Effector State

This study shows that orthogonal gene engineering of CD8+ T cells with IL-2 variant, PD1-decoy, and IL-33 enables tumor control through a novel PD-1+ TOX-indifferent synthetic effector state.

High-throughput single-cell TCR - pMHC dissociation rate measurements performed by an autonomous microfluidic cellular processing unit

The paper develops a microfluidic device to measure TCR-pMHC dissociation rates in single cells and demonstrates its high-throughput capability.

Deciphering the landscape of phosphorylated HLA-II ligands

The paper identifies 1,113 unique phosphorylated HLA-II ligands and develops a predictor for their presentation on HLA-II molecules.

Bedside formulation of a personalized multi-neoantigen vaccine against mammary carcinoma

This paper develops a personalized multi-neoantigen vaccine using long peptides linked to virus-like particles, showing improved anti-tumor effects in a murine mammary carcinoma model.

Probing the killing potency of tumor-infiltrating lymphocytes on microarrayed autologous tumoroids

This paper develops a microarray-based assay to assess tumor-infiltrating lymphocyte (TIL) activity against autologous tumoroids, identifying responders to immunotherapy.

Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands

The paper curates phosphorylated HLA-I ligands and develops a predictor for their interaction with HLA-I molecules.

Integrated Proteogenomic Deep Sequencing and Analytics Accurately Identify Non-Canonical Peptides in Tumor Immunopeptidomes

The paper develops an MS-based proteogenomic approach to identify non-canonical HLA peptides in tumors, finding hundreds of shared and tumor-specific peptides, including an immunogenic one from ABCB5.

Deep motif deconvolution of HLA-II peptidomes for robust class II epitope predictions

The paper improves HLA-II epitope prediction by combining mass spectrometry data with a new motif deconvolution algorithm, enhancing motif definition and prediction accuracy.

The length distribution and multiple specificity of naturally presented HLA-I ligands

The paper analyzes HLA-I ligand length distribution and multiple specificity using HLA peptidomics data from human meningioma samples, improving predictions of naturally presented ligands.

The C-terminal extension landscape of naturally presented HLA-I ligands

The paper identifies frequent C-terminal extensions in HLA-I ligands across multiple alleles and demonstrates their recognition by CD8+ T cells.