C. J. Wu

Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma

This study identifies genomic heterogeneity and ploidy as markers of intrinsic resistance to PD-1 blockade in metastatic melanoma, with a decision tree model predicting resistance with high confidence.

Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy

The paper analyzes single-cell data from bone marrow samples to identify immune cell interactions that predict response to adoptive cellular therapy in myeloid leukemia.

Design of Cytotoxic T Cell Epitopes by Machine Learning of Human Degrons

This paper uses machine learning to design cytotoxic T cell epitopes by modeling proteasomal degradation scores and testing their immunogenicity.

Treg cells drive MYCN-mediated immunosuppression and tumor aggressiveness in high-risk neuroblastoma

This study shows Treg cells drive MYCN-mediated immunosuppression and tumor aggressiveness in high-risk neuroblastoma using human and zebrafish models.

Latent human herpesvirus 6 is reactivated in chimeric antigen receptor T cells

The paper identifies HHV-6 reactivation in CAR T cells using single-cell sequencing and links it to clinical neurotoxicity observed in patients.

Optimized liquid and gas phase fractionation increase HLA-peptidome coverage for primary cell and tissue samples

The paper improves HLA-peptidome coverage using optimized liquid and gas phase fractionation methods, enabling detection of more peptides from limited clinical tissue samples.

Integrative Clinical and Molecular Characterization of Translocation Renal Cell Carcinoma

This study characterizes translocation renal cell carcinoma (tRCC) through integrated clinical and molecular analysis of 152 patients, identifying key features like MiT/TFE fusions, NRF2-driven antioxidant response, and differential treatment outcomes.

Comprehensive and Integrated Genomic Characterization of Human Immunome in Cancer

This study develops a network-based immunogenomics model to identify mutations affecting immune responses in cancer and suggests potential immunomodulatory drug candidates.

Tumor-Immune Partitioning and Clustering (TIPC) algorithm reveals distinct signatures of tumor-immune cell interactions within the tumor microenvironment

The paper introduces TIPC, a computational algorithm that identifies tumor-immune spatial patterns in colorectal cancer, linking them to patient survival and tumor features.

Integrative Molecular Characterization of Sarcomatoid and Rhabdoid Renal Cell Carcinoma Reveals Determinants of Poor Prognosis and Response to Immune Checkpoint Inhibitors

This study characterizes the molecular features and immune profile of sarcomatoid and rhabdoid renal cell carcinoma, showing their responsiveness to immune checkpoint inhibitors and identifying key genetic and transcriptional determinants.

Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to graft-versus-leukemia

The paper investigates the evolutionary trajectories of chronic lymphocytic leukemia cells during resistance to graft-versus-leukemia, finding distinct genetic and epigenetic dynamics post-transplant compared to chemotherapy.

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

The paper identifies thousands of novel unannotated proteins in cancer that contribute to the MHC I immunopeptidome, expanding potential targets for immunotherapy.

Expressed barcodes enable clonal characterization of chemotherapeutic responses in chronic lymphocytic leukemia

This paper develops a method to study clonal responses to chemotherapy in CLL by combining barcoding with single-cell RNA sequencing, revealing that rare drug-tolerant clones dominate post-treatment populations.