E. M. Jaffee

Mimicking the breast metastatic microenvironment: characterization of a novel syngeneic model of HER2+ breast cancer

The paper characterizes a novel syngeneic murine breast cancer model (NT2.5-LM) that exhibits rapid and widespread metastases, enabling study of metastatic progression and therapeutic responses.

Tumor- and Nerve-Derived Axon Guidance Molecule Promotes Pancreatic Ductal Adenocarcinoma Progression and Metastasis through Macrophage Reprogramming

This study identifies SEMA3D as a dual driver of pancreatic ductal adenocarcinoma progression and metastasis through tumor- and nerve-derived mechanisms involving macrophage reprogramming.

Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade

This study examines TLS in HCC treated with neoadjuvant immunotherapy, finding TLS correlate with better outcomes and show distinct morphological and functional features in tumor regression.

Informing virtual clinical trials of hepatocellular carcinoma with spatial multi-omics analysis of a human neoadjuvant immunotherapy clinical trial

The paper develops a spatial quantitative systems pharmacology model for virtual clinical trials in HCC, validated with spatial multi-omics data from a neoadjuvant immunotherapy trial.

Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence

This study uses spatial transcriptomics to analyze HCC tumors treated with cabozantinib and nivolumab, identifying distinct immune and fibrotic mechanisms linked to response and recurrence.

PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration

This paper develops a new protocol for spatial transcriptomics analysis of FFPE PanIN specimens and integrates it with imaging and scRNA-seq to study the progression from PanIN to PDAC.

Inflammatory Signaling in Pancreatic Cancer Transfers Between a Single-cell RNA Sequencing Atlas and Co-Culture

This paper integrates single-cell RNA sequencing data with organoid co-cultures to study inflammatory signaling in pancreatic cancer and validates findings through transfer learning and mechanistic experiments.

Phenotypic shifts of tumor associated macrophages and STAT3 mediated suppression of myeloid derived suppressor cells drive sensitization of HER2+ tumor immunity.

The paper uses single-cell RNA-sequencing to show entinostat shifts tumor microenvironment cell states, reducing immunosuppression and enhancing immune checkpoint inhibitor responses in HER2+ breast tumors.

Transfer learning between preclinical models and human tumors identifies conserved NK cell activation signature in anti-CTLA-4 responsive tumors

The paper uses transfer learning to identify a conserved NK cell activation signature in anti-CTLA-4 responsive tumors across preclinical models and humans, showing its clinical relevance.