Christine A. Iacobuzio–Donahue

Neoantigen-reactive CD8+ T cell engagement marks exceptional survivors of pancreatic cancer

The paper identifies TIE CD8+ T cell clonotypes associated with prolonged survival in pancreatic cancer patients and links resistance to stromal and immune barriers.

SPINK1-COL18A1 Crosstalk Shapes Epigenome and Drives Cancer Stemness in Pancreatic Ductal Adenocarcinoma

This study identifies SPINK1 as a regulator of epigenomic states and stemness in PDAC through its interaction with COL18A1 and endostatin release.

Hierarchical classification of immune cell transcriptomes at population-scale

The paper introduces Suco and Compocyte to classify immune cells from 3,965 patients, identifying new macrophage and monocyte states and T cell memory erosion in metastases.

POLQ-driven repair scars shape the immunogenic landscape of homologous recombination-deficient pancreatic cancer

The paper identifies MDF, a repair scar linked to POLQ-driven error-prone repair, as a marker of immune-responsive HRD pancreatic cancer with increased neoantigens and favorable clinical outcomes.

A Genetically Engineered Human Organoid Model Reveals Distinct Genetic and Epigenetic Barriers of Lineage Plasticity in Early PDAC Transformation

This paper develops a human organoid model of early PDAC that identifies genetic and epigenetic barriers to lineage plasticity, showing CDKN2A loss is essential with KRAS/TP53 mutations and TET1 suppression links ERK signaling to transcription factor silencing.

Genomic evolution of pancreatic cancer at single-cell resolution

This study uses single-nucleus DNA sequencing to analyze pancreatic cancer evolution, revealing patterns of mutation and copy number variation across clinical scenarios.

Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer

The paper analyzes transcriptomic changes in metastatic pancreatic cancer using a patient's autopsy data to identify site-specific gene programs and clonal phylogeny.

Metastatic site influences driver gene function in pancreatic cancer

This study shows that metastatic site influences the function of driver genes like SMAD4 in pancreatic cancer, with organ-specific epigenetic states affecting tumor growth.

Mechanism of neurodegeneration mediated by clonal inflammatory microglia

The paper identifies clonal inflammatory microglia as a cause of neurodegeneration in LCH and ECD, showing their association with neuronal loss and suggesting CSF1R inhibitors as a therapeutic option.

A microglia clonal inflammatory disorder in Alzheimer's Disease

The paper identifies microglia-specific somatic clones with pathogenic variants in Alzheimer's Disease patients that drive neuro-inflammation through the MAPK pathway.

ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model

ConDoR improves tumor phylogeny inference by integrating copy-number constraints with SNV data, outperforming existing methods on simulated data and producing more plausible phylogenies in real datasets.

Clonal evolution during metastatic spread in high-risk neuroblastoma

This study traces clonal evolution in high-risk neuroblastoma using genomic data from 470 samples, showing metastatic clones can remain dormant and later cause relapses.

The mutational landscape of human somatic and germline cells

This study compares mutational landscapes in somatic and germline cells across 29 anatomical structures, identifying key mutational signatures and their contributions to different cell types.

Enabling cross-study analysis of RNA-Sequencing data

This paper presents a pipeline to unify RNA-seq data from different studies by removing batch effects, enabling cross-study analysis.