Faiyaz Notta

Loss of the Y chromosome drives basal identity and metastatic potential via epigenetic reprogramming in pancreatic cancer

This study identifies LOY as a driver of aggressive PDAC through epigenetic reprogramming, linking it to EMT and metastasis, and highlights its clinical relevance as a biomarker.

HMGA2 Expression in Pancreatic Ductal Adenocarcinoma Controls Tumor Microenvironment and Immunosuppression via IL1α

This study shows HMGA2 in PDAC drives immunosuppressive TME by upregulating IL1α, which promotes CAFs and reduces CD8+ T cells, and blocking IL1 improves tumor control with KRAS inhibitors.

Integrated whole-genome and transcriptome sequencing reveals divergent evolutionary processes across biliary tract cancer subtypes

The paper uses whole-genome and transcriptome sequencing to identify two consensus cancer subtypes in biliary tract cancer, revealing divergent molecular landscapes that better explain tumor heterogeneity than anatomical classification.

Extra-lineage tissue programs define the transcription states of human pancreatic cancer

The paper identifies four epithelial transcription states in pancreatic cancer and links their origins to early developmental processes.

Transcriptomic, Genomic, and Clinical Characterization of Morphological Classes in Localized and Metastatic Pancreatic Cancer

This study characterizes morphological classes in pancreatic cancer using transcriptomic, genomic, and clinical data to identify molecular associations and prognostic implications.

The subclonal footprint of pervasive early dissemination in pancreatic cancer

This study analyzes ctDNA shedding in pancreatic cancer using paired tissue and plasma whole genomes, finding that subclones contribute significantly to early dissemination and ctDNA levels.

Integrated spatial proteomics of human PDAC uncovers an expanded tumour-immune-stroma spectrum with genomic associations

This study integrates spatial proteomics and genomics in PDAC to identify tumour-immune-stroma interactions and their genomic associations, showing multi-omics models improve patient survival prediction.

Single-cell analysis of an engineered organoid-based model of pancreatic cancer identifies hypoxia as a contributing factor in the determination of transcriptional subtypes

This study uses single-cell transcriptomics to show that hypoxia in organoid models influences transcriptional subtypes in pancreatic cancer.

NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism

NEST detects cell-cell communication patterns using a deep learning-based attention mechanism, outperforming existing tools and identifying biologically relevant communication in various tissues and diseases.

Inferring tumour microenvironment ecosystems from scRNA-seq atlases

The paper infers multicellular ecosystems from nonspatial scRNA-seq data and shows they predict therapy response and are linked to somatic mutations.

Macrophages heterogeneity and significance during human fetal pancreatic development

The paper identifies fetal pancreatic macrophage subsets and shows their role in promoting endocrine cell differentiation and tissue engraftment.