Enrico G. Petretto

This study uses spatial transcriptomics to identify disease-responsive compartments and immune-fibrotic signaling in AAV kidney biopsies, linking them to histopathology and fibrotic injury.

This paper identifies causal genes in diabetic nephropathy using a cross-species systems genetics framework, finding 192 candidate genes with 40% validated in humans.

The paper identifies Wnt-regulated genes repressed by or independent of β-catenin in a cancer model, revealing a cis-regulatory motif involved in repression.

This study identifies a circRNA-miRNA-mRNA network in ischemic heart disease, revealing circNPHP1's role in enhancing angiogenesis by sponging miR-221-3p to upregulate VEGF-A and BCL2.

The paper compares three proteomic platforms in a multi-ethnic Asian cohort, finding limited overlap, platform-specific performance metrics, and ethnicity-related protein differences.

This paper constructs a mutation-disease dataset and proposes CGM to predict mutation-disease associations, identifying 22 unknown protein interaction pairs.

scPanel identifies a minimal gene panel for patient classification from scRNA-seq data, achieving high accuracy with fewer than 20 genes across multiple datasets.

The paper identifies parvalbumin interneurons in the temporal lobe as highly vulnerable to genetic risk factors and psychoactive drugs in neuropsychiatric disorders.

This study compares scRNA-seq methods with and without sample multiplexing, showing Parse detects rare cell types better despite lower efficiency, while 10X has platform-specific gene length and GC content distributions.

This paper identifies FAXDC2 as a cholesterol biosynthesis enzyme that links Wnt/beta-catenin to RTK/MAPK signaling, showing its role in cancer progression and cellular differentiation.

The paper identifies a matrisome-associated macrophage polarization state in fibrotic tissues across multiple organs using single-cell RNA sequencing.

The paper uses time-series spatial transcriptomics to study human cell grafts in pig hearts after myocardial infarction, identifying Midkine signaling as a key pathway for vascularization.

The paper identifies and functionally validates Wnt-regulated lncRNAs using in vivo models and CRISPRi screens, finding more functional lncRNAs in vivo than in vitro.

This study shows that expanded CAG repeats in HTT disrupt neural progenitor expansion and differentiation in human cerebral organoids, suggesting abnormal neurodevelopment in Huntington disease.

The paper identifies drugs for leukaemia differentiation therapy using network pharmacology, finding that dimaprit and mebendazole enhance ATRA-mediated differentiation in leukaemia cells.

This study identifies that amyloid plaque phagocytosis through Hif1α controls microglial phenotypes in Alzheimer’s disease in both mice and humans.

This paper creates a single-cell brain atlas of Alzheimer’s disease, identifying cell-type specific gene expression patterns and regulatory networks associated with disease.

This paper develops a reproducible method to generate cardiac muscle progenitors from human stem cells using laminin-221, which can form human heart muscle in vivo after transplantation.

This study shows that 2i conditions increase transcriptional heterogeneity in pluripotent stem cells, driven by signaling pathways and negative feedback loss.

The paper shows Wnt/STOP signaling regulates ribosome biogenesis in Wnt-addicted cancers by modulating transcription and protein abundance of key factors.

The paper develops an in vivo Drosophila assay to distinguish Wnt pathway transcriptional responses, identifying gene sets regulated by β-catenin, TCF, and non-canonical Wnt4.

This paper identifies DLG4 (PSD95) expression in microglia and links genetic variation in DLG4 to white matter structure in preterm infants.

This paper introduces CRAFT, a computational framework for drug target identification, and validates Csf1R as a novel anti-epileptic target using pre-clinical models.

ABBA detects differentially methylated regions in WGBS data, identifies disease-associated methylation changes, and proposes a mechanism for glomerulonephritis via Ifitm3 promoter hypermethylation.