Simon Knott

Tryptophan degradation by intestinal Bacteroides induces anti-tumor immunity and limits melanoma growth

This study shows that intestinal Bacteroides species degrade tryptophan into indoles, which enhance anti-tumor immunity and limit melanoma growth.

AI-Driven Spatial Transcriptomics Unlocks Large-Scale Breast Cancer Biomarker Discovery from Histopathology

Path2Space predicts spatial gene expression and tumor microenvironment from histopathology slides, identifying new breast cancer subgroups and improving biomarker prediction.

IL-17RC signaling connects intestinal microbiota and neuroimmune interactions in atherosclerosis

This study shows IL-17RC signaling in the intestine prevents atherosclerosis by controlling microbiota and perivascular innervation, with loss of IL-17RC increasing inflammation and disease.

Lesion-remote astrocytes govern microglia-mediated white matter repair

This study identifies lesion-remote astrocytes (LRAs) that drive microglia-mediated white matter repair after spinal cord injury through Ccn1-dependent mechanisms.

EZH2-TTP-mTORC1 Axis Drives Phenotypic Plasticity and Therapeutic Vulnerability in Lethal Prostate Cancer

This paper identifies the EZH2-TTP-mTORC1 axis as a driver of phenotypic plasticity and therapeutic vulnerability in prostate cancer, showing that combined inhibition of EZH2 and PI3K/mTORC1 improves anti-tumor activity.

The mutational landscape defines the proteome and spatial organization of tumor, stroma and immune cells in ovarian cancer

This study profiles the proteome of ovarian cancer tumors before and after chemotherapy, revealing how HRD status affects immune pathways and identifies potential therapeutic targets.

Single-cell-guided identification of logic-gated antigen combinations for designing effective and safe CAR therapy

This paper introduces LogiCAR designer, a computational method using single-cell transcriptomics to identify logic-gated antigen combinations for CAR therapy, showing improved efficacy and safety compared to existing approaches.

Targeting the translation initiation complex in therapy-resistant and metastatic melanoma

This study identifies M19-6 as a small molecule that disrupts the eIF4F complex, reducing melanoma growth and metastasis while sparing melanocytes.

Single RNA molecule resolution spatial imaging of immunotherapy response in triple negative breast tumors harboring tertiary lymphoid structures

The paper uses single RNA molecule resolution imaging to analyze immunotherapy response in triple negative breast tumors with tertiary lymphoid structures, identifying two tumor types based on immune infiltration and their differential responses to pembrolizumab and radiation therapy.

A Comparative Analysis of Imaging-Based Spatial Transcriptomics Platforms

Head-to-head on serial prostate adenocarcinoma sections: Xenium gave higher sensitivity, wider dynamic range and closer agreement with snRNA-seq; CosMx segmented cells better out of the box.

The molecular consequences of androgen activity in the human breast

This study investigates the molecular effects of androgen in the human breast using single-cell transcriptome, chromatin, and spatial profiling of transgender men undergoing androgen therapy, revealing changes in gene expression, immune populations, vasculature, and metabolism.

Transcriptome and interactome analyses identify the TP53 interacting gene RCCD1 as a candidate susceptibility gene at the 15p26.1 breast and ovarian cancer risk locus

The paper identifies RCCD1 as a susceptibility gene for breast and ovarian cancer by fine-mapping a risk locus and showing its expression and interaction patterns are associated with cancer risk.

LncRNA Spehd regulates hematopoietic stem cells and progenitors and is required for multilineage differentiation

The paper identifies lncRNA Spehd as essential for hematopoietic stem cell differentiation and multilineage potential in mice.

SmartCodes : functionalized barcodes that enable targeted retrieval of clonal lineages from a heterogeneous population

This paper introduces SmartCodes, functionalized barcodes that allow targeted retrieval and manipulation of clonal lineages in heterogeneous populations using CRISPR-based readers.