Kelly V. Ruggles

Rethinking the Benign Nature of Class II Lupus Nephritis

This study defines the single-cell landscape of Class II lupus nephritis and identifies fibroblast transcriptional programs and chronicity index as potential predictors of kidney outcomes.

Pan-cancer proteogenomic interrogation of the Ubiquitin Proteasome System

Proteogenomic analysis of up to 11 CPTAC cohorts shows ubiquitin-proteasome proteins often diverge from transcripts; TP53-mutant tumors elevate UBR5 protein, while TRIM28 prognosis is lineage-dependent.

Cell autonomous inflammation in VEXAS is mediated by cGAS-STING

This study identifies cGAS-STING pathway activation as a key mechanism of inflammation in VEXAS, showing that UBA1 mutations disrupt ERAD and mitochondrial homeostasis, leading to STING-driven inflammation.

IFNγ-dependent metabolic reprogramming restrains an immature, pro-metastatic lymphatic state in melanoma

This study shows that IFNγ suppresses lymphatic vessel growth and metastasis by altering metabolism and immune function in melanoma.

Pan-cancer analysis reveals context-dependent roles of LINE-1 ORF1p in immune regulation and copy number alterations

The paper analyzes ORF1p expression across cancers, finding it correlates with immune suppression in some tumors and activation in others, linked to copy number alterations.

Pathogenic strains of a gut commensal drive systemic platelet activation and thromboinflammation in lupus nephritis

This study shows that pathogenic Ruminococcus gnavus strains in the gut drive platelet activation and thromboinflammation in lupus nephritis, with antibodies against its lipoglycan as a potential biomarker.

The carnosinase dipeptidase CNDP1 is a novel metabolic vulnerability in brain metastasis

This study identifies CNDP1 as a metabolic vulnerability in brain metastasis, showing its inhibition suppresses metastasis and its expression confers metastatic potential.

The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1

This study identifies ASCL1 as a critical driver of neuroendocrine lineage transition in prostate cancer using an in vivo model and spatial transcriptomics.

Stabilization of GTSE1 by cyclin D1-CDK4/6 promotes cell proliferation: relevance in cancer prognosis

The paper shows cyclin D1-CDK4/6 stabilizes GTSE1, promoting cell proliferation and poor cancer prognosis.

Functional high capacity exosome-encapsulating bioinspired hydrogel promotes microvascularbed expansion in diabetic mice

The paper introduces Exo-Q, a hydrogel that promotes microvascular expansion in diabetic wounds, reducing closure time compared to non-diabetic wounds.

BlackSheep: A Bioconductor and Bioconda package for differential extreme value analysis

BlackSheep identifies molecules aberrantly enriched in small sample cohorts using non-parametric differential extreme value analysis.

Spatially Interacting Phosphorylation Sites and Mutations in Cancer

The paper introduces HotPho, a tool that identifies 3D co-clustering of phosphosites and cancer mutations on protein structures, revealing 474 hybrid clusters with potential functional significance.

Predictive Metagenomic Analysis of Autoimmune Disease Identifies Robust Autoimmunity and Disease Specific Microbial Signatures

The paper re-analyzes 42 studies on gut microbiome in autoimmune diseases to identify microbial signatures predictive of MS, IBD, RA, and general autoimmunity using machine learning.

Hypercluster: a flexible tool for parallelized unsupervised clustering optimization

Hypercluster automates and accelerates unsupervised clustering by testing multiple models and hyperparameters in parallel, providing reproducible results.