Judith A. James

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.

Identification and evaluation of 41 risk loci for juvenile idiopathic arthritis informs precision medicine: mechanistic implications of DNA topology and an HLA-A*02:01-ERAP2 interaction

This paper identifies 41 risk loci for juvenile idiopathic arthritis, including 14 novel ones, and presents a polygenic risk score associated with age of onset, along with functional mechanisms involving DNA topology and an HLA-A*02:01-ERAP2 interaction.

Serial Immunohistochemistry for High-Dimensional Single-Cell Spatial Analysis of Human Kidney Biopsies

This paper develops a serial immunohistochemistry method to detect multiple antigens on kidney biopsy slides, enabling high-dimensional single-cell spatial analysis.

ARID3a-Expressing Naive B Cells in SLE have an Activated Phenotype and Transiently Express Surface CD68

The paper identifies ARID3a and CD68 as markers of activated naive B cell precursors in SLE, showing their association with autoimmunity and disease activity.

SPP1hi macrophages in fibrin niches promote hyperplastic tissue remodeling in rheumatoid arthritis synovium

SPP1hi macrophages in RA synovial fibrin deposits promote tissue hyperplasia.

Serum proteomic atlas reveals distinct molecular signatures of lupus nephritis activity, chronicity, and treatment response

The paper uses serum proteomics to identify molecular signatures that classify lupus nephritis, differentiate disease activity and chronicity, and predict treatment response.

Deep profiling of lupus nephritis kidneys reveals dynamic changes in myeloid cells associated with disease progression

This study uses single-cell RNA-sequencing and spatial transcriptomics to analyze myeloid cell dynamics in lupus nephritis, showing shifts in immune responses linked to disease progression.

Early and late RNA eQTL are driven by different genetic mechanisms

The paper identifies distinct genetic mechanisms for early (nuclear) and late (cellular) RNA eQTL by comparing their genomic localization and functional effects across tissues.

Persistent CD4+ T cell functional deficits during recovery from prolonged symptomatic SARS-CoV-2 infection

This study identifies persistent CD4+ T cell functional deficits in individuals with prolonged SARS-CoV-2 symptoms, characterized by low CD4 expression and impaired activation responses.

A population-scale atlas of blood and tissue in lupus nephritis

A single-cell atlas of blood and tissue samples from lupus nephritis patients and healthy controls identifies stromal and immune populations, including scar-associated macrophages, which correlate with disease activity.

Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland

The paper identifies five SNPs in the DDX6-CXCR5 locus associated with autoimmune diseases and shows their functional effects on gene regulation in immune and epithelial cells.

Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis

The paper identifies activated lymphocyte phenotypes in individuals at risk for rheumatoid arthritis using mass cytometry and develops an immunophenotype score to distinguish these individuals from controls.

Granzyme K drives a newly-intentified pathway of complement activation

This study identifies granzyme K as a driver of a novel complement activation pathway independent of classical, lectin, or alternative pathways.

Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles

The paper develops SCENT, a method to create cell-type-specific enhancer-gene maps from single-cell multimodal data, identifying causal variants and genes for diseases.

Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

The paper maps cell-type-specific eQTLs for HLA genes across multiple tissues and identifies dynamic regulation of HLA-DQ genes in immune cells.

Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritis

The paper deconstructs RA synovium using single-cell data to identify six cell type abundance phenotypes associated with distinct inflammatory states.