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Spatial profiling of temporal artery biopsies from patients with giant cell arteritis using NanoString GeoMx Whole Transcriptome Atlas

ABSTRACT: This study used the NanoString GeoMx Digital Spatial Profiler (DSP) platform to spatially profile gene expression in temporal artery biopsy tissue from patients with giant cell arteritis (GCA), taken at the time of diagnosis. Tissue sections were hybridised with the Human Whole Transcriptome Atlas panel and segmented to isolate immune-enriched (CD45⁺) and full-tissue regions across anatomical layers (adventitia, media, intima). Gene expression data were stratified according to clinical trajectory, comparing patients who later achieved sustained remission (SR) under glucocorticoid monotherapy with those who relapsed or failed to remit (non-remission, NR). Non-GCA controls (C) were also included for comparisons. Data from two sequencing batches were merged and normalised using DESeq2 for downstream analysis. This submission includes: (1) unnormalised digital counts and segment metadata; (2) normalised processed data and associated metadata; and (3) clinical information to aid re-analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE299070 | GEO | 2025/10/20

REPOSITORIES: GEO

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Methylome and transcriptome profiling of giant cell arteritis monocytes reveals novel pathways involved in disease pathogenesis and molecular response to glucocorticoids [array]

Project description:Giant cell arteritis (GCA) is a complex systemic vasculitis mediated by the interplay between both genetic and epigenetic factors. Monocytes are crucial players of the inflammation occurring in GCA. Therefore, characterization of the monocyte methylome and transcriptome in GCA would be helpful to better understand disease pathogenesis. We performed an integrated epigenome- and transcriptome-wide association study in CD14+ monocytes from 82 patients with GCA, cross-sectionally classified into three different clinical status (active, in remission with or without glucocorticoid (GC)-treatment), and 31 healthy controls. We identified a global methylation and gene expression dysregulation in GCA monocytes. Specifically, monocytes from active patients showed a more pro-inflammatory phenotype compared with healthy controls and patients in remission. In addition to inflammatory pathways known to be involved in active GCA, such as response to interleukin (IL)-6 and IL-1, we identified a significant number of chemokines, such as CCRL2, and integrins. Furthermore, monocytes from patients in remission with treatment showed downregulation of genes involved in inflammatory processes as well as overexpression of GC receptor-target genes. Finally, we identified changes in DNA methylation correlating with alterations in expression levels of genes with a potential role in GCA pathogenesis, such as ITGA7 and CD63, as well as genes mediating the molecular response to GC, including FKBP5, ETS2, ZBTB16, and ADAMTS2. Our results revealed profound alterations in the methylation and transcriptomic profiles of monocytes from GCA patients, uncovering novel genes and pathways involved in GCA pathogenesis and in the molecular response to GC treatment.

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Methylome and transcriptome profiling of giant cell arteritis monocytes reveals novel pathways involved in disease pathogenesis and molecular response to glucocorticoids [RNA-Seq]

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CTLA-4 pathway is instrumental in Giant Cell Arteritis

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2023-07-03 | GSE236367 | GEO

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2016-04-22 | GSE64486 | GEO

Targeted RNA sequencing of archived giant cell arteritis temporal artery biopsies reveals viral signatures

Project description:Formalin-fixed, paraffin-embedded (FFPE) temporal artery sections from GCA subjects were stained for VZV antigen. Samples testing positive (VZV+) and negative (VZV-) from both GCA and control subjects without GCA were analyzed by targeted RNA sequencing of the whole-human transcriptome (BioSpyder TempO-Seq™).

2021-05-20 | GSE174694 | GEO

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