Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrated long-read transcriptomic profiling of peripheral blood from ankylosing spondylitis patients reveals regulatory shifts and core genes associated with programmed cell death

ABSTRACT: Ankylosing spondylitis (AS) is a chronic immune-mediated arthritis marked by persistent inflammation and progressive structural damage. Although dysregulation of programmed cell death (PCD) is increasingly recognized in AS pathogenesis, the full spectrum of transcript-level regulation remains unclear. Here, we employed Oxford Nanopore Technologies (ONT) long-read RNA sequencing to comprehensively profile peripheral blood transcriptomes from six AS patients and six matched healthy controls. Our analysis identified 1,088 differentially expressed genes (DEGs) and 1,812 differentially expressed transcripts (DETs), with upregulated transcripts enriched in apoptosis, autophagy, and transcriptional regulation. We further detected 50 transcripts with significant differential usage and 304 alternative splicing events affecting immune- and PCD-related genes, including FCGR2B, TLR2, and STAT5B. Integrative multi-omic analysis revealed 26 core genes, such as NAMPT, GATA2, and DDIT3, showing consistent dysregulation at gene, isoform, and splicing levels, highlighting convergent regulatory networks underlying immune imbalance and cell death in AS. These findings provide the first isoform-resolved transcriptomic landscape of PCD regulation in AS, revealing extensive regulatory complexity and novel core genes that may represent promising targets for future mechanistic and therapeutic studies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE299639 | GEO | 2025/06/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Differentially expressed genes and transcript isoforms in mouse NSCs expressing miR-128

2011-04-28 | GSE28889 | GEO

Differentially expressed genes and transcript isoforms in mouse NSCs expressing miR-128

Project description:We identify a brain-specific microRNA—miR-128—that represses Nonsense Mediated mRNA Decay (NMD) and thereby controls batteries of transcripts in neural cells. miR-128 represses NMD by targeting the RNA helicase UPF1 and the exon-junction complex core component MLN51. We employed exon arrays for this analysis, as this platform detects expression levels of individual exons and thus allows detection of not only differentially expressed transcripts (DETs), but also alternative isoform transcripts (AITs). The latter is particularly relevant to our study because alternative RNA processing events (e.g., RNA splicing, alternative promoter usage, and alternative polyadenylation-site usage) often place a translation termination codon in a premature context and thereby trigger NMD. Compare different expressed genes and transcript isoforms in mouse NSCs miR-128 positive vs miR-128 negative (Control). Mouse NSCs, that do not normally express miR-128, were nucleofected with either miR-128 (biological triplicates were analysed) or miR-Control (biological triplicates). RNA was extracted 72hrs later, and Exon Array was performed to identify target genes.

2011-04-28 | E-GEOD-28889 | biostudies-arrayexpress

Pseudo-albino or pigmented Solea senegalensis (Senegalese sole) anterior gut and dorsal skin transcriptomes (RNA-seq), raw sequence reads

Project description:Pseudo-albinism is a complex condition, caused by a multitude of factors and negatively affecting flatfish aquaculture. The majority of studies have targeted genes involved in pigmentation, the most notable change in these animals. In this study, a global transcriptome approach was taken to understand the underlying basis of Senegalese sole pseudo-albinism, using as targets two important innate immune barriers, the skin and intestine. RNA-seq transcriptome analysis identified 573 differentially expressed transcripts (DETs) between pseudo-albino and pigmented soles in the skin and/or the gut. DETs were mainly linked to pigment production, skin structure and regeneration, mucus production and smooth muscle contraction.

2019-12-31 | E-MTAB-7434 | biostudies-arrayexpress

CircCDYL association with hnRNPL modulates CDYL isoform switching in Breast Cancer cells

Project description:Circular RNAs (circRNAs) are covalently closed transcripts involved in the regulation of different cellular processes, and their dysregulation has been frequently observed in cancer. In this study, we investigated the role of circCDYL, a circRNA generated from the CDYL gene, in modulating alternative splicing (AS) and isoform switching in breast cancer cells. Analysis of circRNA profiles in breast cancer cells showed that circCDYL expression increased in estrogen receptor alpha (ERα)-downregulated cells, suggesting a potential link between circCDYL-mediated regulation and ERα signaling pathways. RNA-Sequencing analysis following circCDYL knock-down in MCF-7 cells revealed significant alterations in the splicing pattern, with over 2,900 splicing events significantly affected. Through RNA immunoprecipitation and RNA pull-down assays, we found evidence of an association between circCDYL and the splicing factor hnRNPL. To explore the consequences of this association, we performed AS and isoform switching analysis after circCDYL and hnRNPL silencing, revealing significant effects on AS and a weaker modulation of isoform switching events. Furthermore, we observed that circCDYL and hnRNPL modulated CDYL isoform expression, as confirmed by isoform-specific qRT-PCR analysis. Chromatin immunoprecipitation assays also indicated changes in chromatin marks at the CDYL locus upon knock-down of circCDYL and hnRNPL. These results suggested a possible association between circCDYL and hnRNPL, which contributed to the regulation of alternative splicing in breast cancer cells and may be involved in the modulation of isoform expression and chromatin dynamics of CDYL gene.

2025-04-18 | GSE295065 | GEO

RNA-seq dynamic transcriptomic pipeline

Project description:Purpose: Develop an analytical pipeline for dynamic RNA-seq experiments and highlight the importance of considering surgery effect in MI-induced models Methods: Mice have undergone surgery, hearts were harvested and RNA was extracted, sequenced and analyzed by DESeq2 R package. Differentially expressed transcripts were clustered by WGCNA and then analyzed to identify enriched biological processes and transcription factors. Results: Our pipeline enabled the detection of 1027 DETs. Enriched biological processes were mainly cell signilisation and inflammatory related. IL-6 was found as a key controller of the identified TFs and DETs. Immune cells were recruited to the myocardium later post surgery and some possessed phenotypic changes.

2019-04-13 | GSE127244 | GEO

single cell-RNA sequencing for Immune cells from mouse brain tumor post anti PD-1 treatment

Project description:To evaluate the influence of ablating Fcgr2b on anti-PD-1 treatment efficacy, we administered GL261 cells to both Fcgr2b knockout and wild-type (WT) mice, followed by treatment with anti-PD-1. Afterwards, we isolated immune cells from the brains of these mice for further analysis.

2024-11-06 | GSE262592 | GEO

Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn’s Disease

Project description:Background & Aims: Perianal fistulizing Crohn’s disease (PCD) is a common and debilitating complication with elusive pathophysiology. We examined biopsies from patients with PCD and related conditions using a multi-omics approach. Methods: Patients with PCD (n=24), CD without perianal disease (NPCD, n=10), and idiopathic perianal fistulas (IPF, or cryptoglandular fistulas, n=25) were recruited. Biopsies were taken from fistula tracts, fistula opening, and rectal mucosa during examination under anesthesia or colonoscopy. Single-cell RNA-sequencing (scRNA-seq), mass cytometry (CyTOF), spatial transcriptomics (ST), immunohistochemistry (IHC), and integrated analysis of published datasets were performed. Results: ScRNA-seq, CyTOF, and ST unraveled immune and non-immune cell compartments in PCD and IPF fistula tracts. PCD fistulas showed hyperactivated pathogenic pathways including interferon (IFN)G response, TNF signaling, and IL6-JAK-STAT3 in myeloid cells. Similarly, stromal cells from PCD fistulas exhibited elevated IFNG and TNF response, TNF signaling, and epithelial-mesenchymal transition (EMT). Further analysis revealed cellular modules associated with anti-TNF therapy in PCD patients. In addition to fistula tracts, intestinal cells from PCD patients also expressed greater levels of IFNG-responsive and EMT genes compared to CD patients without perianal disease. In addition, we showed that both fistula tracts and ileal mucosa from PCD patients harbored expanded IFNG+ Th17 cells, which expressed elevated inflammatory mediators. The findings were independently validated using ST and IHC. Conclusion: Multi-omics analysis revealed immune and nonimmune cell landscapes of PCD. and highlights the pathogenic role of hyperactivated IFNG signaling in both fistula tracts and luminal mucosa of patients with PCD. This study identified IFNG as a potential therapeutic target for PCD.

2025-06-17 | GSE277387 | GEO

Bulk RNA-sequencing of synovial macrophages (Fcgr2b-KO mice)

Project description:Bulk RNA-sequencing of three types of synovial macrophages in Fcgr2b-KO mice stimulated with or without immune complexes

2024-09-30 | GSE247476 | GEO

Pervasive 3'-UTR isoform switches during mouse oocyte maturation

Project description:Oocyte maturation is the foundation for developing healthy individuals of mammals. Upon germinal vesicle breakdown, oocyte meiosis resumes and the synthesis of new transcripts ceases. To quantitatively profile the transcriptomic dynamics after meiotic resumption throughout the oocyte maturation, we generated transcriptome sequencing data with individual mouse oocytes at three main developmental stages: germinal vesicle (GV), metaphase I (MI), and metaphase II (MII). When clustering the sequenced oocytes, results showed that isoform-level expression analysis outperformed gene-level analysis, indicating isoform expression provided extra information that was useful in distinguishing oocyte stages. Comparing transcriptomes of the oocytes at the GV stage and the MII stage, in addition to identification of differentially expressed genes (DEGs), we detected many differentially expressed transcripts (DETs), some of which came from genes that were not identified as DEGs. When breaking down the isoform-level changes into alternative RNA processing events, we found the main source of isoform composition changes was the alternative usage of polyadenylation sites. With detailed analysis focusing on the alternative usage of 3'-UTR isoforms, we identified, out of 3810 tested genes, 512 (13.7%) exhibiting significant switches of 3'-UTR isoforms during the process of moues oocyte maturation. Altogether, our data and analyses suggest the importance of examining isoform abundance changes during oocyte maturation, and further investigation of the pervasive 3'-UTR isoform switches in the transition may deepen our understanding on the molecular mechanisms underlying mammalian early development.

2021-10-05 | GSE178836 | GEO

Exon arrays from HeLa cells transfected with GFP-ZRANB2 vector

Project description:Human ZRANB2 mRNA is alternatively spliced to give two variants with different 3M-bM-^@M-^Y ends. Both isoforms are present in the nucleus of human cells. ZRANB2 binds to mRNA, as well as the essential splicing factors U170K and U2AF35, and the novel splicing component SFRS17A (formerly known as XE7). It has been shown to alter splicing patterns of Tra2M-NM-21 minigene primary transcripts in a dose-dependent manner. It is still unclear what role ZRANB2 plays in the regulation of alternative splicing. To determine the endogenous transcripts that are targeted by ZRANB2 at the genome wide level, we decided to perform exon microarray studies and analyzed the suitability of this method to examine splicing differences in human cells overexpressing a splicing factor. GFP-ZRANB2 construct containing isoform 2 (short form, SF) of ZRANB2 was used. This construct includes exon 1 through to alternative exon 10. Isoform 2 was chosen since it has been shown previously to affect alternative splicing of a Tra2M-NM-21 minigene. HeLa cells were transfected with GFP-ZRANB2, control vector GFP or were left untransfected. RNA was extracted using a Qiagen RNA extraction kit. Experiments were run in 5 replicates.

2012-12-15 | E-GEOD-32932 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data