GEO series
Integrated bulk and spatial transcriptomic analysis identifies progression-associated molecular signatures in biopsy-proven hypertensive nephropathy [RNA-seq]
GSE339456
Homo sapiens
Expression profiling by high throughput sequencing
35 samples
Submitted 2026/07/22
Platform GPL24676
Summary
Hypertensive nephropathy (HN) is a leading cause of chronic kidney disease (CKD), but molecular mechanisms underlying disease progression remain poorly understood. We aimed to identify transcriptomic signatures associated with disease progression and to localize these signatures within renal architectures. Patients with biopsy-proven HN were selected from the Norwegian Kidney Biopsy Registry and stratified after ≥5 years of follow-up into early stable (ES), early progressor (EP), late stable (LS) and late progressor (LP) based on baseline kidney function and annual eGFR decline. Bulk transcriptomic profiling was performed in a discovery cohort and validated in an independent cohort using nCounter profiling. Spatial transcriptomics was applied to map progression-associated signatures to nephron compartments. Bulk RNA sequencing identified 415 differentially expressed genes (DEGs) between ES and EP, and 692 between LS and LP samples. ES was enriched in circadian rhythm pathways, with reduced NR1D1 and NR1D2 expression in EP. LP was associated with metabolic reprogramming including glutathione, retinol and amino acid metabolism. Random forest modelling identified NR1D1 gene expression as a key classifier, validated in an independent cohort. Spatial transcriptomics revealed nephron segment-specific expression patterns, including a proximal tubule cluster enriched in ferroptosis in LP. Comparative nephron-segment analyses across groups revealed progression-associated biomarkers, including CHGA, CCN2 and SFRP2 in glomeruli, and APOE in proximal tubules. HN progression appears to involve stage-specific and compartmentalized molecular programs. Integration of bulk and spatial transcriptomics identifies candidate biomarkers and pathways, potentially supporting innovative prognostic stratification and therapeutic strategies.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE339456_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 35 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1498894 and SRA study SRP720251. Searching any of these in the dataset finder brings you back here.
Study design
10 × FFPE, EarlyStable,n vs 10 × FFPE, EarlyProgressive,n vs 8 × FFPE, LateProgressive,n vs 7 × FFPE, LateStable,n
Supports a between-group comparison across 35 samples.
4 replicated groups read from 35 sample titles; they account for 35 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9895924 FFPE, EarlyStable,nr20
- GSM9895925 FFPE, EarlyStable,nr22
- GSM9895926 FFPE, EarlyStable,nr24
- GSM9895927 FFPE, EarlyStable,nr31
- GSM9895928 FFPE, EarlyStable,nr32
- GSM9895929 FFPE, EarlyStable,nr33
- GSM9895930 FFPE, EarlyStable,nr39
- GSM9895931 FFPE, EarlyStable,nr76
- GSM9895932 FFPE, EarlyStable,nr79
- GSM9895933 FFPE, EarlyStable,nr80
- GSM9895934 FFPE, EarlyProgressive,nr43
- GSM9895935 FFPE, EarlyProgressive,nr45
- GSM9895936 FFPE, EarlyProgressive,nr69
- GSM9895937 FFPE, EarlyProgressive,nr75
- GSM9895938 FFPE, EarlyProgressive,nr81
- GSM9895939 FFPE, EarlyProgressive,nr90
- GSM9895940 FFPE, EarlyProgressive,nr94
- GSM9895941 FFPE, EarlyProgressive,nr98
- GSM9895942 FFPE, EarlyProgressive,nr111
- GSM9895943 FFPE, EarlyProgressive,nr122
- GSM9895944 FFPE, LateStable,nr84
- GSM9895945 FFPE, LateStable,nr85
- GSM9895946 FFPE, LateStable,nr91
- GSM9895947 FFPE, LateStable,nr107
- GSM9895948 FFPE, LateStable,nr108
- GSM9895949 FFPE, LateStable,nr109
- GSM9895950 FFPE, LateStable,nr112
- GSM9895951 FFPE, LateProgressive,nr67
- GSM9895952 FFPE, LateProgressive,nr68
- GSM9895953 FFPE, LateProgressive,nr70
- GSM9895954 FFPE, LateProgressive,nr72
- GSM9895955 FFPE, LateProgressive,nr73
- GSM9895956 FFPE, LateProgressive,nr92
- GSM9895957 FFPE, LateProgressive,nr102
- GSM9895958 FFPE, LateProgressive,nr105
Similar datasets
- GSE319969 Spatial and Bulk Transcriptomic Profiling Defines the Molecular Evolution of Cutaneous Squamous Cell Carcinoma and Reveals Stage-Specific Biomarkers of Clinical Relevance [RNA-Seq] 24 samples
- GSE317207 Transcriptomic profiling of human hepatocellular carcinoma biopsy samples using bulk RNA-seq 33 samples
- GSE278688 Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC [scRNA-Seq] 29 samples
- GSE272409 Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[scRNA-seq] 13 samples
- GSE342462 Integrated transcriptomic and bioelectrical profiling of stem-like cellular states in a colorectal cancer using SdFFF and UHF-DEP 12 samples
- GSE342455 Transcriptomic profiling of tumor-associated macrophages following pharmacological SYK inhibition in a human breast cancer co-culture model 6 samples
- GSE330697 Delayed molecular aging, preservation of energy metabolism and enhanced exercise response in exercise-trained human muscle 93 samples
- GSE202379 Single Nuclei RNA-Seq to map progression of non-alcoholic fatty liver disease (NAFLD) in patients II 59 samples
Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.