Omics · study · 2026
Rapid liquid biopsy assessment through gene profiling from the kidney biopsy transport medium: a technical validation and a proof-of-concept pilot study
Listed in NCBI GEO
Rapid diagnosis is pivotal in kidney disease for timely and precision therapy.
Description
Conventional microscopic and molecular assessments from biopsy tissues rely on extra sample processing, making same-day diagnosis impractical. Therefore, we introduce the biopsy transport medium (BTM), a byproduct of the biopsy tissue storage process that could serve as a source of biomarkers, accelerating the assessment workflow.
Biopsies from tumor-free nephrectomy tissues were used to create mimicked BTM, allowing optimization of RNA extraction procedure. RNA yield and integrity were then systematically evaluated prior to downstream analyses. Subsequently, gene expression analysis was performed through multiple techniques: qPCR, RNA sequencing, and NanoString nCounter system.
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The results showed that storage time (the duration a biopsy is stored in BTM), ranging from 0.5 to 24 hours, did not significantly affect RNA quality and yield. The transcriptomic signals detected in biopsy tissues are largely recapitulated in the corresponding BTM samples. The differential gene expression analysis based on BTM identified rejection-associated profiles, which are aligned with Banff lesion scores.
This study confirms BTM’s ability to provide transcriptomic information relevant to the state of the kidney and supports BTM’s potential for same-day molecular diagnosis, especially with tailored qPCR panels for rapid, targeted analysis.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE308nnn/GSE308751 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE308751 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1332652 ncbi.nlm.nih.gov/bioproject/PRJNA1332652 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- Disease 75% · Genetics 68% · RNA sequencing 75% · Sequencing 75%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE308751 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:disease | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].anzsrc:group:3105 | enrichment · NCBI GEO | taxonomy-embedding@1.1.0 | title+keywords+description (68%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |