Omics · study · 2026
Multi-platform genomic analysis of matched well- and dedifferentiated liposarcomas identify novel risk and progression determinants [aCGH]
Listed in NCBI GEO
To define mechanisms that regulate biological behavior in well- and dedifferentiated liposarcoma (WD/DDLS) subsets, we describe an integrative analysis of DNA sequence, copy number and gene expression in 9 paired WDLS and DDLS samples with validation cohorts and in vitro studies.
Description
Amplification of 12q13-15 was common to all WDLS; 6q23-25 amplifications were observed 18% of WDLS and were associated with increased TAB2 and higher local recurrence risk versus non-6q-amplified WDLS.
TAB2 knockdown decreased MDM2 protein expression and induced markers of cellular senescence in 6q23-25-amplified WDLS cells but not in non-amplified WDLS of amplified DDLS cells. Amplification of 6q23-25 was not associated with DDLS recurrence risk or progression from WDLS to DDLS. Instead, pathogenic ATRX mutations, recurrent losses in 13q and gains in 8q12-21 accompanied dedifferentiation.
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Downregulation of the 13q-encoded genes MYCBP2 and IRS2 was observed in DDLS versus WDLS; in vitro, these genes were essential for WDLS cell differentiation. Taken together, this study defines a copy number-driven model of liposarcoma initiation, progression, and differentiation. Array comparative genomic hybridization (aCGH) was performed using Agilent 244K or 1M arrays and analyzed using the RAE pipeline as previously reported (Barretina J, et. al, Nat Genet. 2010;42(8):715-21, PMC2911503 and Crago AM, et. al, Clin Cancer Res. 2012;18(5):1334-40, PMC3294014)
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE336nnn/GSE336156 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE336156 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1480777 ncbi.nlm.nih.gov/bioproject/PRJNA1480777 ↗
project · from NCBI GEO
Topics
- Stated by source
- Genome variation profiling by genome tiling array · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- Bioinformatics and computational biology 74% · Cancer 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE336156 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].anzsrc:group:3102 | enrichment · NCBI GEO | taxonomy-embedding@1.1.0 | title+keywords+description (74%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:genome-variation-profiling-by-genome-tiling-array | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| 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 |