Cross-lineage anomaly detection of microRNA expression: a framework for deriving exploratory candidate biomarkers in sarcoma.
7 affiliations
- 1Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.
- 2Medical Faculty, Medical University of Warsaw, Warsaw, Poland.
- 3Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland.
- 4Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
- 5Institute of Biochemistry and Biophysics Polish Academy of Science, Warsaw, Poland.
- 6Department of Experimental Pharmacology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland.
- 7Outpatient Chemotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.
Abstract
Introduction
Sarcomas are rare, heterogeneous malignancies of mesenchymal origin whose diagnosis and molecular classification remain challenging. We introduced a oneclass anomaly detection framework to microRNA expression profiles to test whether sarcoma-associated miRNA features are distinguishable from those of epithelial, haematological, and neurological cancers and if these features carry any biological relevance.Methods
Candidate miRNAs meeting cross-lineage significance criteria were further evaluated through differential expression analysis against subtype-matched normal mesenchymal reference tissue, pathway enrichment, and survival analysis. A five-miRNA index ("Index 5"), derived by Fisher's linear discriminant analysis with leave-one-out cross-validation in a TCGA-SARC training cohort, was applied without refitting to an independent external cohort (GSE36982).Results
The five-miRNA index ("Index 5") achieved an AUC of 0.93 and, applied without refitting to an independent external cohort (GSE36982), an AUC of 0.97. After Benjamini-Hochberg correction, one candidate miRNA (miR-1305) remained significantly associated with overall survival.Discussion
These findings identify a computationally derived, externally tested candidate miRNA signature associated with sarcoma. While this study lacks experimental and clinical validation, the broader aim of this study was to come up with a framework that would assist and speedup the exploratory candidate biomarker discovery process in rare malignancies.
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BibTeX
@article{dey2026crosslineage,
title = {{Cross-lineage anomaly detection of microRNA expression: a framework for deriving exploratory candidate biomarkers in sarcoma.}},
author = {Mritunjoy Dey and Piotr Remiszewski and Ewelina Perdas and Paweł Golik and Jakub Piątkowski and Anna M Czarnecka},
journal = {Frontiers in genetics},
year = {2026},
month = oct,
doi = {10.3389/fgene.2026.1907450},
url = {https://europepmc.org/article/MED/42928931},
note = {CC BY},
}
RIS
TY - JOUR
TI - Cross-lineage anomaly detection of microRNA expression: a framework for deriving exploratory candidate biomarkers in sarcoma.
AU - Mritunjoy Dey
AU - Piotr Remiszewski
AU - Ewelina Perdas
AU - Paweł Golik
AU - Jakub Piątkowski
AU - Anna M Czarnecka
PY - 2026
DA - 2026/10/12
JO - Frontiers in genetics
DO - 10.3389/fgene.2026.1907450
UR - https://europepmc.org/article/MED/42928931
AB - Introduction Sarcomas are rare, heterogeneous malignancies of mesenchymal origin whose diagnosis and molecular classification remain challenging. We introduced a oneclass anomaly detection framework to microRNA expression profiles to test whether sarcoma-associated miRNA features are distinguishable from those of epithelial, haematological, and neurological cancers and if these features carry any biological relevance.Methods Candidate miRNAs meeting cross-lineage significance criteria were further evaluated through differential expression analysis against subtype-matched normal mesenchymal reference tissue, pathway enrichment, and survival analysis. A five-miRNA index ("Index 5"), derived by Fisher's linear discriminant analysis with leave-one-out cross-validation in a TCGA-SARC training cohort, was applied without refitting to an independent external cohort (GSE36982).Results The five-miRNA index ("Index 5") achieved an AUC of 0.93 and, applied without refitting to an independent external cohort (GSE36982), an AUC of 0.97. After Benjamini-Hochberg correction, one candidate miRNA (miR-1305) remained significantly associated with overall survival.Discussion These findings identify a computationally derived, externally tested candidate miRNA signature associated with sarcoma. While this study lacks experimental and clinical validation, the broader aim of this study was to come up with a framework that would assist and speedup the exploratory candidate biomarker discovery process in rare malignancies.
SN - 1664-8021
ER -