Biology subjects

Barahona, P.

Publications and source records attributed to Barahona, P..

3 recordsLinked to original sources

bioRxiv2025

Single-cell RNA-sequencing of cerebral spinal fluid identifies circulating tumour cells in children with brain cancer

Paediatric central nervous system (CNS) tumours are the leading cause of cancer-related death in children, yet disease monitoring remains challenging. Conventional approaches, including imaging and cytology, lack sensitivity, delaying intervention. Liquid biopsy offers a minimally invasive alternative, but the utility of circulating tumour cells (CTCs) in paediatric CNS tumours as biomarkers is poorly defined. We developed a CTC detection and characterisation workflow from cerebrospinal fluid (CSF) utilising single-cell RNA-sequencing (scRNA-seq) and applied this to ten CNS tumour subtypes in 16 patients. CTCs were identified in all cases, with higher burdens in pineoblastoma, medulloblastoma and atypical teratoid rhabdoid tumours. Longitudinal profiling revealed CTC dynamics correlated with clinical disease course and anticipated relapse. Critically, scRNA-seq uncovered a sub-clonal canonical driver alteration at diagnosis that only became detectable by bulk RNA-seq at progression, underscoring its potential to resolve clonal dynamics. This workflow enables real-time molecular profiling, offering a transformative strategy for disease monitoring and personalised therapy in paediatric brain tumours.

cancer biology↗

bioRxiv2025

Expanding the utility of transcriptome analysis for mutation detection in high-risk childhood precision oncology

In precision oncology, whole transcriptome sequencing (RNA-seq) excels at identifying oncogenic fusions. Here, using a cohort of 477 high-risk paediatric tumours, we demonstrate that RNA-seq can identify all mutation classes found previously using whole genome sequencing (WGS) and provides additional functional insights into their pathogenicity. By incorporating reference-guided fusion, and reference-free structural variant (SV) detection algorithms with RNA abundance assessment, RNA-seq identified 96% of SVs and resolved 33 complex SVs that WGS failed to identify. Furthermore, RNA-seq identified 92% of all single nucleotide variants and small insertions and deletions. Importantly RNA-seq informed the pathogenicity assessment in 22% of variants through identification of allele specific expression or the functional consequence of splice-altering variants. The utility of RNA-seq extends beyond fusion identification to the interpretation of mutation pathogenicity and the discovery of important mutations that would otherwise go undetected. We propose that RNA-seq is an indispensable companion to WGS in precision medicine.

genomics↗

bioRxiv2023

Comprehensive multi-platform tyrosine kinase profiling reveals novel actionable FGFR aberrations across pediatric and AYA sarcomas

No targeted agents are approved for pediatric sarcomas. Tyrosine kinase (TK) inhibitors represent attractive therapeutic candidates, however, beyond rare TK-activating fusions or mutations, predictive biomarkers are lacking. RNA overexpression of TKs is more commonly observed in pediatric sarcomas, however, an unresolved question is when upregulated TK expression is associated with kinase activation and signaling dependence. We explored the TK molecular landscape of 107 sarcoma patients from the ZERO Childhood Cancer precision medicine program using whole genomic and transcriptomic sequencing. Phosphoproteomic analyses of tyrosine phosphorylation (pY) and functional in vitro and in vivo assays were also performed in cell lines and patient-derived xenografts (PDXs). Our integrated analysis shows that although novel genomic driver lesions are rare, they are present and therapeutically actionable in selected patients as exemplified by a novel LSM1-FGFR1 fusion identified in an osteosarcoma patient. We further show that in certain contexts, TK expression data can be used to indicate TK pathway activity and predict TK-inhibitor sensitivity. We exemplify the utility of FGFR-inhibitors in PAX3-FOXO1 fusion-positive rhabdomyosarcomas (FP-RMS) mediated by high FGFR4 and FGF8 RNA expression levels, and overt activation of FGFR4 (FGFR4_pY). We demonstrate marked tumor growth inhibition in all FP-RMS PDXs treated with single agent FGF401 (FGFR4-specific inhibitor) and single agent lenvatinib (multi-kinase FGFR-inhibitor). Clinical benefit of lenvatinib in a relapsed metastatic FP-RMS patient further exemplifies that FGFR-inhibitors deserve additional investigation in FP-RMS patients. Statement of significanceOur multi-omic interrogation of sarcomas in the ZERO Childhood Cancer program illustrates how an RNA-expression biomarker signature (FGFR4+/FGF8+) in association with FGFR4 activation identifies that PAX3-FOXO1-positive rhabdomyosarcoma patients could benefit from FGFR-inhibitors.

cancer biology↗