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Transcriptomic profiling of organoids derived from malignant effusions uncovers lncRNA MEG3 and target genes potentially involved in platinum resistance in serous ovarian carcinoma - 11/11/25

Doi : 10.1016/j.biopha.2025.118668 
Naiade Calanca a, b , Claudia Aparecida Rainho b , Debora Kazumi Maeda a, b , Luiza Côrtes a, c , Rolando André Rios Villacis a, d , Daniela Bizinelli e , Hellen Kuasne f , Mads Malik Aagaard a , Lars Ulrik Fokdal g, h , Karina Dahl Steffensen g, h , Lars Henrik Jensen g, h, 1 , Silvia Regina Rogatto a, c, h, ⁎, 1
a Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle 7100, Denmark 
b Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP 18618-689, Brazil 
c Botucatu Medical School Hospital, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil 
d Department of Genetics and Morphology, University of Brasília (UnB), Brasília, DF 70910-900, Brazil 
e Interunit Graduate Program in Bioinformatics, Institute of Chemistry, University of São Paulo (USP), São Paulo, SP 05508-090, Brazil 
f Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada 
g Department of Oncology, University Hospital of Southern Denmark, Vejle 7100, Denmark 
h Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark 

⁎ Correspondence to: Botucatu Medical School Hospital, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil. Botucatu Medical School Hospital, São Paulo State University (UNESP) Botucatu SP 18618-687 Brazil

Abstract

Serous ovarian carcinoma (SOC) is an aggressive disease, characterized by advanced-stage tumors that are often associated with relapse and poor outcomes. Although platinum-based chemotherapy is a cornerstone of the treatment, most of the relapsed tumors become resistant to these agents. We explored organoids derived from SOC malignant effusions to identify targets actionable by epigenetic drugs (epi-drugs) to enhance platinum response. Tumor-derived organoids (TDOs) were established using malignant effusions of SOC patients. Histological and transcriptomic (RNA-Seq) characterization (18 TDOs versus 7 normal ovarian samples) was performed, followed by cross-validation with external RNA-Seq datasets (337 SOC samples, 4 TDOs, and 180 normal tissues). Predicted interactions between long noncoding RNAs (lncRNAs) and epigenetic effectors were investigated. We selected the epi-drugs decitabine and tazemetostat, whose targets were overexpressed in SOC, to treat carboplatin-resistant SOC cell lines and TDOs. Subsequently, these models were challenged with carboplatin. Twelve lncRNAs and 168 protein-coding genes differentially expressed were involved in epigenetic regulation. Abnormal expression levels of lncRNA MEG3 and epigenetic effectors DNMT3B and EZH2 were confirmed in external datasets. Increased carboplatin sensitivity and MEG3 upregulation were observed after treating the cell lines and TDOs with epi-drugs. Altogether, our findings provide novel insights into using organoids derived from malignant effusions as preclinical models and hint at potential targets for overcoming platinum resistance in SOC.

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Graphical Abstract




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Highlights

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Organoids were successfully derived from serous ovarian carcinoma effusions.
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LncRNAs involved in epigenetic regulation showed altered expression in organoids.
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Increased levels of lncRNA MEG3 were noted after in vitro treatment with epi-drugs.
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Organoids pretreated with epi-drugs showed increased sensitivity to carboplatin.

Il testo completo di questo articolo è disponibile in PDF.

Keywords : Serous ovarian carcinoma, Tumor-derived organoids, Long noncoding RNAs, Epigenetic drugs, MEG3


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© 2025  The Authors. Pubblicato da Elsevier Masson SAS. Tutti i diritti riservati.
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