HOXD8 hypermethylation as a fully sensitive and specific biomarker for biliary tract cancer detectable in tissue and bile samples
Eleonora Loi 1, Cesare Zavattari # 2, Alessandro Tommasi # 2, Loredana Moi # 1, Matteo Canale 3, Agnese Po 4, Claudia Sabato 5, Ana Florencia Vega-Benedetti 1, Pina Ziranu 6, Marco Puzzoni 6, Eleonora Lai 6, Luca Faloppi 7, María Rullán 8 9, Juan Carrascosa 8 9, Irene Amat 9 10, Jesús M Urman 8 9, Maria Arechederra 9 11, Carmen Berasain 9 11 12, Elisabetta Ferretti 5, Andrea Casadei-Gardini 13, Matías A Avila 9 11 12, Sergio Alonso # 14, Mario Scartozzi # 6, Patrizia Zavattari # 15
Background: Biliary tract cancers (BTC) are rare but highly aggressive tumours with poor prognosis, usually detected at advanced stages. Herein, we aimed at identifying BTC-specific DNA methylation alterations.
Methods: Study design included statistical power and sample size estimation. A genome-wide methylation study of an explorative cohort (50 BTC and ten matched non-tumoral tissue samples) has been performed. BTC-specific altered CpG islands were validated in over 180 samples (174 BTCs and 13 non-tumoral controls). The final biomarkers, selected by a machine-learning approach, were validated in independent tissue (18 BTCs, 14 matched non-tumoral samples) and bile (24 BTCs, five non-tumoral samples) replication series, using droplet digital PCR.
Results: We identified and successfully validated BTC-specific DNA methylation alterations in over 200 BTC samples. The two-biomarker panel, selected by an in-house algorithm, showed an AUC > 0.97. The best-performing biomarker (chr2:176993479-176995557), associated with HOXD8, a pivotal gene in cancer-related pathways, achieved 100% sensitivity and specificity in a new series of tissue and bile samples.
Conclusions: We identified a novel fully efficient BTC biomarker, associated with HOXD8 gene, detectable both in tissue and bile by a standardised assay ready-to-use in clinical trials also including samples from non-invasive matrices.