Plasma tumour DNA dynamics and circulating subclones patterns in patients with metastatic castration-resistant prostate cancer (mCRPC) treated with cabazitaxel in a prospective biomarker trial (NCT03381326).
Authors: Brighi Nicole , Wetterskog Daniel , Gurioli Giorgia , Orlando Francesco , Conteduca Vincenza , Vainauskas Osvaldas , Giunta Emilio Francesco , Bleve Sara , Casadei Chiara , Cremaschi Paolo , Basso Umberto , Pierantoni Francesco , Fornarini Giuseppe , Mosca Alessandra , Nicodemo Maurizio , Banna Giuseppe Luigi , Ulivi Paola , Demichelis Francesca , De Giorgi Ugo , Attard Gerhardt 
Published: June 2024

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Background: Liquid biopsies enable non-invasive detection of circulating biomarkers for disease monitoring and treatment resistance interrogation. We aimed to study circulating tumour DNA (ctDNA) and its early changes during treatment to identify biomarkers of resistance to cabazitaxel in mCRPC patients (pts). We also designed and validated a Circulating Subclonality Index (CSI) to capture subclonal events in plasma and correlate with outcomes. Methods: mCRPC pts (N=104) candidate for cabazitaxel were enrolled in a prospective biomarker multicentre trial. Plasma was collected at baseline (BL), prior to cycle 3/4 (C3) and at progression (PD) and analyzed using a bespoke prostate cancer capture panel (PCF_SELECT [Orlando et al, NAR Cancer 2022]). ctDNA fraction was calculated using allele specific quantitation of hemi-deletions. We optimised PCF_SELECT to use non-integer copy numbers (CN) as a sub-clonality measure of circulating clones. CSI was defined as the proportion of CN-altered genes (derived from CLONETv2 output) where the CN value of either allele had a distance >0.1 from the nearest integer value. Primary outcome measures were overall survival (OS) and progression-free survival (PFS). Medians and [95% CI] are reported. Results: Early ctDNA dynamics (change from BL to C3) strongly associated with outcomes: pts with increasing ctDNA levels had the shortest OS (7.5 months (mo), HR 4.6 [2.1-10.3], p<0.0001) compared to pts with decreasing ctDNA (15.7 mo, HR 2.4 [1.3-4.4], p=0.0015) and pts with no detectable tumour at either timepoint (29.9 mo). Pts with early ctDNA increase had a higher risk of PD (OR 14.1 [3.5-44.5], p<0.0001), and ctDNA dynamics were independently related to OS (HR 6.6 [3.5-12.6], p<0.0001] and PFS (HR 7.6 [3.8-15.2], p<0.0001). Median CSI proved to be a robust statistical value for outcomes. Pts with lower BL CSI had shorter OS (7.8 [4.0-10.0] vs 12.1 [9.7-15.7] mo, HR 2.0 [1.1-3.5], p=0.011) and PFS (2.7 [2.3-4.4] vs 5.6 [4.6-7.3] mo, HR 1.9 [1.1-3.4], p=0.013) compared to those with higher CSI. BL CSI was independently related to PFS (HR 2.1 [1.2-3.7], p=0.014). A significant CSI decrease was observed upon cabazitaxel PD compared to BL (p=0.003). Conclusions: Early ctDNA dynamics identified pts with worse outcomes during cabazitaxel. Lower subclonality, representative of fewer circulating subclones, was observed at PD and associated with shorter PFS. This suggests that a treatment-resistant clone, associated with a lower index of subclonality, dominates in ctDNA. Clinical trial information: NCT03381326 .