Spatial transcriptomics reveals clonal relationships between intraductal carcinoma and adjacent invasive prostate cancer

AIMS: The pathogenesis of intraductal carcinoma (IDC) is still controversial. Contrary to current opinion, where IDC represents retrograde spread of invasive prostate cancer (PCa), we recently presented an alternative, unifying hypothesis named 'Repetitive Invasion, Precursor Progression' (RIPP). Little is known about genomic alterations in high-grade Prostatic Intraepithelial Neoplasia (HGPIN), IDC and adjacent invasive PCa. Our objective was to clarify the mutual clonal relationships among HGPIN, IDC, and adjacent PCa using spatial transcriptomics. METHODS AND RESULTS: Regions of interest containing HGPIN, IDC and adjacent invasive PCa were selected from six Gleason score 3 + 4 = 7 radical prostatectomy specimens. Spatial transcriptomic profiling and library preparation were executed according to the Visium workflow. Pathologist-guided manual annotations were utilized to delineate regions of interest for the integrated analysis of chromosomal copy number variants (CNV) and spatiotemporal trajectories. Adjacent HGPIN, IDC and invasive PCa shared common CNV signatures across all samples, with various subclonal events. Unsupervised clonal analysis revealed that across three samples, the adjacent invasive subclone had acquired additional genomic alterations. In two samples, HGPIN, IDC and adjacent invasive PCa had identical CNVs. Finally, in one sample, IDC had additional CNVs compared with HGPIN and invasive glands. Supervised trajectory analysis consistently placed adjacent invasive PCa as the final step in the trajectory, after HGPIN and/or IDC. CONCLUSIONS: Spatial transcriptomics revealed strong clonal relationships among adjacent HGPIN, IDC and invasive PCa. Supervised trajectory analysis did not support retrograde spread in this limited number of samples, while unsupervised analysis revealed a complex mutual relationship among HGPIN, IDC and adjacent PCa.