Quantifying Y chromosome loss in primary and metastatic prostate cancer by chromosome painting.

Somatic Y chromosome loss in hematopoietic cells is associated with higher mortality in men. However, the status of the Y chromosome in cancer tissue is not fully known due to technical limitations, such as difficulties in labelling and sequencing DNA from the Y chromosome. We have developed a system to quantify Y chromosome gain or loss in patient-derived prostate cancer organoids. Using our system, we observed Y chromosome loss in 4 of the 13 (31%) patient-derived metastatic castration-resistant prostate cancer (mCRPC) organoids; interestingly, loss of Yq (long arm of the Y chromosome) was seen in 38% of patient-derived organoids. Additionally, potential associations were observed between mCRPC and Y chromosome nullisomy. The prevalence of Y chromosome loss was similar in primary and metastatic tissue, suggesting that Y chromosome loss is an early event in prostate cancer evolution and may not a result of drug resistance or organoid derivation. This study reports quantification of Y chromosome loss and gain in primary and metastatic prostate cancer tissue and lays the groundwork for further studies investigating the clinical relevance of Y chromosome loss or gain in mCRPC

Prostate cancer organoid demonstrating no Y loss XY paint of organoids demonstrating no Y loss.

Prostate cancer organoid demonstrating no Y loss XY paint of organoids demonstrating no Y loss.</p

Characteristics of the Y chromosome in primary prostate cancer samples from patients using Mitelman’s Database.

(A) Y chromosome status in primary prostate cancer samples. (B) Y chromosome heterogeneity in primary prostate adenocarcinoma samples. Chi-square test reported significance.</p

Characteristics of patient-derived prostate cancer organoids.

(A) Percentage of organoids with loss of the chromosome Y (left) and Yq (right). (B) Doubling times of organoids. (C) Breakdown of organoids, stratified by type of prostate cancer tissue used for patient-derived organoid development and Y chromosome status. Chr, chromosome; CRPC, castration-resistant prostate cancer.</p

Characteristics of patient-derived metastatic prostate cancer organoids labelled with the XY paint FISH probes.

Characteristics of patient-derived metastatic prostate cancer organoids labelled with the XY paint FISH probes.</p

Prostate cancer organoid demonstrating Y loss XY paint of organoid demonstrating complete Y loss.

Prostate cancer organoid demonstrating Y loss XY paint of organoid demonstrating complete Y loss.</p

Prostate cancer organoid demonstrating partial Y loss XY paint of organoid demonstrating Y loss in some cells and no Y loss in others.

Prostate cancer organoid demonstrating partial Y loss XY paint of organoid demonstrating Y loss in some cells and no Y loss in others.</p

Y chromosome paint FISH probe design and validation.

(A) FISH probe design. (B) XY paint probe validation in prostate cancer cell lines, LNCaP (left) and LAPC4 (negative control; right). Cen X, centromere X; FISH, fluorescence in situ hybridization.</p

The Impact of PIK3R1 Mutations and Insulin–PI3K–Glycolytic Pathway Regulation in Prostate Cancer

Abstract Purpose: Oncogenic alterations of the PI3K/AKT pathway occur in &amp;gt;40% of patients with metastatic castration-resistant prostate cancer, predominantly via PTEN loss. The significance of other PI3K pathway components in prostate cancer is largely unknown. Experimental Design: Patients in this study underwent tumor sequencing using the MSK-IMPACT clinical assay to capture single-nucleotide variants, insertions, and deletions; copy-number alterations; and structural rearrangements, or were profiled through The Cancer Genome Atlas. The association between PIK3R1 alteration/expression and survival was evaluated using univariable and multivariable Cox proportional-hazards regression models. We used the siRNA-based knockdown of PIK3R1 for functional studies. FDG-PET/CT examinations were performed with a hybrid positron emission tomography (PET)/CT scanner for some prostate cancer patients in the MSK-IMPACT cohort. Results: Analyzing 1,417 human prostate cancers, we found a significant enrichment of PIK3R1 alterations in metastatic cancers compared with primary cancers. PIK3R1 alterations or reduced mRNA expression tended to be associated with worse clinical outcomes in prostate cancer, particularly in primary disease, as well as in breast, gastric, and several other cancers. In prostate cancer cell lines, PIK3R1 knockdown resulted in increased cell proliferation and AKT activity, including insulin-stimulated AKT activity. In cell lines and organoids, PIK3R1 loss/mutation was associated with increased sensitivity to AKT inhibitors. PIK3R1-altered patient prostate tumors had increased uptake of the glucose analogue 18F-fluorodeoxyglucose in PET imaging, suggesting increased glycolysis. Conclusions: Our findings describe a novel genomic feature in metastatic prostate cancer and suggest that PIK3R1 alteration may be a key event for insulin–PI3K–glycolytic pathway regulation in prostate cancer. </jats:sec