Analysis of BRCA2 Copy Number Loss and Genomic Instability in Circulating Tumor Cells from Patients with Metastatic Castration-resistant Prostate Cancer

Single circulating tumor cell sequencing based on improved high-porosity membranes and nanoporous microchambers

Circulating tumor cells (CTCs) are crucial for understanding tumor heterogeneity and progression. Despite extensive research over the years, most studies have focused on CTCs counting, with fewer efforts directed toward single-cell sequencing (SCS) of CTCs. In this study, we developed two novel nanodevices---a high-porosity ultrathin filter membrane and a nanowell chip--- to isolate single CTCs. Automated scanning and single-cell picking systems were employed to locate and isolate individual CTCs, enabling the establishment of an efficient and automated workflow for single CTC sequencing using filter-based systems. We conducted an in-depth comparison to evaluate the effects of different filter membranes and cell adhesion types on genomic integrity, cell viability, sequencing coverage, and depth. The results showed that the high-porosity filter membrane outperformed other photolithographic filters for SCS of CTCs. Validation using NCI-H358 cell lines and patient-derived CTCs demonstrated that this workflow could accurately and comprehensively detect gene mutations, amplifications, and copy number variations (CNVs). CNV profiles of CTCs from patients with the same tumor type were highly consistent, while intra-patient CTCs revealed significant heterogeneity. Furthermore, we identified and overcame challenges related to cell adhesion to the filter membrane and the impact of cell viability on sequencing outcomes during CTC enrichment. This workflow offers new insights into the development of CTC-based approaches for exploring tumor progression, heterogeneity, and mechanisms of drug resistance.

Prognostic Value of PARP1 and PARP2 Copy Number Alterations in Prostate Cancer

PARP1/2 have overlapping yet nonredundant biological functions in DNA repair and androgen receptor-transcriptional regulation. Studies on PARP alterations in human tumors have yielded conflicting results. In prostate cancer (PCa), PARP1/2 protein overexpression has been related to androgen deprivation therapy resistance, biochemical recurrence, and progression to metastases. PARP inhibitors have been approved for treating metastatic castration-resistant PCa with homologous recombination repair gene mutations. However, the significance of PARP1/2 genomic alterations is not fully studied. We aimed to analyze PARP1/2 alterations in PCa, assess their value as prognostic markers, and explore their relevance for potential therapeutic stratification. PARP1/2 copy number status was evaluated in 121 PCa primary tumors using real-time PCR. In 29 of them, a regional pelvic lymph node involvement was also analyzed. BRCA1/2 somatic mutations were analyzed in 24 PCa cases. Relationship with clinicopathological features, progression to metastases, and prostate-specific antigen recurrence was assessed. PARP1 loss and PARP2 gain were detected in 34.7% and 32.2% of primary tumors, respectively, with a high frequency of co-occurrence (P < .001). Both alterations were statistically associated with locally advanced disease at the time of diagnosis (P = .036; P = .006), metastatic dissemination (P = .014; P = .003), and other aggressive clinicopathological characteristics (such as the presence of Gleason pattern 5, high-grade, and high-stage). Cases with exclusive PARP2 gain had the shortest time to prostate-specific antigen recurrence, whereas double wt patients displayed the best outcome (P = .007). In 29 paired primary tumors and regional pelvic lymph node involvement, PARP1 loss showed strong concordance (P = .001), whereas PARP2 gain did not (P = .411). In conclusion, loss of PARP1 and gain of PARP2 show strong co-occurrence and are associated with clinicopathological characteristics of aggressiveness. PARP2 alterations appear to have a particularly significant impact on disease prognosis. Furthermore, these data suggest that the analysis of PARP1/2 copy number status could be useful in predicting PCa outcomes. Its role in therapy warrants further evaluation.

Advances in metastatic prostate cancer circulating tumor cell enrichment technologies and clinical studies

Circulating tumor cells (CTCs) have emerged as a pivotal tool that enables molecular interrogation of patient tumor cells and association with clinical outcomes. In prostate cancer specifically, where tumor biopsies from patients with bone metastasis are extremely challenging, CTCs offer a viable and established source of tumor "biopsy". While the prognostic value of CTC enumeration in metastatic prostate cancer is established, there is a compelling need for molecular CTC characterization for effective patient stratification and disease management. The clinical utility of CTCs has been advanced by the evolution of enrichment technologies and their molecular characterization. Enrichment technologies have evolved from strictly EpCAM-based enrichment to antigen-agnostic enrichment, while their clinical utility has evolved from enumeration to advanced downstream analyses including CTC proteomics, transcriptomics and genomics. This chapter offers a comprehensive overview of recent advancements in CTC enrichment and analytical technologies while highlighting pivotal clinical studies in prostate cancer, that utilize CTCs to determine the molecular basis of clinical response and resistance, to assist in disease management and treatment customization.

Liquid biopsy to personalize treatment for metastatic prostate cancer

Liquid biopsy is an innovative approach that provides a more complete understanding of treatment response and prognosis in monitoring metastatic prostate cancer. It complements invasive tissue biopsy and involves the assessment of various biomarkers in body fluids such as blood, semen, and urine. Liquid biopsy analyzes circulating tumor cells, extracellular vesicles, circulating tumor DNA, and the secretome. This is particularly important given the heterogeneity of prostate cancer and the need for better prognostic biomarkers. Liquid biopsy can personalize the treatment of homonosensitive and castration-resistant metastatic prostate cancer by acting as a predictive and prognostic tool. This review discusses various biomarkers, assay techniques, and potential applications in daily clinical practice, highlighting the exciting possibilities that this emerging field holds for improving patient outcomes.

Feasibility of Next-generation Sequencing of Liquid Biopsy (Circulating Tumor DNA) Samples and Tumor Tissue from Patients with Metastatic Prostate Cancer in a Real-world Clinical Setting in Germany

BACKGROUND AND OBJECTIVE

With European Medicines Agency approval of PARP inhibitors in metastatic castration-resistant prostate cancer and ongoing trials in metastatic hormone-sensitive prostate cancer, detection of genetic alterations in BRCA1/2 and other homologous recombination repair genes has gained an important role. Our aim was to investigate the feasibility and comparability of comprehensive next-generation sequencing (NGS) of liquid biopsy (LB; circulating tumor DNA) and tumor tissue (TT) samples in a real-world clinical setting.

METHODS

The study cohort consisted of 50 patients with metastatic prostate cancer (mPC) who had TT NGS performed for BRCA1/2 alterations and consent for additional LB NGS. The Oncomine Comprehensive Assay v3 (Thermo Fisher Scientific, Waltham, MA, USA) was used for TT NGS. The Guardant360 83-gene assay (Guardant Health, Palo Alto, CA, USA) was used for LB NGS, including all types of somatic alterations, microsatellite instability, and blood tumor mutational burden. We calculated BRCA1/2 alteration rates and the negative percentage agreement (NPA) and positive percentage agreement (PPA) between TT and LB results.

KEY FINDINGS AND LIMITATIONS

TT NGS was successful in 44/50 patients (88%), with pathogenic BRCA1/2 alterations detected in four (9%). LB NGS was successful in all 50 patients (100%), with BRCA1/2 alterations detected in ten (20%). In a subgroup analysis for the 44 patients with successful TT NGS, NPA was 85% and PPA was 50%. The median time between TT sample collection and blood sampling for NGS was 132 wk (IQR 94-186). The limited sample size and differences in the time of NGS assessment are limitations.

CONCLUSIONS AND CLINICAL IMPLICATIONS

LB NGS resulted in a higher detection rate for BRCA1/2 alterations in comparison to conventional TT NGS (20% vs 9%). Ideally, BRCA1/2 testing should be based on both approaches to identify all patients with mPC eligible for PARP inhibitor therapy.

PATIENT SUMMARY

Our study shows that genetic tests for both tumor tissue and blood samples results in higher rates of detection of BRCA1/2 gene alterations in patients with metastatic prostate cancer.

Circulating Tumor Cells: How Far Have We Come with Mining These Seeds of Metastasis?

Circulating tumor cells (CTCs) are cancer cells that slough off from the tumor and circulate in the peripheral blood and lymphatic system as micro metastases that eventually results in macro metastases. Through a simple blood draw, sensitive CTC detection from clinical samples has proven to be a useful tool for determining the prognosis of cancer. Recent technological developments now make it possible to detect CTCs reliably and repeatedly from a simple and straightforward blood test. Multicenter trials to assess the clinical value of CTCs have demonstrated the prognostic value of these cancer cells. Studies on CTCs have filled huge knowledge gap in understanding the process of metastasis since their identification in the late 19th century. However, these rare cancer cells have not been regularly used to tailor precision medicine and or identify novel druggable targets. In this review, we have attempted to summarize the milestones of CTC-based research from the time of identification to molecular characterization. Additionally, the need for a paradigm shift in dissecting these seeds of metastasis and the possible future avenues to improve CTC-based discoveries are also discussed.

Development and validation of a circulating tumor cells-related signature focusing on biochemical recurrence and immunotherapy response in prostate cancer

Background

Studies have shown that the circulating tumor cells (CTCs) play a key role for invasion and formation of distant metastases in prostate cancer (PCa). However, few CTCs-related genes (CRGs) have been developed for biochemical recurrence (BCR) prediction and clinical applications of PCa patients.

Materials and methods

Bioinformatics analysis with public PCa datasets were used to investigate the relationship between the differentially expressed CRGs and BCR. Lasso-COX regression analysis was used to constructed and validated a CRGs-based BCR prediction signature for PCa. Single-cell data were used to validate the expression levels of signature genes in different cell types and then explored the cell-cell communication relationships. Finally, the expression levels of signature genes were verified and the CRGs involved in immunotherapy response were further identified.

Results

Thirteen CRGs were differentially expressed and closely associated with BCR in PCa. Then we constructed and validated a BCR prediction signature for PCa patients based on 3 differentially expressed CRGs (EMID1, SPP1 and UBE2C), and the signature was an independent factor to predict BCR for PCa. Single-cell data showed the specific expression patterns of the signature genes, while the SPP1 pathway plays an important role in cell-cell communication. Further analyses suggested UBE2C was highly expressed in BCR group and high expression of UBE2C had a better response for patients who received immunotherapy. Moreover, the expression levels of UBE2C in CTCs were higher than other cells and tissues, indicated that UBE2C may affect the BCR event of PCa patients through CTCs.

Conclusion

Our findings demonstrated that CRGs were significantly associated with BCR and immunotherapy efficacy in PCa and CRGs may influence the BCR event through CTCs.

OCT4‑positive circulating tumor cells may predict a poor prognosis in patients with metastatic castration‑resistant prostate cancer treated with abiraterone plus prednisone therapy

Octamer-binding transcription factor 4 (OCT4) and circulating tumor cells (CTCs) are key factors associated with tumor metastasis and drug resistance in cancer. The present prospective study aimed to investigate the prevalence of OCT4-positive (OCT4+) CTCs and the potential association with the clinical features and survival of patients with metastatic castration-resistant prostate cancer (mCRPC) treated with abiraterone + prednisone. In total, 70 patients with mCRPC treated with abiraterone + prednisone were enrolled in the present study and peripheral blood samples were collected prior to treatment initiation to determine CTC count via a Canpatrol system. RNA in situ hybridization was performed for OCT4+ CTC quantification. Lactate dehydrogenase (LDH) was detected by automatic biochemical analyzer (AU54000, OLYMPUS). Results demonstrated that 34 (48.6%), 21 (30.0%) and 15 (21.4%) patients harbored OCT4+ (CTC+/OCT4+) or OCT4-negative CTCs (CTC+/OCT4-) or were CTC-negative (CTC-), respectively. Notably, CTC+/OCT4+ occurrence was associated with visceral metastasis and high levels of LDH. In addition, radiographic progression-free survival [rPFS; median, 15.0, 95% confidence interval (CI), 9.6-20.4 vs. not reached vs. median, 29.5, 95% CI, 18.6-40.4 months; P=0.001] and overall survival (OS) were significantly decreased (median, 27.3, 95% CI, 20.1-34.5 vs. not reached vs. not reached; P=0.016) in CTC+/OCT4+ compared with CTC+/OCT4- and CTC- patients. Subsequently, the adjustment was performed by multivariate Cox regression models, which revealed that CTC+/OCT4+ (vs. CTC+/OCT4- or CTC-) was independently associated with decreased rPFS [hazard ratio (HR), 3.833; P<0.001] and OS (HR, 3.938; P=0.008). In conclusion, OCT4+ CTCs were highly prevalent in patients with mCRPC and associated with visceral metastasis and increased levels of LDH. Thus, the presence of OCT4+ CTCs may serve as an independent prognostic factor for patients with mCRPC treated with abiraterone + prednisone.

Recent Advances in Blood-Based Liquid Biopsy Approaches in Prostate Cancer

ABSTRACT

The advent of high-throughput technologies has enabled the analysis of minute amounts of tumor-derived material purified from body fluids, termed "liquid biopsies." Prostate cancer (PCa) management, like in many other cancer types, has benefited from liquid biopsies at several stages of the disease. Although initially describing circulating tumor cells in blood, the term "liquid biopsy" has come to more prominently include cell-free, circulating tumor DNA, as well as RNA, proteins, and other molecules. They provide tumor molecular information representing the entire, often-heterogeneous disease, relatively noninvasively and longitudinally. Blood has been the main liquid biopsy specimen in PCa, and urine has also proven beneficial. Technological advances have allowed clinical implementation of some liquid biopsies in PCa, in disease monitoring and precision oncology. This narrative review introduces the main types of blood-based PCa liquid biopsies focusing on advances in the past 5 years. Clinical adoption of liquid biopsies to detect and monitor the evolving PCa tumor biology promises to deepen our understanding of the disease and improve patient outcomes.