Influencing Best Practices for Genomic and Germline Testing in Urology.

INTRODUCTION: We evaluated germline and somatic testing practices and compared results from tissue and liquid biopsy specimens in a large community urology setting. METHODS: A retrospective analysis was performed on advanced prostate cancer patients from a single community practice between June 2016 and September 2021. Clinical data and sequencing results from tissue and liquid biopsy specimens were available for 389 patients. Genomic data were available for 81 tissues and 74 liquid biopsy specimens. Comparison of genomic findings included 81 tissues and 27 liquid biopsy specimens. The number of actionable biomarkers and patients screened and enrolled in clinical trials was assessed from germline and somatic testing. Frequency of pathogenically altered genes, alteration types, and biomarkers were assessed from tissue and liquid specimens. Alteration frequency was compared between specimen types for the top 25 altered genes. RESULTS: Clinically relevant alterations were found from germline and somatic testing in both tissue and liquid biopsy specimens. The frequency of microsatellite instability-high, tumor mutational burden-high, or alterations in homologous recombination repair genes was consistent with published findings. Concordance between tissue and liquid findings varied with low circulating tumor DNA. CONCLUSIONS: Germline and somatic testing is critical for treatment decisions and should be standard of care for community practices. Liquid biopsy is a viable alternative when circulating tumor DNA is high.

Clinical Utility of Liquid Biopsy to Identify Genomic Heterogeneity and Secondary Cancer Diagnoses: A Case Report.

Liquid biopsy is a valuable tool in advanced and metastatic cancers for detection of genomic alterations in tumors that facilitate personalized targeted therapy approaches. Analyzing circulating tumor DNA (ctDNA) using next-generation sequencing (NGS) provides an opportunity to detect tumor genomic changes during therapy and capture inter- and intra-heterogeneity of genomically divergent cancer cell evolution. Herein, we present a patient with metastatic castration-resistant prostate cancer, with progression to soft tissues, bone, and regional lymph nodes, who was treated with abiraterone plus prednisone, with excellent prostate-specific antigen response. At the time of progression, NGS analysis of ctDNA using the FoundationOne®Liquid test revealed a CHEK2 mutation and a BRAF V600E mutation, the latter being exceedingly rare in prostate cancer. At the time of biochemical recurrence, the patient was referred to hematology for evaluation of chronic but stable thrombocytopenia prior to initiating new systemic therapy. Results of a bone marrow biopsy were consistent with hairy-cell leukemia, where the BRAF V600E mutation is considered the disease-defining mutation detectable in nearly all cases at diagnosis. In this case, liquid biopsy served as a noninvasive, highly sensitive approach to help reveal tumor genomic heterogeneity but also identified an unexpected genomic alteration leading to secondary cancer diagnosis and changes to treatment-related decision-making.

Comparative Effectiveness of Immune Checkpoint Inhibitors vs Chemotherapy by Tumor Mutational Burden in Metastatic Castration-Resistant Prostate Cancer.

Importance: The most useful biomarkers for clinical decision-making identify patients likely to have improved outcomes with one treatment vs another. Objective: To evaluate treatment class-specific outcomes of patients receiving immune checkpoint inhibitor (ICI) vs taxane chemotherapy by tumor mutational burden (TMB). Design, Setting, and Participants: This comparative effectiveness analysis of clinical variables and outcomes used prospectively defined biomarker-stratified genomic data from a deidentified clinicogenomic database. Data included men with previously treated metastatic castration-resistant prostate cancer (mCRPC) receiving ICI or single-agent taxane chemotherapy from January 2011 to April 2021 at approximately 280 US academic or community-based cancer clinics (approximately 800 sites of care). Data were analyzed from July to August 2021. Exposures: Single-agent ICI or single-agent taxanes. Treatments were assigned at discretion of physician and patient without randomization. Imbalances of known factors between treatment groups were adjusted with propensity weighting. Main Outcomes and Measures: Prostate-specific antigen (PSA) response, time to next therapy (TTNT), and overall survival (OS). Results: A total of 741 men (median [IQR], 70 [64-76] years) with mCRPC received comprehensive genomic profiling and were treated with ICI or single-agent taxane therapy. At baseline, the median (IQR) PSA level was 79.4 (19.0-254) ng/mL, 108 men (18.8%) had Eastern Cooperative Oncology Group Performance Status scores of 2 or greater, and 644 men (86.9%) had received prior systemic treatments for mCRPC. A total of 45 patients (6.1%) received ICI therapy and 696 patients (93.9%) received taxane therapy. Among patients with TMB of fewer than 10 mutations per megabase (mt/Mb) receiving ICI, compared with those receiving taxanes, had worse TTNT (median [IQR], 2.4 [1.1-3.2] months vs 4.1 [2.2-6.3] months; hazard ratio [HR], 2.65; 95% CI, 1.78-3.95; P < .001). In contrast, for patients with TMB of 10 mt/Mb or greater, use of ICIs, compared with use taxanes, was associated with more favorable TTNT (median [IQR], 8.0 [3.4 to unknown] months vs 2.4 [2.4-7.3] months; HR, 0.37, 95% CI, 0.15-0.87; P = .02) and OS (median 19.9 [8.06 to unknown] months vs 4.2 [2.69 - 6.12] months; HR, 0.23; 95% CI, 0.10-0.57; P = .001). Among all 741 patients, 44 (5.9%) had TMB of 10 mt/Mb or greater, 22 (3.0%) had high microsatellite instability, and 20 (2.7%) had both. Treatment interactions with TMB of 10 mt/Mb or greater (TTNT: HR, 0.10; 95% CI, 0.32-0.31; P < .001; OS: HR, 0.25; 95% CI, 0.076-0.81; P = .02) were stronger than high microsatellite instability alone (TTNT: HR, 0.12; 95% CI, 0.03-0.51; P = .004; OS: HR, 0.38; 95% CI, 0.13-1.12; P = .08). Conclusions and Relevance: In this comparative effectiveness study, ICIs were more effective than taxanes in patients with mCRPC when TMB was 10 mt/Mb or greater but not when TMB was fewer than 10 mt/Mb. The results add validity to the existing TMB cutoff of 10 mt/Mb for ICI use in later lines of therapy, and suggest that ICIs may be a viable alternative to taxane chemotherapy for patients with mCRPC with high TMB.

Young-Onset Colon Cancer and Recurrence Risk by Gene Expression.

The incidence and mortality from colorectal cancer in younger adults (younger than 55 years) is increasing. We reviewed the complete database of a gene-expression test, Oncotype DX Colon Recurrence Score test, to determine age-related differences in recurrence score (RS) and single-gene results (7 cancer-related of the 12-gene assay). We included 20 478 stage II and III A and B colon cancer patients submitted to Genomic Health. RS results were grouped by low-, intermediate-, and high-risk groups. Single-gene scores were described using median and interquartile range. Of all patients 72.5% and 72.6% of those younger than 40 years had low-risk RS. Comparing older with younger patients, RS or single-gene expression did not differ by age group or stage. Young-onset colon cancer does not differ by expression of the RS component genes. Most patients with stage II and III colon cancer have low-risk disease as measured by the 12-gene assay, regardless of age.

Safety and efficacy of neratinib in combination with weekly paclitaxel and trastuzumab in women with metastatic HER2­positive breast cancer: an NSABP Foundation Research Program phase I study.

PURPOSE: Neratinib is an oral, small-molecule inhibitor that irreversibly binds to pan-HER (ErbB) receptor tyrosine kinases. Studies suggest that dual anti-HER therapies utilized in breast cancer patients are more efficacious than single agents in both the metastatic and neoadjuvant settings. In this phase I study, neratinib was combined with trastuzumab and paclitaxel in metastatic HER2-positive patients. METHODS: Twenty-one patients entered this dose-escalation study to determine the maximum-tolerated dose, safety, and efficacy of neratinib (120 up to 240 mg/day) with trastuzumab (4 mg/kg IV loading dose, then 2 mg/kg IV weekly), and paclitaxel (80 mg/m(2) IV days 1, 8, and 15 of a 28-day cycle) in women with HER2-positive metastatic breast cancer previously treated with anti-HER agent(s) and a taxane. RESULTS: The recommended phase II dose of neratinib with trastuzumab and paclitaxel was 200 mg/day. Common grade 3/4 adverse events were diarrhea (38 %), dehydration (14 %), electrolyte imbalance (19 %), and fatigue (19 %). With mandated primary diarrheal prophylaxis, ≥grade 3 diarrhea was not observed. Objective responses, complete (CR) and partial (PR), occurred in eight patients (38 %), with a clinical benefit of CR + PR+ stable disease (SD) ≥24 weeks in 11 patients (52 %). Median time-to-disease progression was 3.7 months. CONCLUSIONS: Dual anti-HER blockade with neratinib and trastuzumab resulted in significant clinical benefit despite prior exposure to trastuzumab, lapatinib, T-DM1, a taxane, and multiple lines of chemotherapy. In selected populations, inhibiting multiple ErbB-family receptors may be more advantageous than single-agent inhibition. Based on favorable tolerance and efficacy, this three-drug combination will be further assessed in a randomized phase II neoadjuvant trial (NSABP FB-7:NCT01008150).