Repeat Next-Generation Sequencing Testing on Progression in Men With Metastatic Prostate Cancer Can Identify New Actionable Alterations

PURPOSE

There are limited data available on the real-world patterns of molecular testing in men with advanced prostate cancer. We thus sought to evaluate next-generation sequencing (NGS) testing in the United States, focused on single versus serial NGS testing, the different disease states of testing (hormone-sensitive v castration-resistant, metastatic vs nonmetastatic), tissue versus plasma circulating tumor DNA (ctDNA) assays, and how often actionable data were found on each NGS test.

METHODS

The Prostate Cancer Precision Medicine Multi-Institutional Collaborative Effort clinical-genomic database was used for this retrospective analysis, including 1,597 patients across 15 institutions. Actionable NGS data were defined as including somatic alterations in homologous recombination repair genes, mismatch repair deficiency, microsatellite instability (MSI-high), or a high tumor mutational burden ≥10 mut/MB.

RESULTS

Serial NGS testing (two or more NGS tests with specimens collected more than 60 days apart) was performed in 9% (n = 144) of patients with a median of 182 days in between test results. For the second NGS test and beyond, 82.1% (225 of 274) of tests were from ctDNA assays and 76.1% (217 of 285) were collected in the metastatic castration-resistant setting. New actionable data were found on 11.1% (16 of 144) of second NGS tests, with 3.5% (5 of 144) of tests detecting a new BRCA2 alteration or MSI-high. A targeted therapy (poly (ADP-ribose) polymerase inhibitor or immunotherapy) was given after an actionable result on the second NGS test in 31.3% (5 of 16) of patients.

CONCLUSION

Repeat somatic NGS testing in men with prostate cancer is infrequently performed in practice and can identify new actionable alterations not present with initial testing, suggesting the utility of repeat molecular profiling with tissue or blood of men with metastatic castration-resistant prostate cancer to guide therapy choices.

Mechanisms of tyrosine kinase inhibitor resistance in renal cell carcinoma

Renal cell carcinoma (RCC), the most prevalent type of kidney cancer, is a significant cause of cancer morbidity and mortality worldwide. Antiangiogenic tyrosine kinase inhibitors (TKIs), in combination with immune checkpoint inhibitors (ICIs), are among the first-line treatment options for patients with advanced RCC. These therapies target the vascular endothelial growth factor receptor (VEGFR) tyrosine kinase pathway and other kinases crucial to cancer proliferation, survival, and metastasis. TKIs have yielded substantial improvements in progression-free survival (PFS) and overall survival (OS) for patients with advanced RCC. However, nearly all patients eventually progress on these drugs as resistance develops. This review provides an overview of TKI resistance in RCC and explores different mechanisms of resistance, including upregulation of alternative proangiogenic pathways, epithelial-mesenchymal transition (EMT), decreased intracellular drug concentrations due to efflux pumps and lysosomal sequestration, alterations in the tumor microenvironment including bone marrow-derived cells (BMDCs) and tumor-associated fibroblasts (TAFs), and genetic factors such as single nucleotide polymorphisms (SNPs). A comprehensive understanding of these mechanisms opens the door to the development of innovative therapeutic approaches that can effectively overcome TKI resistance, thereby improving outcomes for patients with advanced RCC.

Comparison of circulating tumor DNA between African American and Caucasian patients with metastatic castrate-resistant prostate cancer post-abiraterone and/or enzalutamide

BACKGROUND

African American men are much more likely than Caucasian men to be diagnosed with and to die of prostate cancer. Genetic differences likely play a role. The cBioPortal database reveals that African American men with prostate cancer have higher rates of CDK12 somatic mutations compared to Caucasian men. However, this does not account for prior prostate cancer treatments, which are particularly important in the castrate-resistant setting. We aimed to compare somatic mutations based on circulating tumor DNA (ctDNA) in metastatic castration-resistant prostate cancer (mCRPC) between African American and Caucasian men after exposure to abiraterone and/or enzalutamide.

METHODS

This single-institution retrospective study characterizes the somatic mutations detected on ctDNA for African American and Caucasian men with mCRPC who had progressed after abiraterone and/or enzalutamide from 2015 through 2022. We evaluated the gene mutations and types of mutations in this mCRPC cohort.

RESULTS

There were 50 African American and 200 Caucasian men with CRPC with available ctDNA data. African American men were younger at the time of diagnosis (p = 0.008) and development of castration resistance (p = 0.006). African American men were more likely than Caucasian men to have pathogenic/likely pathogenic (P/LP) mutations in CDK12 (12% vs. 1.5%; p = 0.003) and copy number amplifications and P/LP mutations in KIT (8.0% vs. 1.5%; p = 0.031). African American men were also significantly more likely to have frameshift mutations (28% vs. 14%; p = 0.035).

CONCLUSIONS

Compared to Caucasian men, African American men with mCRPC after exposure to abiraterone and/or enzalutamide had a higher incidence of somatic CDK12 P/LP mutations and KIT amplifications and P/LP mutations based on ctDNA. African American men also had more frameshift mutations. We hypothesize that these findings have potential implications for tumor immunogenicity.

Characterization of ctDNA findings at the end of life in patients with prostate cancer

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Background: Somatic alterations change over time in response to treatment and disease progression in patients with prostate cancer (PCa). We report ctDNA findings of patients who died from PCa within 3 months of a ctDNA assessment to better characterize patients with fatal disease. Methods: A total of 118 patients with PCa specific mortality who had been treated at Tulane Cancer Center and had ctDNA assessments between 2015 and 2022. The ctDNA was assessed by Guardant360 (Guardent Health, Inc) assays to identify alterations, pathogenic mutations and/or copy number alterations (CNAs) in cancer-related genes. Clinical annotation including treatment history, genetics, and staging were also obtained. Statistical analyses included Fischer’s Exact and Wilcoxon tests. Results: Of the 118 patients with PCa specific mortality, 42% (49/118) had a ctDNA assessment <3 months from death. Of 49 CRPC patients tested within 3 months of death, the median number of life extending therapies (LET) at death was 5 (2-9). Patients had a median of 2 (0-6) LET prior to first ctDNA screening and 3 (0-7) LET in between first and last ctDNA assessment. Of the total gene alterations detected on ctDNA analysis, within 3 months of death, the most common alterations detected were 65.3% (32/49) TP53, 44.9% (22/49) AR, 28.6% (14/49) EGFR, 24.5% (12/49) PIK3CA, 22.4% (11/49) MYC, and 20.4% (10/49) CDK6. In a paired analysis(n= 45) of first and last ctDNA screening, AR (OR= 2.35, 95% C.I. (0.99, 5.62), p= 0.05), CDK6 (OR= 4.00, 95% C.I. (1.02, 15.68), p= 0.04), FGFR1 (OR= 9.51, 95% C.I. (1.14, 79.61), p= 0.03), and EGFR (OR= 9.71, 95% C.I. (2.06, 45.83), p= 0.0009) were significantly more likely to be detected in ctDNA screening within 3 months of death. In addition, ctDNA alterations in general were significantly more likely to be detected at the end-of-life (p=< 0.00001). Other ctDNA gene mutations did not have statistically significant increases. Conclusions: An analysis of patients with PCa mortality showed most frequent gene alterations in TP53, AR, EGFR, PIK3CA, MYC, and CDK6. When comparing patients’ first and last ctDNA, alterations were significantly more likely by time of death in AR, CDK6, EGFR, FGFR and there was a significant increase in overall detection of somatic alterations in ctDNA. These analyses are limited to the genes assessed on the ctDNA panel and may or may not reflect all of the functionally relevant alterations. Further the CNAs reported herein may reflect broad genomic changes rather than specific gene alterations.

Comparison of ctDNA between African American and Caucasian patients with CRPC post abiraterone and/or enzalutamide

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Background: Genetic differences between African American and Caucasian patients with advanced prostate cancer may contribute to racial disparities in terms of treatment outcomes and survival, hence further exploration is warranted. We assessed ctDNA differences between African American and Caucasian men in the setting of CRPC post treatment with abiraterone and/or enzalutamide. Methods: From 2015 through 2022 at Tulane Cancer Center, 250 patients with CRPC including 50 African Americans and 200 Caucasian with prior abiraterone and/or enzalutamide treatment were included. All patients had ctDNA assessed via Guardant360. Data including both gene mutations and types of mutations were for between 73-80 genes. Clinical annotation including initial staging, treatment history, and genetic testing were obtained. Statistical analyses included Fisher’s exact test and Wilcoxon rank-sum test. Results: The most common pathogenic/likely pathogenic (P/LP) alterations in both African Americans and Caucasians were TP53 (44% and 46%, respectively), AR (50% and 39%), and PIK3CA (14% and 9%). CDK12 (OR= 8.955, 95% C.I. [2.156, 37.192], p=0.003) and KIT (OR= 5.710, 95% C.I. [1.235, 26.397]. p=0.031) alterations were more frequently detected in African Americans. In terms of pathologic mutation type, frameshift mutations were significantly more frequent in African Americans (OR= 2.293, 95% C.I. [1.103, 4.769], p=0.035). All patients were CRPC at the time of testing and had prior abiraterone and/or enzalutamide, but there were no significant differences between African American and Caucasian patients with regards to prior life-extending therapies. Conclusions: African Americans with CRPC post treatment with abiraterone and/or enzalutamide had a higher frequency of P/LP CDK12 and KIT mutations, which have both been shown to lead to aggressive clinical features and treatment resistance. African Americans also had a higher incidence of frameshift mutations, a finding not previously noted. [Table: see text]

Evaluation of ctDNA in patients with CRPC with pathogenic germline mutations in BRCA2

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Background: Approximately 3-5% of advanced prostate cancer patients have pathogenic BRCA2 mutations in germline tests. In this study, we examine the relationship between pathogenic germline BRCA2 mutation and somatic changes in ctDNA. Methods: Germline screenings were performed by Invitae multi-cancer gene panel which includes 50-84 genes. ctDNA alterations were detected by Guardant 360 assays which report somatic changes in 70-83 genes. All ctDNA samples were collected in post-abiraterone and/or enzalutamide (in CRPC patients). Any pathogenic/likely pathogenic somatic alterations in the ctDNAs with more than 0.1% of allelic fraction were included in this cohort. The type of mutation detected in ctDNA was also assessed (truncating, point, etc.). Statistical significance for comparison is calculated with Fischer Exact Probablity Test and Chi-Square Test. Results: A total of 11 patients had germline BRCA2 pathogenic mutations and ctDNA assays; 267 patients had no germline DNA pathogenic alterations and ctDNA assays. Compared to germline normal patients, the germline BRCA2 mutations were less likely to have AR alterations on ctDNA (OR=0.2133, 95% C.I. [0.087, 0.525], p-value = 0.0003). BRCA2 germline positive patients were also more likely to have a mutated BRCA1, BRCA2, and TP53 ctDNA (OR=7.899, 95% C.I. [1.2745, 48.9548], p=0.055), (OR=7.899, 95% C.I. [1.7529, 16.059], p=0.008), and (OR=6.442, 95% C.I. [2.449, 16.946], p=0.00001), respectively. All other ctDNA assessed genes were mutated at a similar frequency between germline BRCA2 mutated and “normal” germline patients. BRCA2 germline mutations patients are less likely to have copy number alterations (CNVs) (OR=0.3992, 95% C.I. [0.2168, 0.7352], p=0.0031) and more likely to have frameshift mutations (OR=2.3182, 95% C.I. [1.169, 4.5972], p=0.0183). Conclusions: The ctDNA testing in this CRPC population (after abiraterone and/or enzalutamide) was less likely to find AR alterations and more likely to find pathogenic mutations for BRCA1, BRCA2, and TP53 in BRCA2 germline positive patients. In addition, BRCA2 germline positive CRPC patients were more likely to have frameshift mutations and less likely to have CNVs than those with an intact germline. Characterizing the mutational landscape in BRCA2 germline mutated patients may help to better define underlying disease biology. Those with BRCA mutated germline may be less likely to have AR driven tumors. More study is needed to better understand patients with underlying DNA repair defects.

Analysis of TP53 gain of function mutations in metastatic castration-resistant prostate cancer

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Background: TP53, an oncogene implicated in the development of many malignancies, is commonly altered in mCRPC. Gain-of-function mutations in TP53 confer increased oncogenic properties of this gene and play a role in mCRPC. The goal of this study was to characterize somatic TP53 mutations, specifically gain-of-function mutations, in the ctDNA of mCRPC patients in the context of prior therapies. Methods: A retrospective analysis of mCRPC patients at Tulane Cancer Center between 2015-2022 was performed. All patients had ctDNA testing performed with the Guardant360 multigene panel assay. Clinical annotation including initial diagnosis, staging, treatment history, and family history were obtained. TP53 mutations were classified based on existing published functional studies and/or in silico evaluation. Statistical analyses were performed with Fisher's exact and Chi-squared tests where appropriate. Results: 338 mCRPC patients with ctDNA testing were included in this analysis. 76 patients had no prior treatment with either abiraterone or enzalutamide, while 262 patients had been treated with abiraterone and/or enzalutamide. Somatic TP53 mutations were similar in frequency between those with or without abiraterone/enzalutamide pretreatment; 46% (35/76) of patients in the abiraterone/enzalutamide naïve subset had a somatic TP53 mutation, compared to 41% (108/262) of patients previously treated with abiraterone and/or enzalutamide. Only 9% (7/76) of abiraterone/enzalutamide naïve patients had a TP53 gain-of-function mutation, compared to 19% (49/262) of patients previously treated with one or both drugs ( p = 0.05). The most common type of TP53 mutation was loss-of-function. There were no significant associations between TP 53 mutations and occurrence of other common mutations. Conclusions: mCRPC patients with prior treatment of abiraterone and/or enzalutamide were significantly more likely to have a gain-of-function TP53 mutation. Further studies are needed to investigate therapeutic implications of these findings.

Genomic alterations in patients with prostate cancer with liver metastases

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Background: mCRPC patients with liver metastases have a poor prognosis and often progress rapidly on a variety of treatments. Previously, preliminary ctDNA analyses of mCRPC patients with liver metastases showed a range of commonly altered genes in patients with liver metastases (Ranasinghe et al; 2019). In this follow-up, we evaluated ctDNA alterations in an expanded cohort of mCRPC patients with liver metastases. Methods: From Tulane Cancer Center, retrospective review of mCRPC patients was used to identify patients with confirmed liver metastasis. All liver metastases were confirmed based on imaging data. All patients included had ctDNA evaluated with a multi-gene cancer panel via Guardant 360 assay (Guardant Health, Inc). Additional clinical annotation including family history, germline testing, staging, imaging, and laboratory values. Statistical analyses were performed with Fisher’s Exact and Wilcoxon Rank Sum tests. Results: 158 mCRPC patients with appropriate diagnostic imaging as well as ctDNA testing. From this group, 8% (n= 12) had confirmed liver metastases. Among the patients with liver metastasis, the most common alterations detected were in AR (50%; 6/12) and PIK3CA (25%; 3/12). Patients with liver metastasis were more likely to have amplifications in FGFR1 detected in their ctDNA (OR= 14.40; 95% C.I. (1.83, 113.22); p= 0.03). In addition to ctDNA, germline data was assessed, and it was found that patients with liver metastasis were more likely to have a pathogenic germline mutation (OR= 7.61; 95% C.I. (2.85, 20.31); p<.0001). The most common germline mutations detected in patients with liver metastasis were in BRCA2 (n= 3) and TP53 (n= 2). Conclusions: Though liver metastasis are less common in prostate cancer, it often occurs following extensive treatment and results in a poor prognosis for patients. In patients with liver metastasis, FGFR1 amplification was more often detected in ctDNA. Importantly, patients with liver metastasis were significantly more likely to have a pathogenic germline alteration.

Evaluation of ctDNA in patients treated with lutetium-177-PSMA-617

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Background: Lutetium-177- PSMA-617 (Lu-177) is a radioligand therapy that delivers radiation to PSMA-expressing cells in patients with advanced prostate cancer. In this study, we aimed to analyze ctDNA in responders and non-responders after Lu-177 treatments. Methods: Data was retrospectively collected on 31 heavily pre-treated metastatic CRPC patients who received Lu-177 treatment at Tulane Cancer Center. All patients fulfilled VISION criteria for treatment and all had ctDNA assessment with Guardant 360 within 30 days prior to first treatment with Lu-177. Of the 31 patients, 7 had paired ctDNA assessment both prior initiation of treatment and at the end of treatment. Clinical data such as PSA response (PSA decline 50% or more) to Lu-177, initial diagnosis, pathology, treatment history, and relevant germline genetic data were collected. Results: Of the 31 patients who received Lu-177 treatment, 18 had PSA response to Lu-177 (responders) and 13 did not (non-responders). In ctDNA mutational analyses, there were no significant differences detected prior to treatment between responders and non-responders. There was, however, a significant increase in the presence of copy number amplifications in non-responders (n= 11/13) when compared to responders (n= 7/18) (OR= 8.64, 95% C.I. [1.46, 51.25)], p = 0.0250). Amplification was detected in 10 genes in non-responders, whereas responders only had amplifications in AR (7/18) and EGFR (1/18). The most frequently amplified genes in non-responders were AR (8/13), CCNE1 (6/13), EGFR (4/13), and FGFR1 (4/13). Furthermore, in analysis of the 7 patients with paired ctDNA assessments, amplifications increased during treatment with Lu-177. Conclusions: Radioligand therapy with Lu-177 has been shown to prolong life and reduce disease progression. Our analysis of the cohort of Lu-177 treated patients showed that the presence of gene amplifications in ctDNA may play a role in predicting resistance to treatment with Lu-177.

Advanced papillary renal cell carcinoma: Epidemiology, genomic drivers, current therapies, and ongoing trials

Papillary renal cell carcinoma (PRCC) is the most common subtype of non-clear cell renal cell carcinoma. PRCC can be subdivided into types 1 and 2 based on histology, each associated with different genetic mutations. The MET gene is commonly altered in type 1 PRCC while multiple alterations are involved in type 2 PRCC. PRCC is an aggressive cancer with a predominance in male and black patients and poor prognosis. Due to its rarity, there was a lack of convincing prospective data to guide treatment; hence, therapies were previously extrapolated from clear cell renal cell carcinoma with mixed results. More recently, some phase 2 trials focused on PRCC have been promising. Tyrosine kinase inhibitor (TKI) monotherapy is considered the standard of care, and combination strategies with TKIs and immune checkpoint inhibitors are emerging. Genetic profiling and large-scale clinical trials are needed to inform targeted treatment of PRCC.

Association of Uric Acid-Lowering Therapy With Incident Chronic Kidney Disease

IMPORTANCE

Uric acid is a waste metabolite produced from the breakdown of purines, and elevated serum uric acid levels are associated with higher risk of hypertension, cardiovascular disease, and mortality and progression of chronic kidney disease (CKD). Treatment of hyperuricemia in patients with preexisting CKD has not been shown to improve kidney outcomes, but the associations of uric acid-lowering therapies with the development of new-onset kidney disease in patients with estimated glomerular filtration rate (eGFR) within reference range and no albuminuria is unclear.

OBJECTIVE

To examine the association of initiating uric acid-lowering therapy with the incidence of CKD.

DESIGN, SETTING, AND PARTICIPANTS

This cohort study included patients with eGFR of 60 mL/min/1.73 m2 or greater and no albuminuria treated at US Department of Veterans Affairs health care facilities from 2004 to 2019. Clinical trial emulation methods, including propensity score weighting, were used to minimize confounding. Data were analyzed from 2020 to 2022.

EXPOSURE

Newly started uric acid-lowering therapy.

MAIN OUTCOMES AND MEASURES

The main outcomes were incidences of eGFR less than 60 mL/min/1.73 m2, new-onset albuminuria, and end-stage kidney disease.

RESULTS

A total of 269 651 patients were assessed (mean [SD] age, 57.4 [12.5] years; 252 171 [94%] men). Among these, 29 501 patients (10.9%) started uric acid-lowering therapy, and 240 150 patients (89.1%) did not. Baseline characteristics, including serum uric acid level, were similar among treated and untreated patients after propensity score weighting. In the overall cohort, uric acid-lowering therapy was associated with higher risk of both incident eGFR less than 60 mL/min/1.73 m2 (weighted subhazard ratio [SHR], 1.15 [95% CI, 1.10-1.20; P < .001) and incident albuminuria (SHR, 1.05 [95% CI, 1.01-1.09; P < .001) but was not associated with the risk of end-stage kidney disease (SHR, 0.96 [95% CI, 0.62-1.50]; P = .87). In subgroup analyses, the association of uric acid-lowering therapy with worse kidney outcomes was limited to patients with baseline serum uric acid levels of 8 mg/dL or less.

CONCLUSIONS AND RELEVANCE

These findings suggest that in patients with kidney function within reference range, uric acid-lowering therapy was not associated with beneficial kidney outcomes and may be associated with potential harm in patients with less severely elevated serum uric acid levels.

Elevated neutrophil-lymphocyte ratios in extremely preterm neonates with histologic chorioamnionitis

OBJECTIVE

Histologic chorioamnionitis (HCA) is a placental inflammation linked to preterm birth and adverse neonatal outcome. The neutrophil-lymphocyte ratio (NLR) can identify various inflammatory disorders, however its utility in HCA is not clear. Our goal was to examine NLR values and HCA diagnoses in at-risk pregnancies and neonates.

STUDY DESIGN

We retrospectively analyzed the EHR of mothers and preterm (<33 wk GA) neonates with or without HCA (identified by placental histology). The NLR was calculated from complete blood counts in laboring women and in their neonates (0-24 h of life).

RESULT

In 712 consecutive gestations, 50.8% had HCA (26.5% fetal HCA). The neonatal NLR (0-12 h, 13-24 h) predicted fetal HCA better than chance alone (p = 0.01 and 0.002, respectively).

CONCLUSION

Early NLR elevation in preterm neonates is consistent with a diagnosis of fetal HCA. The NLR may identify preterm neonates at risk for HCA-related complications.

PD-L1 Expression and Treatment Implications in Metastatic Clear Cell Renal Cell Carcinoma: A Systematic Review

BACKGROUND: Over the past decade, immune checkpoint inhibitors (ICIs) have increasingly become the standard of care for various advanced malignancies, including metastatic clear cell renal cell carcinoma (mccRCC). Most ICIs currently used in clinical practice inhibit the interaction between the programmed cell death protein-1 (PD-1) and programmed death ligand-1 (PD-L1) complex. A deeper understanding of this interaction and PD-L1 expression in tumors has led to more effective therapies in the treatment of advanced cancers, but the debate regarding the utility of PD-L1 as a biomarker continues. OBJECTIVE: We aimed to systematically evaluate the role of PD-L1 in mccRCC in terms of expression and treatment implications. METHODS: Following PRISMA guidelines, we performed a systematic literature search using PubMed and Embase through August 31, 2020. Titles and abstracts were screened to identify articles for full-text review. A hand search was also performed using Google Scholar and the bibliography to relevant studies. RESULTS: A total of 26 articles were identified, and relevant data were extracted and organized. The available information regarding PD-L1 expression in mccRCC from both prospective clinical trials and retrospective studies were summarized. We discussed the utility of PD-L1 as a predictive and prognostic biomarker in mccRCC, its association with other potential biomarkers, and the pattern and level of expression of PD-L1 in primary versus metastatic tumors. CONCLUSIONS: Although significant progress has been made, much more remains to be learned regarding the differences between PD-L1+ and PD-L1- ccRCC tumors, in terms of both the underlying biology and clinical responses to immunotherapy and other agents.

Scaling and root planing with and without periodontal flap surgery

Complete removal of calculus is a primary part of achieving a "biologically acceptable" tooth surface in the treatment of periodontitis. Rabbani et al. reported that a single episode of scaling did not completely remove subgingival calculus and that the deeper the periodontal pocket, the less complete the calculus removal. The purpose of the present study was to evaluate the effectiveness of scaling relative to calculus removal following reflection of a periodontal flap. Each of 21 patients who required multiple extractions had 2 teeth scaled, 2 teeth scaled following the reflection of a periodontal flap, and 2 teeth serve as controls. Local anesthesia was used. Following extraction, the % of subgingival tooth surfaces free of calculus was determined using the method described by Rabbani with a stereomicroscope. Results showed that while scaling only (SO) and scaling with a flap (SF) increased the % of root surface without calculus, scaling following the reflection of a flap aided calculus removal in pockets 4mm and deeper. Comparison of SO versus SF at various pocket depths for % of tooth surfaces completely free of calculus showed 1 to 3 mm pockets to be 86% versus 86%, 4 to 6 mm pockets to be 43% versus 76% and greater than 6 mm pockets to be 32% versus 50%. The extent of residual calculus was directly related to pocket depth, was greater following scaling only, and was greatest at the CEJ or in association with grooves, fossae or furcations. No differences were noted between anterior and posterior teeth or between different tooth surfaces.