Genomic analysis of advanced breast cancer tumors from talazoparib-treated gBRCA1/2mut carriers in the ABRAZO study

These analyses explore the impact of homologous recombination repair gene mutations, including BRCA1/2 mutations and homologous recombination deficiency (HRD), on the efficacy of the poly(ADP-ribose) polymerase (PARP) inhibitor talazoparib in the open-label, two-cohort, Phase 2 ABRAZO trial in germline BRCA1/2-mutation carriers. In the evaluable intent-to-treat population (N = 60), 58 (97%) patients harbor ≥1 BRCA1/2 mutation(s) in tumor sequencing, with 95% (53/56) concordance between germline and tumor mutations, and 85% (40/47) of evaluable patients have BRCA locus loss of heterozygosity indicating HRD. The most prevalent non-BRCA tumor mutations are TP53 in patients with BRCA1 mutations and PIK3CA in patients with BRCA2 mutations. BRCA1- or BRCA2-mutated tumors show comparable clinical benefit within cohorts. While low patient numbers preclude correlations between HRD and efficacy, germline BRCA1/2 mutation detection from tumor-only sequencing shows high sensitivity and non-BRCA genetic/genomic events do not appear to influence talazoparib sensitivity in the ABRAZO trial.ClinicalTrials.gov identifier: NCT02034916.

Abstract CT031: TALAPRO-1: Talazoparib monotherapy in metastatic castration-resistant prostate cancer (mCRPC) with tumor DNA damage response alterations (DDRm)– Exploration of genomic loss of heterozygosity (gLOH) and potential associations with antitumor activity

Background: TALAPRO-1 enrolled men with progressive mCRPC, measurable soft-tissue disease, and tumor DDRm involved directly or indirectly in homologous recombination repair (HRR) (11 gene panel). Men had received 1-2 taxane-based chemotherapy regimens and progressed on ≥1 novel hormonal therapy. The primary endpoint was objective response rate ([ORR] per RECIST 1.1; blinded independent central review [BICR]). Exploratory ad hoc biomarker analyses assessed gLOH and associations with antitumor activity.

Methods: gLOH was calculated as previously described (Sokol et al., JCO Precis Oncol 2020; PMID: 32903788). Of 104 men in the HRR-deficient measurable disease population (hereafter referred to as the efficacy population), 55 were evaluable for gLOH, 45 were non-evaluable for gLOH, and four lacked central lab gLOH results. Potential association of gLOH high/low status with response was explored using two high/low thresholds: 8.8% based on literature showing that this threshold optimally distinguished prostate cancers bearing BRCA biallelic alterations from BRCA-wildtype (Sokol et al., JCO Precis Oncol 2020; PMID: 32903788), and an agnostic threshold based on the median gLOH score in TALAPRO-1 (9.2%) in the gLOH-evaluable efficacy population. Data cutoff was Sept 4, 2020 (primary completion date).

Results: gLOH ranged from 1.39% to 30.2% in the gLOH-evaluable efficacy population. Based on the 8.8% gLOH threshold, ORR was significantly higher for gLOH-high (53.3% [16/30], 95% confidence interval [CI] 34.3-71.7%) vs gLOH-low (12.0% [3/25], 95% CI 2.5-31.2%; odds ratio [OR] 8.381, 2-sided P=0.0017; Fisher’s exact test). Similar results were yielded based on the 9.2% gLOH threshold. Next, potential associations of gLOH score with response within HRR gene alteration groups of the efficacy population were explored using the 8.8% threshold. Within the BRCA2 group, ORR was robust regardless of gLOH status, but was significantly higher for gLOH-high (70.6%, 12/17) than for gLOH-low (23.1%, 3/13) (P=0.0253). Within the ATM group, ORR was numerically higher for gLOH-high (50.0%, 2/4) than gLOH-low (0%, 0/6), but not significantly (P=0.1333). Radiographic progression-free survival (RECIST 1.1; BICR) in the gLOH-evaluable efficacy population was numerically superior for gLOH-high versus gLOH-low using either threshold (hazard ratio 0.68), but not significantly.

Conclusions: Based on these retrospective, exploratory analyses of TALAPRO-1, gLOH-high status was associated with response within the gLOH-evaluable efficacy population. Further exploration of gLOH as a candidate predictive biomarker for talazoparib in prostate cancer is warranted.

Citation Format: Johann S. de Bono, Niven Mehra, A. Douglas Laird, Elena Castro, Philippe Barthelemy, Remy Delva, Giorgio V. Scagliotti, Marco Maruzzo, Adam Stirling, Jean-Pascal Machiels, Herlinde Dumez, Vincent Renard, Julia F. Hopkins, Lee A. Albacker, Hsiang-Chun Chen, Cynthia G. Healy, Jijumon Chelliserry, Tanya Dorff, Karim Fizazi. TALAPRO-1: Talazoparib monotherapy in metastatic castration-resistant prostate cancer (mCRPC) with tumor DNA damage response alterations (DDRm)– Exploration of genomic loss of heterozygosity (gLOH) and potential associations with antitumor activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT031.

Determinants of Response to Talazoparib in Patients with HER2-Negative, Germline BRCA1/2-Mutated Breast Cancer

PURPOSE

PARP inhibitors (PARPi) have demonstrated efficacy in tumors with germline breast cancer susceptibility genes (gBRCA) 1 and 2 mutations, but further factors influencing response to PARPi are poorly understood.

EXPERIMENTAL DESIGN

Breast cancer tumor tissue from patients with gBRCA1/2 mutations from the phase III EMBRACA trial of the PARPi talazoparib versus chemotherapy was sequenced using FoundationOne CDx.

RESULTS

In the evaluable intent-to-treat population, 96.1% (296/308) had ≥1 tumor BRCA (tBRCA) mutation and there was strong concordance (95.3%) between tBRCA and gBRCA mutational status. Genetic/genomic characteristics including BRCA loss of heterozygosity (LOH; identified in 82.6% of evaluable patients), DNA damage response (DDR) gene mutational burden, and tumor homologous recombination deficiency [assessed by genomic LOH (gLOH)] demonstrated no association with talazoparib efficacy.

CONCLUSIONS

Overall, BRCA LOH status, DDR gene mutational burden, and gLOH were not associated with talazoparib efficacy; however, these conclusions are qualified by population heterogeneity and low patient numbers in some subgroups. Further investigation in larger patient populations is warranted.

TALAPRO-1: Talazoparib monotherapy in metastatic castration-resistant prostate cancer (mCRPC) with tumor DNA damage response alterations (DDRm)—Exploration of germline DDR alteration landscape and potential associations with antitumor activity

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Background: TALAPRO-1 enrolled men with progressive mCRPC with measurable soft-tissue disease and tumor DDRm involved directly or indirectly in homologous recombination repair (HRR) (11 gene panel). These men had received 1–2 taxane chemotherapy and progressed on ≥1 novel hormonal therapy. The primary endpoint was objective response rate ([ORR] per RECIST 1.1; central review). Exploratory ad hoc biomarker analyses assessed germline DDR/HRR (gHRR) alteration landscape and associations with antitumor activity. Methods: Alterations were defined as known/likely pathogenic variants. gHRR alteration (gHRRm) frequency was assessed in the study population evaluable for saliva sequencing (n = 91) using Ambry CustomNext-Cancer (9/11 genes from the tumor panel assessed). Potential associations between gHRRm status and antitumor activity were explored in the HRR-deficient measurable disease population evaluable for gHRRm (n = 70). The potential association of germline vs somatic tumor HRRm and antitumor activity was also assessed in the HRR-deficient measurable disease population (n = 104) using saliva data and somatic-germline-zygosity (SGZ) prediction (when saliva results were unavailable) to annotate tumor alteration origin. This analysis was limited to short variants. Data cutoff was Sept 4, 2020 (primary completion date). Results: Using Ambry saliva results, 19 gHRRm were identified in 18/91 (20%) evaluable patients (pts) ( BRCA2 = 10; ATM = 4; CHEK2 = 4; RAD51C = 1; 1 pt had both ATM and RAD51C). As expected for germline sequencing, all 19 alterations were short variants (12 SNV, 7 InDels). For 17/19 gHRRm, central lab tumor F1CDx records were available: in all 17 cases, identical tumor alterations were found. Of these 17 tumor HRRm, 16 were evaluable for tumor SGZ prediction of origin or zygosity: 15/16 germline, with 1/16 somatic; 9/16 homozygous (incl 7/9 BRCA2), with 7/16 heterozygous (incl 2/9 BRCA2). ORR was 31% (5/16) in men with gHRRm and 26% (14/54) in men without gHRRm ( P = 0.7519, 2-sided Fisher exact test). Based on tumor sequencing results, annotated using saliva results and SGZ predictions, ORR was 25% (10/40) in men with gHRRm and 19% (4/21) in men with only somatic HRRm ( P = 0.7528). Conclusions: Here we report a 20% incidence of gHRRm for this population of men with mCRPC preselected based on tumor HRRm status, which may be impacted by low Ns and assay specific differences in variant calling. In this population, no association with differential antitumor activity was observed with gHRRm status as assessed using germline results alone, or assessed holistically using a combination of tumor and saliva results and SGZ prediction.

Abstract P5-13-08: Identification of PD-L1+ status as a candidate predictive biomarker of response to talazoparib (TALA) in the phase 3 EMBRACA study

Background: Loss-of-function mutations in genes encoding components of the homologous recombination DNA damage response (DDR) machinery, notably BRCA1/2, are associated with tumor sensitivity to poly(ADP-ribose) polymerase inhibitors (PARPi). In EMBRACA, the PARPi TALA improved progression-free survival (PFS) (HR [95% CI] 0.54 [0.41-0.71], P<0.001) vs chemotherapy (CT) in germline BRCA-mutated (gBRCAm) HER2− advanced breast cancer. BRCA1/2 deficiency is associated with elevated PD-L1 expression in ovarian cancers, and PARP inhibition has been associated with PD-L1 upregulation in nonclinical models (Stewart et al, Cancer Res 2018;78:6717-25). Little is known about the potential for PD-L1 expression to modulate sensitivity to PARPi monotherapy in the clinic. Recently, a neoadjuvant study of olaparib in unselected, primary triple-negative breast cancer (TNBC), demonstrated a significant correlation between PD-L1 expression (using the 22C3 antibody) and response to olaparib (Eikesdal et al, Ann Oncol 2021;32:240-9). In contrast, this EMBRACA analysis assessed the contribution of PD-L1 status to TALA sensitivity in a uniformly gBRCAm patient (pt) population. Methods: Available baseline tumor tissue blocks from 120 of 431 EMBRACA pts (28% of intent-to-treat) were sectioned and slides immunostained using SP142/Ventana anti-PD-L1 at HistoGeneX (Naperville, Illinois). PD-L1 immunohistochemistry (IHC) status was assessed as the proportion of tumor area occupied by PD-L1 stained immune cells (IC) of any intensity, with ≥1% defined as PD-L1+. The overall response rate (ORR), defined as unconfirmed complete or partial response (CR/PR), was assessed by investigators. PFS was assessed by an Independent Review Facility. Results: 92/120 (77%) tumors were evaluable for PD-L1 IHC status. Of these 92 evaluable tumors, 9/36 (25%) TNBC and 15/56 (27%) hormone receptor-positive (HR+) tumors were PD-L1+ (24/92, 26% combined TNBC and HR+). In the TALA arm, the ORR was similar for PD-L1+ and PD-L1− tumors for TNBC pts: 2/5 (40%) and 6/19 (32%), respectively. In contrast, the ORR was higher for PD-L1+ vs PD-L1− tumors for HR+ pts: 11/12 (92%) vs 12/31 (39%), exact P value=0.002 (for combined TNBC and HR+, 13/17 [76%] vs 18/50 [36%], P=0.005). For the CT arm, the limited numbers evaluable for both PD-L1 and response (n=25 total), with only one response, precluded similar analysis. Based on the imbalanced results in ORR according to PD-L1 status in pts with HR+ disease, Cox regression analysis was used to explore potential associations of PD-L1 status with PFS. In the TALA arm, median PFS was similar for TNBC independent of PD-L1 status (6.3 mo and 7.0 mo, respectively; HR [95% CI] 1.207 [0.371-3.929]). Median PFS was numerically longer for PD-L1+ vs PD-L1− for HR+ tumors; this difference was not significant (20.2 mo vs 9.2 mo; HR [95% CI] 1.154 [0.395-3.367]). In the CT arm, PD-L1 status was not associated with PFS, although the PD-L1 subgroups were small (For HR+: PD-L1+, n=3; PD-L1−, n=10). Conclusions: Based on these exploratory, retrospective subgroup analyses, PD-L1 positivity by SP142/Ventana was lower in EMBRACA than previously reported in TNBC using the same scoring algorithm: 24/92 (26%) vs 369/902 (41%) in IMpassion130 (Schmid et al, Lancet Oncol 2020;21:44-59). PD-L1+ status was associated with higher ORR in HR+ EMBRACA pts receiving TALA. Interestingly, the enhanced responsiveness for PD-L1+ was not associated with improved PFS, although this assessment is complicated by low pt numbers. Further research is warranted to explore the relationship between baseline tumor PD-L1 status and sensitivity to PARPi, particularly in light of ongoing clinical studies evaluating combinations of immunotherapy and PARPi.

Citation Format: Hope S. Rugo, Joanne L. Blum, A. Douglas Laird, Sara A. Hurvitz, Johannes Ettl, Lida A. Mina, Kyung-Hun Lee, Anthony Gonçalves, Rinat Yerushalmi, Young-Hyuck Im, Miguel Martin, Louis Fehrenbacher, Henri H. Roché, Ying Chen, Silvana Lanzalone, Jijumon Chelliserry, Wolfgang Eiermann, Jennifer K. Litton. Identification of PD-L1+ status as a candidate predictive biomarker of response to talazoparib (TALA) in the phase 3 EMBRACA study [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-13-08.

Abstract CT072: Exploration of impact of tumor BRCA zygosity and genomic loss-of-heterozygosity (gLOH) on efficacy in Phase 3 EMBRACA study of talazoparib in patients (pts) with HER2-negative (HER2−) advanced breast cancer (ABC) and a germline BRCA1/2 (gBRCA1/2) mutation

Background: Loss-of-function mutations in genes encoding components of the homologous recombination machinery, notably BRCA1/2, are associated with tumor sensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors. In EMBRACA, the PARP inhibitor talazoparib (TALA) demonstrated a significant improvement in the primary endpoint of progression-free survival (PFS) (HR [95% CI] 0.54 [0.41-0.71], P < 0.001) vs physician's choice of chemotherapy (PCT) in pts with HER2− ABC and a gBRCA1/2 mutation.

Methods: Baseline tumor tissue (primary or metastatic sites) from 308 pts (71%) in the intent-to-treat population was sequenced using the FoundationOne CDx NGS panel. Mutations summarized below were known/likely pathogenic single-nucleotide variants, insertions, deletions, or rearrangements. Additional exploratory computational analyses pertinent to homologous recombination deficiency were performed, including somatic-germline-zygosity (SGZ) and gLOH assessments.

Results: 296/308 (96%) of evaluable pts exhibited ≥1 tumor BRCA mutation, with BRCA1 and BRCA2 mutations mainly mutually exclusive (4/308 [1%] pts had both BRCA1 and BRCA2 mutations). Of 12 pts with no apparent BRCA mutations, 7 exhibited tumor BRCA copy number alterations deemed pathogenic and 2 had BRCA single-nucleotide variants deemed of unknown pathogenicity. 195/236 (83%) BRCA-mutant (BRCAm) pts evaluable for BRCA LOH status were predicted to exhibit BRCA LOH by SGZ analysis. The potential impact of tumor BRCA mutational zygosity on PFS was explored in the TALA arm calculating HR by Cox proportional hazards model, comparing 122 pts with BRCA LOH with 27 pts without BRCA LOH. This analysis demonstrated no difference in PFS [HR (95% CI): 1.152 (0.680-1.951); P = 0.597)]. gLOH scores were variable, but mostly high: median (range), 21.8% (0.0, 52.7) and 20.5% (0.2, 40.5) for TALA and PCT arms, respectively. The potential association of gLOH scores with selected measures of efficacy was explored. Within both arms gLOH was similar in those pts achieving vs pts not achieving clinical benefit as defined by complete response, partial response, or stable disease ≥24 wks per RECIST v.1.1 as determined by investigator (P = 0.976 and 0.492, respectively, using 2-tailed t-test). In both arms, pts with gLOH ≥ median vs gLOH < median exhibited similar PFS: HR (95% CI) 1.247 (0.828-1.879) for TALA; 1.238 (0.693-2.211) for PCT, with HR <1 favoring gLOH ≥ median.

Conclusions: Selection based on gBRCA mutational status is appropriate to identify HER2− ABC pts with potential for clinical benefit with PARP inhibitors, with tumor BRCA zygosity and gLOH not impacting outcome (within the gBRCAm subset). Additional exploratory correlative analyses are ongoing and will be reported.

Citation Format: Jennifer K. Litton, A. Douglas Laird, Hope S. Rugo, Johannes Ettl, Sara A. Hurvitz, Miguel Martin, Henri Roché, Young-Hyuck Im, Annabel Goodwin, Joanne L. Blum, Wolfgang Eiermann, Ying Chen, Silvana Lanzalone, Jijumon Chelliserry, Akos Czibere, Lee A. Albacker, Garrett M. Frampton, Lida A. Mina. Exploration of impact of tumor BRCA zygosity and genomic loss-of-heterozygosity (gLOH) on efficacy in Phase 3 EMBRACA study of talazoparib in patients (pts) with HER2-negative (HER2−) advanced breast cancer (ABC) and a germline BRCA1/2 (gBRCA1/2) mutation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT072.

Exploring impact of mutations in non-BRCA DNA damage response (DDR) and non-DDR genes on efficacy in phase III EMBRACA study of talazoparib (TALA) in patients (pts) with germline BRCA1/2 mutated (gBRCAm) HER2-negative (HER2-) advanced breast cancer (ABC)

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Background: Loss-of-function mutations in genes encoding components of the homologous recombination DNA damage response (DDR) machinery, notably BRCA1/2, are associated with tumor sensitivity to poly(ADP-ribose) polymerase inhibitors (PARPi). In EMBRACA, the PARPi TALA showed an improvement in progression-free survival (PFS) (HR [95% CI] 0.54 [0.41-0.71], P < 0.001) vs physician's choice of chemotherapy (PCT) in g BRCAm HER2− ABC. Methods: Baseline tumor tissue from 308 pts (71%; intent-to-treat) was sequenced using the FoundationOne CDx panel. Mutations summarized below were known/likely pathogenic single-nucleotide variants, insertions, deletions, or rearrangements. Best tumor response (BOR) was using RECIST 1.1 by Investigator (confirmation of CR or PR not required). Results: 296/308 (96%) of evaluable pts exhibited ≥1 tumor BRCA mutation, with 7 of the remaining 12 exhibiting BRCA copy number alterations deemed pathogenic. Mutations in other genes implicated in DDR and/or potential sensitization to PARPi were rare, with mutations detected in BARD1, CDK12, FANCG, STAG2 (each 0.3%), ATR, BRD4, FANCC, PALB2, RAD51B (0.6%), ATM, BRIP1 (1.0%), NBN (1.3%), CHEK2, FANCA (1.6%), and ARID1A (2.3%). No association was observed between total number of DDR mutations, including BRCA1/2, and best tumor response (BOR) [odds ratio of 1 vs ≥2 DDR mutations (95% CI): TALA, 0.76 (0.31-1.87), P = 0.55; PCT, 0.98 (0.27-3.51), P = 0.97]. TP53 and PIK3CA were the most commonly mutated non- BRCA genes in BRCAm tumors (52.0 and 10.8%, respectively). TP53 mutations were more prevalent in BRCA1m vs BRCA2m tumors (85.2 vs 24.8%). PIK3CA mutations were more prevalent in BRCA2m vs BRCA1m tumors (15.9 vs 5.2%). With TALA, PFS was significantly shorter in pts with TP53 mutations than without [HR (95% CI) 1.693 (1.186-2.418), P = 0.0033]. A similar, non-significant, trend was evident with PCT [HR (95% CI) 1.439 (0.859-2.411), P = 0.1614]. PIK3CA mutational status had no impact on PFS in either arm. Conclusions: Selection based on g BRCA mutational status is appropriate to identify HER2─ ABC pts with potential for clinical benefit from TALA, with the total number of tumor mutations in BRCA1/2 and other DDR genes not impacting response (within the g BRCAm subset). TP53 mutations were associated with shorter PFS, likely reflecting the worse outcomes observed in g BRCA1m patients. Additional correlative analyses are ongoing. Clinical trial information: NCT01945775 .

The diverse genomic landscape of low−risk prostate cancer

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Background: Among men with clinically low-risk prostate cancer, we have previously documented heterogeneity in terms of clinical characteristics and genomic risk scores. In this study, we aimed to study the underlying tumor biology of this patient population, by interrogating patterns of gene expression among men with clinically low-risk tumors. Methods: Prostate biopsies from 427 patients considered potentially suitable for active surveillance underwent central pathology review and genome-wide expression profiling. These cases were compared to 1290 higher-risk biopsy cases with diverse clinical features from a prospective genomic registry. Average genomic risk (AGR) was determined from 18 published prognostic signatures, and MSigDB Hallmark gene sets were analyzed using bootstrapped clustering methods. These sets were examined in relation to clinical variables and pathologic and biochemical outcomes using multivariable regression analysis. Results: 408 (96%) of biopsies passed RNA quality control. Based on average genomic risk quartiles defined by the high-risk multicenter cases, the UCSF low-risk patients were distributed across the quartiles as 219 (54%), 107 (26%), 61 (15%), and 21 (5%). Unsupervised clustering analysis of the Hallmark gene set scores revealed 3 clusters, which were enriched for the previously described PAM50 luminal A, luminal B and basal subtypes. These three clusters did not associate with existing clinical or known genomic risk characteristics, suggesting a novel and independent classification for low-risk prostate cancer. AGR was associated with both pathological (OR: 1.3, p < 0.001) and biochemical outcomes (OR: 1.5, p = 0.001 ) but the clusters were not. Conclusions: Prostate cancers that are largely homogeneously low-risk by traditional characteristics demonstrate substantial diversity at the level of genomic expression. Molecular sub-stratification of low-risk prostate cancer may facilitate better decision-making with respect to both timing and intensity of cancer surveillance and treatment.

Development and Validation of a Novel Integrated Clinical-Genomic Risk Group Classification for Localized Prostate Cancer

Purpose It is clinically challenging to integrate genomic-classifier results that report a numeric risk of recurrence into treatment recommendations for localized prostate cancer, which are founded in the framework of risk groups. We aimed to develop a novel clinical-genomic risk grouping system that can readily be incorporated into treatment guidelines for localized prostate cancer. Materials and Methods Two multicenter cohorts (n = 991) were used for training and validation of the clinical-genomic risk groups, and two additional cohorts (n = 5,937) were used for reclassification analyses. Competing risks analysis was used to estimate the risk of distant metastasis. Time-dependent c-indices were constructed to compare clinicopathologic risk models with the clinical-genomic risk groups. Results With a median follow-up of 8 years for patients in the training cohort, 10-year distant metastasis rates for National Comprehensive Cancer Network (NCCN) low, favorable-intermediate, unfavorable-intermediate, and high-risk were 7.3%, 9.2%, 38.0%, and 39.5%, respectively. In contrast, the three-tier clinical-genomic risk groups had 10-year distant metastasis rates of 3.5%, 29.4%, and 54.6%, for low-, intermediate-, and high-risk, respectively, which were consistent in the validation cohort (0%, 25.9%, and 55.2%, respectively). C-indices for the clinical-genomic risk grouping system (0.84; 95% CI, 0.61 to 0.93) were improved over NCCN (0.73; 95% CI, 0.60 to 0.86) and Cancer of the Prostate Risk Assessment (0.74; 95% CI, 0.65 to 0.84), and 30% of patients using NCCN low/intermediate/high would be reclassified by the new three-tier system and 67% of patients would be reclassified from NCCN six-tier (very-low- to very-high-risk) by the new six-tier system. Conclusion A commercially available genomic classifier in combination with standard clinicopathologic variables can generate a simple-to-use clinical-genomic risk grouping that more accurately identifies patients at low, intermediate, and high risk for metastasis and can be easily incorporated into current guidelines to better risk-stratify patients.

Comprehensive Determination of Prostate Tumor ETS Gene Status in Clinical Samples Using the CLIA Decipher Assay

ETS family gene fusions are common in prostate cancer and molecularly define a tumor subset. ERG is the most commonly rearranged, leading to its overexpression, followed by ETV1, ETV4, and ETV5, and these alterations are generally mutually exclusive. We validated the Decipher prostate cancer assay to detect ETS alterations in a Clinical Laboratory Improvement Amendments-accredited laboratory. Benchmarking against ERG immunohistochemistry and ETV1/4/5 RNA in situ hybridization, we examined the accuracy, precision, and reproducibility of gene expression ETS models using formalin-fixed, paraffin-embedded samples. The m-ERG model achieved an area under curve of 95%, with 93% sensitivity and 98% specificity to predict ERG immunohistochemistry status. The m-ETV1, -ETV4, and -ETV5 models achieved areas under curve of 98%, 88%, and 99%, respectively. The models had 100% robustness for ETS status, and scores were highly correlated across sample replicates. Models predicted 41.5% of a prospective radical prostatectomy cohort (n = 4036) to be ERG⁺, 6.3% ETV1⁺, 1% ETV4⁺, and 0.4% ETV5⁺. Of prostate tumor biopsy samples (n = 509), 41.2% were ERG⁺, 8.6% ETV1⁺, 0.4% ETV4⁺, and none ETV5⁺. Higher Decipher risk status tumors were more likely to be ETS⁺ (ERG or ETV1/4/5) in the radical prostatectomy and the biopsy cohorts (P < 0.05). These results support the utility of microarray-based ETS status prediction models for molecular classification of prostate tumors.

Encoding phenotype in bacteria with an alternative genetic set

An unnatural base-pair architecture with base pairs 2.4 Å larger than the natural DNA-based genetic system (xDNA) is evaluated for its ability to function like DNA, encoding amino acids in the context of living cells. xDNA bases are structurally analogous to natural bases but homologated by the width of a benzene ring, increasing their sizes and resulting in a duplex that is wider than native B-DNA. Plasmids encoding green fluorescent protein were constructed to contain single and multiple xDNA bases (as many as eight) in both strands and were transformed into Escherichia coli. Although they yielded fewer colonies than the natural control plasmid, in all cases in which a modified plasmid (containing one, two, three, or four consecutive size-expanded base pairs) was used, the correct codon bases were substituted, yielding green colonies. All four xDNA bases (xA, xC, xG, and xT) were found to encode the correct partners in the replicated plasmid DNA, both alone and in longer segments of xDNA. Controls with mutant cell lines having repair functions deleted were found to express the gene correctly, ruling out repair of xDNA and confirming polymerase reading of the unnatural bases. Preliminary experiments with polymerase deletion mutants suggested combined roles of replicative and lesion-bypass polymerases in inserting correct bases opposite xDNA bases and in bypassing the xDNA segments. These experiments demonstrate a biologically functioning synthetic genetic set with larger-than-natural architecture.