Unraveling the potential clinical utility of circulating tumor DNA detection in colorectal cancer-evaluation in a nationwide Danish cohort

BACKGROUND

Increasingly, circulating tumor DNA (ctDNA) is proposed as a tool for minimal residual disease (MRD) assessment. Digital PCR (dPCR) offers low analysis costs and turnaround times of less than a day, making it ripe for clinical implementation. Here, we used tumor-informed dPCR for ctDNA detection in a large colorectal cancer (CRC) cohort to evaluate the potential for post-operative risk assessment and serial monitoring, and how the metastatic site may impact ctDNA detection. Additionally, we assessed how altering the ctDNA-calling algorithm could customize performance for different clinical settings.

PATIENTS AND METHODS

Stage II-III CRC patients (N = 851) treated with a curative intent were recruited. Based on whole-exome sequencing on matched tumor and germline DNA, a mutational target was selected for dPCR analysis. Plasma samples (8 ml) were collected within 60 days after operation and-for a patient subset (n = 246)-every 3-4 months for up to 36 months. Single-target dPCR was used for ctDNA detection.

RESULTS

Both post-operative and serial ctDNA detection were prognostic of recurrence [hazard ratio (HR) = 11.3, 95% confidence interval (CI) 7.8-16.4, P < 0.001; HR = 30.7, 95% CI 20.2-46.7, P < 0.001], with a cumulative ctDNA detection rate of 87% at the end of sample collection in recurrence patients. The ctDNA growth rate was prognostic of survival (HR = 2.6, 95% CI 1.5-4.4, P = 0.001). In recurrence patients, post-operative ctDNA detection was challenging for lung metastases (4/21 detected) and peritoneal metastases (2/10 detected). By modifying the cut-off for calling a sample ctDNA positive, we were able to adjust the sensitivity and specificity of our test for different clinical contexts.

CONCLUSIONS

The presented results from 851 stage II-III CRC patients demonstrate that our personalized dPCR approach effectively detects MRD after operation and shows promise for serial ctDNA detection for recurrence surveillance. The ability to adjust sensitivity and specificity shows exciting potential to customize the ctDNA caller for specific clinical settings.

Comparing single-target and multi-target approaches for postoperative circulating tumor DNA detection in stage II-III colorectal cancer patients

Circulating tumour DNA (ctDNA) detection for postoperative risk stratification in cancer patients has great clinical potential. However, low ctDNA abundances complicates detection. Multitarget (MT) detection strategies have been developed to increase sensitivity. Yet, empirical evidence supporting performance gains of MT vs. single‐target (ST) strategies in a postoperative setting is limited. We compared ctDNA detection in 379 paired plasma samples from 112 stage II–III colorectal cancer patients by ST digital PCR and MT sequencing of 16 patient‐specific variants. The strategies exhibited good concordance (90%, Cohen's Kappa 0.79), with highly correlated ctDNA quantifications (Pearson r = 0.985). A difference was observed in ctDNA detection preoperatively (ST 72/92, MT 88/92). However, no difference was observed immediately after surgery in recurrence (ST 11/22, MT 10/22) or nonrecurrence (both 2/34) patients. In serial samples, detection was similar within recurrence (ST 13/16, MT 14/16) and nonrecurrence (ST 3/49, MT 1/49) patients. Both approaches yielded similar lead times to standard‐of‐care radiology (ST 4.0 months, MT 4.1 months). Our findings do not support significant performance gains of the MT strategy over the ST strategy for postoperative ctDNA detection.

Abstract 1959: Sensitive detection of circulating tumor DNA by whole genome sequencing: Validation of MRDetect using serial blood samples from stage III colorectal cancer patients

Background: While detection of circulating tumor DNA (ctDNA) is associated with poor cancer prognosis, the clinical utility for guiding treatment decisions is unresolved. Patients with minimal residual disease (MRD) often have less than one genome equivalent of ctDNA per 10 mL blood. Consequently, it is stochastic whether a 10 mL sample contains ctDNA from a particular genomic locus. Consequently, the sensitivity of ctDNA detection methods targeting a limited number of tumor loci is heavily affected by sampling bias. To overcome this challenge, we developed MRDetect; a whole genome sequencing (WGS) approach, which detects ctDNA using the patient-specific cumulative signal from tens of thousands of mutations throughout the genome. Recently, we showed how MRDetect found ctDNA fractions down to 10-4. Here, we performed a validation study to confirm the prognostic impact of MRDetect.

Aim: Validation of MRDetect for sensitive ctDNA detection to monitor residual disease in stage III colorectal cancer (CRC) patients treated with curative intent.

Methods: From a large, uniform cohort of stage III CRC patients n = 146), we had plasma samples collected every third month (n = 938, median = 9 per patient) and a median follow-up of 34 months. For each patient, a genome-wide mutational signature was established by WGS of tumor and matched normal DNA. Enhanced by an AI-based error suppression model, this signature was used to detect ctDNA in 1-2 mL plasma samples using WGS (20x coverage). We used de-novo point mutation and copy number variation analysis to investigate cancer evolution after treatment. To evaluate the reproducibility of MRDetect, aliquot samples (n = 2x190 samples) from 5 recurrence and 10 non-recurrence patients were processed and sequenced at two independent laboratories. Outcome measures: ctDNA status, tumor fraction, false positive rate, Time To ctDNA Recurrence (TTcR), and Time To radiological Recurrence (TTrR).

Results: Analysis of paired samples showed great reproducibility with high agreement between both ctDNA status calls (Cohens Kappa = 0.81) and the estimated tumor fractions (r2 = 0.99). MRDetect revealed post-operative ctDNA in all recurrence patients (5/5) with detected tumor fractions down to 2 x 10-4. Median TTcR was 0.9 month (range 0.5 - 7.3 months) while median TTrR was 12.8 months (range 11.3 - 31.1 months). The false positive rate was 1% (1/100), assessed in longitudinal samples from the 10 non-relapsing patients. Tumor evolution dynamics in plasma samples revealed novel amplification and deletions, which were absent in the primary tissue but confirmed in metachronous metastases. We will present results from the full cohort at AACR 2022.

Conclusion: MRDetect detects ctDNA with high sensitivity and specificity and enables effective postoperative assessment of MRD, cancer evolution dynamics and early relapse detection.

Citation Format: Amanda Frydendahl, Thomas Reinert, Jesper Nors, Sunil Deochand, Dillon Maloney, Noah Friedman, Tomer Lauterman, Danielle Afterman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Ravi Kandasamy, Iman Tavassoly, Jonathan Rosenfeld, Anders Husted Andersen, Uffe S. Løve, Per V. Andersen, Ole Thorlacius-Ussing, Lene Hjerrild Iversen, Kåre Andersson Gotschalck, Boris Oklander, Asaf Zviran, Claus Lindbjerg Andersen. Sensitive detection of circulating tumor DNA by whole genome sequencing: Validation of MRDetect using serial blood samples from stage III colorectal cancer patients [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 1959.

Abstract 3398: Exploring the biology of ctDNA release in colon cancer

Background: Colorectal cancer is responsible for 9.4% of cancer-related deaths worldwide. Early detection of the disease has the potential to improve patient outcomes, therefore, developing an efficient and minimally invasive method for carrying out surveillance has been a clinically relevant effort in recent years. Circulating tumour DNA has garnered interest as a marker for early cancer detection, however, deeper understanding of the underlying biology of ctDNA release is needed in order to maximize its utility in clinical practice. In this project, we aimed to investigate whether a phenotype conductive to ctDNA shedding can be defined in a colorectal cancer cohort, including transcriptomic, genomic and clinical data collected from stage I to stage IV colon cancer patients at Aarhus University Hospital.

Methods: Transcriptomic data from 102 patients and whole exome sequencing data from 60 patients were analyzed. Differential gene expression and differential pathway enrichment analyses between ctDNA positive and ctDNA negative patients were conducted by performing Student’s t-test. The resulting p-values were adjusted according to the Benjamini-Hochberg method. The genes in the transcriptomic analyses were assigned to pathways with regard to the MSigDB Hallmark gene sets and pathway enrichment was assessed using Gene Set Variation Analysis (GSVA). Using an extended cohort of 537 patients, we performed Wilcoxon’s signed rank test to investigate the association between tumour size, histological subtypes and ctDNA shedding behavior. Additionally, we modelled the expected ctDNA fraction as a function of birth rate, death rate and tumour mass.

Results: In colon cancer, ctDNA release is primarily associated with tumour size, molecular subtypes and proliferative transcriptomic signatures. A moderate but significant correlation was observed between the tumour’s largest diameter and the detected ctDNA fraction. Furthermore, molecular subtypes associated with less aggressive disease tended to shed lower amounts of ctDNA. Notably, we have found that pathways associated with proliferation are enriched in the ctDNA positive subgroup.

Conclusions: Our results demonstrate that enhanced proliferative capacity in connection with tumour size and molecular subtypes may contribute to a higher ctDNA release rate. We anticipate our study to be a starting point for further investigation of ctDNA shedding dynamics in colorectal cancer.

Citation Format: Judit Kisistok, Tenna Vesterman Henriksen, Jesper Bertram Bramsen, Thomas Reinert, Trine Block Mattesen, Nicolai Juul Birkbak, Claus Lindbjerg Andersen. Exploring the biology of ctDNA release in colon cancer [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 3398.

Circulating Tumor DNA in Stage III Colorectal Cancer, beyond Minimal Residual Disease Detection, toward Assessment of Adjuvant Therapy Efficacy and Clinical Behavior of Recurrences

PURPOSE

Sensitive methods for risk stratification, monitoring therapeutic efficacy, and early relapse detection may have a major impact on treatment decisions and patient management for stage III colorectal cancer patients. Beyond assessing the predictive power of postoperative ctDNA detection, we explored the added benefits of serial analysis: assessing adjuvant chemotherapy (ACT) efficacy, early relapse detection, and ctDNA growth rates.

EXPERIMENTAL DESIGN

We recruited 168 patients with stage III colorectal cancer treated with curative intent at Danish and Spanish hospitals between 2014 and 2019. To quantify ctDNA in plasma samples (n = 1,204), 16 patient-specific somatic single-nucleotide variants were profiled using multiplex-PCR, next-generation sequencing.

RESULTS

Detection of ctDNA was a strong recurrence predictor postoperatively [HR = 7.0; 95% confidence interval (CI), 3.7-13.5; P < 0.001] and directly after ACT (HR = 50.76; 95% CI, 15.4-167; P < 0.001). The recurrence rate of postoperative ctDNA-positive patients treated with ACT was 80% (16/20). Only patients who cleared ctDNA permanently during ACT did not relapse. Serial ctDNA assessment after the end of treatment was similarly predictive of recurrence (HR = 50.80; 95% CI, 14.9-172; P < 0.001), and revealed two distinct rates of exponential ctDNA growth, slow (25% ctDNA-increase/month) and fast (143% ctDNA-increase/month; P < 0.001). The ctDNA growth rate was prognostic of survival (HR = 2.7; 95% CI, 1.1-6.7; P = 0.039). Serial ctDNA analysis every 3 months detected recurrence with a median lead-time of 9.8 months compared with standard-of-care computed tomography.

CONCLUSIONS

Serial postoperative ctDNA analysis has a strong prognostic value and enables tumor growth rate assessment. The novel combination of ctDNA detection and growth rate assessment provides unique opportunities for guiding decision-making.See related commentary by Morris and George, p. 438.

Error Characterization and Statistical Modeling Improves Circulating Tumor DNA Detection by Droplet Digital PCR

BACKGROUND

Droplet digital PCR (ddPCR) is a widely used and sensitive application for circulating tumor DNA (ctDNA) detection. As ctDNA is often found in low abundance, methods to separate low-signal readouts from noise are necessary. We aimed to characterize the ddPCR-generated noise and, informed by this, create a sensitive and specific ctDNA caller.

METHODS

We built 2 novel complimentary ctDNA calling methods: dynamic limit of blank and concentration and assay-specific tumor load estimator (CASTLE). Both methods are informed by empirically established assay-specific noise profiles. Here, we characterized noise for 70 mutation-detecting ddPCR assays by applying each assay to 95 nonmutated samples. Using these profiles, the performance of the 2 new methods was assessed in a total of 9447 negative/positive reference samples and in 1311 real-life plasma samples from colorectal cancer patients. Lastly, performances were compared to 7 literature-established calling methods.

RESULTS

For many assays, noise increased proportionally with the DNA input amount. Assays targeting transition base changes were more error-prone than transversion-targeting assays. Both our calling methods successfully accounted for the additional noise in transition assays and showed consistently high performance regardless of DNA input amount. Calling methods that were not noise-informed performed less well than noise-informed methods. CASTLE was the only calling method providing a statistical estimate of the noise-corrected mutation level and call certainty.

CONCLUSIONS

Accurate error modeling is necessary for sensitive and specific ctDNA detection by ddPCR. Accounting for DNA input amounts ensures specific detection regardless of the sample-specific DNA concentration. Our results demonstrate CASTLE as a powerful tool for ctDNA calling using ddPCR.

Circulating tumor DNA for prognosis assessment and postoperative management after curative-intent resection of colorectal liver metastases

The recurrence rate of colorectal liver metastases (CRLM) patients treated with curative intent is above 50%. Standard of care surveillance includes intensive computed tomographic (CT) imaging as well as carcinoembryonic antigen (CEA) measurements. Nonetheless, relapse detection often happens too late to resume curative treatment. This longitudinal cohort study enrolled 115 patients with plasma samples (N = 439) prospectively collected before surgery, postoperatively at day 30 and every third month for up to 3 years. Droplet digital PCR (ddPCR) was used to monitor serial plasma samples for somatic mutations. Assessment of ctDNA status either immediately after surgery, or serially during surveillance, stratified the patients into groups of high and low recurrence risk (hazard ratio [HR], 7.6; 95% CI, 3.0-19.7; P < .0001; and HR, 4.3; 95% CI, 2.3-8.1; P < .0001, respectively). The positive predictive value (PPV) of ctDNA was 100% in all postoperative analyses. In multivariable analyses, postoperative ctDNA status was the only consistently significant risk marker associated with relapse (P < .0001). Indeterminate CT findings were observed for 30.8% (21/68) of patients. All patients (9/21) that were ctDNA positive at the time of the indeterminate CT scan later relapsed, contrasting 42.6% (5/12) of those ctDNA negative (P = .0046). Recurrence diagnoses in patients with indeterminate CT findings were delayed (median 2.8 months, P < .0001). ctDNA status is strongly associated with detection of minimal residual disease and early detection of relapse. Furthermore, ctDNA status can potentially contribute to clinical decision-making in case of indeterminate CT findings, reducing time-to-intervention.

Serial circulating tumor DNA analysis to assess recurrence risk, benefit of adjuvant therapy, growth rate and early relapse detection in stage III colorectal cancer patients

3540

Background: Challenges in the postoperative management of stage III colorectal cancer include: 1) selection of high-risk patients for adjuvant chemotherapy (ACT), 2) lack of markers to assess ACT efficacy, 3) assessment of recurrence risk after ACT, and 4) lack of markers to guide treatment decisions for high-risk patients e.g. additional therapy or intensified surveillance. Circulating tumor DNA (ctDNA) is a promising marker with potential to mitigate the challenges. Here we used serial ctDNA measurements to assess the correlation between recurrence and ctDNA detection: postoperative, during and after ACT, and during surveillance; and to assess growth rates of metachronous metastases. Uniquely, we also used concurrent CT scans and ctDNA measurements to compare the sensitivity for detecting recurrence. Methods: Stage III CRC patients treated with curative intent at Danish and Spanish hospitals in 2014-2019 were recruited (n = 166). Blood samples (n = 1227) were collected prior to and immediately after surgery, and every third month for up to 36 months. Per patient 16 personal mutations were used to quantify plasma ctDNA (Signatera, bespoke mPCR NGS assay). Results: Detection of ctDNA was a strong recurrence predictor, both postoperatively (HR 7.2, 95% CI 3.8-13.8, P< 0.001), directly after ACT (HR = 18.2, 95% CI 7.1-46, P < 0.001), and when measured serially after end of treatment (HR = 41, 95% CI 16-100, P < 0.001). The recurrence rate of postoperative ctDNA positive patients treated with ACT was 80% (16/20). Patients who stayed ctDNA positive during ACT all recurred. Serial post-treatment ctDNA measurements revealed exponential growth for all recurrence patients following either a SLOW (26%-increase/month) or a FAST (126%-increase/month) pattern (P < 0.001). From ctDNA detection to radiologic recurrence, ctDNA levels of FAST patients increased by a median 117-fold, and up to 554-fold. The 3-year overall survival was 43% for FAST patients and 100% for SLOW and non-recurrence patients (HR = 41.3, 95% CI 7.5-228, P < 0.001). Coinciding CT scans and ctDNA measurements (n = 113 patients, 235 coinciding events, median 2 per patient) showed a high agreement (92%) and ctDNA either detected residual disease before the CT scan (n = 7 patients) or at the same time (n = 14 patients). The median lead-time was 7.5 months. Conclusions: The study confirmed the prognostic power of serial postoperative ctDNA analysis. Moreover, it provided novel analyses demonstrating that ctDNA is more sensitive for recurrence detection than CT scans and can be used for tumor growth rate assessments. The difference between FAST and SLOW growing tumors suggest that growth rates could guide whom to start on systemic therapy rapidly and whom to send for diagnostic imaging. Altogether, the study highlights many potential utilities of ctDNA in guiding clinical decision-making.

Circulating tumor DNA analysis for assessment of recurrence risk, benefit of adjuvant therapy, and early relapse detection after treatment in colorectal cancer patients

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Background: Timely detection of recurrence, as well as identification of patients at high risk of recurrence after surgery and after completion of adjuvant therapy, are major challenges in the treatment of colorectal cancer (CRC). Postsurgical circulating tumor DNA (ctDNA) analysis is a promising tool for the identification of patients with minimal residual disease (MRD) and a high risk of recurrence. The objective of this prospective, multicenter study was to determine whether serial postsurgical ctDNA analysis could identify the patients at high risk of recurrence, provide an assessment of adjuvant therapy efficacy and detect relapse earlier than standard-of-care radiological imaging. Methods: The cohort comprises 265 stage I-III CRC patients, the to-date largest cohort assessed for ctDNA. All patients had the tumor resected and a subset of 62.6% (166 /265) was additionally treated with ACT. Plasma samples (n = 1503) were collected at various time points for a median follow-up of 28.4 months (range: 1.2-51.0 months). Individual tumors and matched germline DNA were whole-exome sequenced and somatic single nucleotide variants (SNVs) were identified. Personalized multiplex PCR assays were designed to track tumor-specific SNVs (Signatera, bespoke mPCR NGS assay) in each patient’s plasma sample. Results: Postoperative ctDNA status prior to ACT was assessed in 218 patients, of which 9.17% (20/218) were identified to be MRD-positive and 75% (15/20) eventually relapsed. The remaining 25% (5/20) of MRD-positive patients that did not relapse, received ACT. In contrast, only 13.6% (27/198) of MRD-negative cases relapsed (HR: 11: 95% CI: 5.7-20; p < 0.001). Longitudinal ctDNA-positive status, post-definitive therapy (n = 202) was associated with a HR of 36 (95% CI: 16-81; p < 0.001). For a subset of 155 patients postoperative CEA and ctDNA measurements were compared, wherein, ctDNA-positive status was found to be significantly associated with RFS (HR, 7.1; 95% CI, 3.4-15; P < 0.001) compared to CEA (HR, 1.2; 95% CI, 0.46-3.1; P = 0.73). Serial ctDNA analysis detected MRD up to a median of 8 months (0.56 - 21.6 months) ahead of radiologic relapse. Conclusion: Postoperative ctDNA positive status was associated with markedly reduced RFS compared to CEA. The study also shows that effective therapy can be curative in a portion of MRD-positive patients. In a longitudinal setting, ctDNA analysis predicted the risk of recurrence and is a more reliable biomarker for treatment response monitoring.

Age-stratified reference intervals unlock the clinical potential of circulating cell-free DNA as a biomarker of poor outcome for healthy individuals and patients with colorectal cancer

Circulating cell-free DNA (cfDNA) has spurred much interest as a biomarker in oncology. However, inter- and intra-individual cfDNA levels vary greatly. Consequently, in order to base clinical decisions on cfDNA measurements, normal reference intervals are essential to avoid that ordinary variation is confused with clinically relevant change. The lack of reference intervals may potentially explain the ambiguous results reported in the field. Our study aimed to establish reference intervals and to evaluate the association between cfDNA and demographic and clinical variables, including colorectal cancer (CRC). Plasma samples and clinical data from 2817 subjects were collected including 1930 noncancer individuals and 887 CRC patients. cfDNA was measured using droplet digital polymerase chain reaction (PCR). The large cohort combined with robust cfDNA quantification enabled establishment of reference intervals (<67 years: 775-4860 copies/mL; ≥67 years: 807-6561 copies/mL). A cfDNA level above the age-stratified 90% percentile was prognostic of reduced survival in both noncancer individuals and CRC patients, with HR values of 2.56 and 2.01, respectively. Moreover, cfDNA levels increased significantly with age, elevated BMI and chronic diseases. In CRC, the cfDNA level was increased for Stage IV, but not Stage I to Stage III cancer. In summary, the use of reference intervals revealed that high cfDNA levels were predictive of shorter survival in both noncancer individuals and CRC patients, and that CRC development did not affect the cfDNA level until metastatic dissemination. Furthermore, cfDNA levels were impacted by age and chronic diseases. Conclusively, our study presents reference intervals that will help pave the way for clinical utilization of cfDNA.

The effect of surgical trauma on circulating free DNA levels in cancer patients-implications for studies of circulating tumor DNA

Detection of circulating tumor DNA (ctDNA) post‐treatment is an emerging marker of residual disease. ctDNA constitutes only a minor fraction of the cell‐free DNA (cfDNA) circulating in cancer patients, complicating ctDNA detection. This is exacerbated by trauma‐induced cfDNA. To guide optimal blood sample timing, we investigated the duration and magnitude of surgical trauma‐induced cfDNA in patients with colorectal or bladder cancer. DNA levels were quantified in paired plasma samples collected before and up to 6 weeks after surgery from 436 patients with colorectal cancer and 47 patients with muscle‐invasive bladder cancer. To assess whether trauma‐induced cfDNA fragments are longer than ordinary cfDNA fragments, the concentration of short (< 1 kb) and long (> 1 kb) fragments was determined for 91 patients. Previously reported ctDNA data from 91 patients with colorectal cancer and 47 patients with bladder cancer were used to assess how trauma‐induced DNA affects ctDNA detection. The total cfDNA level increased postoperatively—both in patients with colorectal cancer (mean threefold) and bladder cancer (mean eightfold). The DNA levels were significantly increased up to 4 weeks after surgery in both patient cohorts (P = 0.0005 and P ≤ 0.0001). The concentration of short, but not long, cfDNA fragments increased postoperatively. Of 25 patients with radiological relapse, eight were ctDNA‐positive and 17 were ctDNA‐negative in the period with trauma‐induced DNA. Analysis of longitudinal samples revealed that five of the negative patients became positive shortly after the release of trauma‐induced cfDNA had ceased. In conclusion, surgery was associated with elevated cfDNA levels, persisting up to 4 weeks, which may have masked ctDNA in relapse patients. Trauma‐induced cfDNA was of similar size to ordinary cfDNA. To mitigate the impact of trauma‐induced cfDNA on ctDNA detection, it is recommended that a second blood sample collected after week 4 is analyzed for patients initially ctDNA negative.

Circulating tumor DNA to detect minimal residual disease, response to adjuvant therapy, and identify patients at high risk of recurrence in patients with stage I-III CRC

4009

Background: The clinical utility of tracking circulating tumor DNA (ctDNA) as a non-invasive biomarker for detecting minimal residual disease (MRD) and stratifying patients based on their risk of developing relapse has been well established in colorectal cancer (CRC). This study evaluates the detection and longitudinal monitoring of ctDNA in CRC patients pre- and post-operatively, during and after adjuvant chemotherapy (ACT). Methods: The prospective, multicenter cohort study recruited patients (n = 193) diagnosed with resected stage I-III CRC. Plasma samples (n = 1052) were collected at various timepoints with a median follow up of 21.6 months (4.6-38.5 months). Individual tumors and matched germline DNA were whole-exome sequenced and somatic mutations identified. Multiplex PCR assays were designed to 16 tumor-specific single-nucleotide variants to track ctDNA in plasma samples. The study evaluated the relationship between ctDNA status and clinical outcomes including radiologic imaging. Cox regression was used to calculate recurrence-free survival (RFS) in patients stratified by ctDNA status postoperatively and post-ACT. Multivariable analysis was performed with all clinical variables. Best model was selected according to Akaike Information Criterion. Results: Pre-operatively ctDNA was detected in 90% (n = 166/185) of the patients. Post-operative ctDNA status prior to ACT was assessed in 152 patients, of which 9.2% (14/152) were identified to be MRD-positive and 78.5% (11/14) eventually relapsed. In contrast, 10.1% (14/138) of MRD-negative cases relapsed (HR: 16.53; 95% CI: 7.19-38.02; p < 0.001). Longitudinal ctDNA-positive status, post-ACT (n = 84) and post definitive therapy (n = 139) was associated with a 27.92 HR (95% CI: 9.16-85.11; p < 0.001) and a 47.52 HR (95% CI: 17.34-130.3.; p < 0.001), respectively. In the multivariable analysis, longitudinal ctDNA status was the only significant prognostic factor associated with RFS (HR: 53.19, 95% CI: 18.87-149.90; p < 0.001). Serial ctDNA analysis detected MRD up to a median of 9.08 months (0.56-16.5 months) ahead of radiologic relapse with a sensitivity of 79.1% and specificity of 99%. Conclusions: Postoperative ctDNA analyses detect patients with high-risk of recurrence, with near 100% specificity. Early detection of MRD and longitudinal monitoring of ctDNA could guide treatment decisions. Intervention trials to assess the clinical benefit of ctDNA use are underway.

Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer

Importance

Novel sensitive methods for detection and monitoring of residual disease can improve postoperative risk stratification with implications for patient selection for adjuvant chemotherapy (ACT), ACT duration, intensity of radiologic surveillance, and, ultimately, outcome for patients with colorectal cancer (CRC).

Objective

To investigate the association of circulating tumor DNA (ctDNA) with recurrence using longitudinal data from ultradeep sequencing of plasma cell-free DNA in patients with CRC before and after surgery, during and after ACT, and during surveillance.

Design, Setting, and Participants

In this prospective, multicenter cohort study, ctDNA was quantified in the preoperative and postoperative settings of stages I to III CRC by personalized multiplex, polymerase chain reaction-based, next-generation sequencing. The study enrolled 130 patients at the surgical departments of Aarhus University Hospital, Randers Hospital, and Herning Hospital in Denmark from May 1, 2014, to January 31, 2017. Plasma samples (n = 829) were collected before surgery, postoperatively at day 30, and every third month for up to 3 years.

Main Outcomes and Measures

Outcomes were ctDNA measurement, clinical recurrence, and recurrence-free survival.

Results

A total of 130 patients with stages I to III CRC (mean [SD] age, 67.9 [10.1] years; 74 [56.9%] male) were enrolled in the study; 5 patients discontinued participation, leaving 125 patients for analysis. Preoperatively, ctDNA was detectable in 108 of 122 patients (88.5%). After definitive treatment, longitudinal ctDNA analysis identified 14 of 16 relapses (87.5%). At postoperative day 30, ctDNA-positive patients were 7 times more likely to relapse than ctDNA-negative patients (hazard ratio [HR], 7.2; 95% CI, 2.7-19.0; P < .001). Similarly, shortly after ACT ctDNA-positive patients were 17 times (HR, 17.5; 95% CI, 5.4-56.5; P < .001) more likely to relapse. All 7 patients who were ctDNA positive after ACT experienced relapse. Monitoring during and after ACT indicated that 3 of the 10 ctDNA-positive patients (30.0%) were cleared by ACT. During surveillance after definitive therapy, ctDNA-positive patients were more than 40 times more likely to experience disease recurrence than ctDNA-negative patients (HR, 43.5; 95% CI, 9.8-193.5 P < .001). In all multivariate analyses, ctDNA status was independently associated with relapse after adjusting for known clinicopathologic risk factors. Serial ctDNA analyses revealed disease recurrence up to 16.5 months ahead of standard-of-care radiologic imaging (mean, 8.7 months; range, 0.8-16.5 months). Actionable mutations were identified in 81.8% of the ctDNA-positive relapse samples.

Conclusions and Relevance

Circulating tumor DNA analysis can potentially change the postoperative management of CRC by enabling risk stratification, ACT monitoring, and early relapse detection.

Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma

PURPOSE

Novel sensitive methods for early detection of relapse and for monitoring therapeutic efficacy may have a huge impact on risk stratification, treatment, and ultimately outcome for patients with bladder cancer. We addressed the prognostic and predictive impact of ultra-deep sequencing of cell-free DNA in patients before and after cystectomy and during chemotherapy.

PATIENTS AND METHODS

We included 68 patients with localized advanced bladder cancer. Patient-specific somatic mutations, identified by whole-exome sequencing, were used to assess circulating tumor DNA (ctDNA) by ultra-deep sequencing (median, 105,000×) of plasma DNA. Plasma samples (n = 656) were procured at diagnosis, during chemotherapy, before cystectomy, and during surveillance. Expression profiling was performed for tumor subtype and immune signature analyses.

RESULTS

Presence of ctDNA was highly prognostic at diagnosis before chemotherapy (hazard ratio, 29.1; P = .001). After cystectomy, ctDNA analysis correctly identified all patients with metastatic relapse during disease monitoring (100% sensitivity, 98% specificity). A median lead time over radiographic imaging of 96 days was observed. In addition, for high-risk patients (ctDNA positive before or during treatment), the dynamics of ctDNA during chemotherapy was associated with disease recurrence (P = .023), whereas pathologic downstaging was not. Analysis of tumor-centric biomarkers showed that mutational processes (signature 5) were associated with pathologic downstaging (P = .024); however, no significant correlation for tumor subtypes, DNA damage response mutations, and other biomarkers was observed. Our results suggest that ctDNA analysis is better associated with treatment efficacy compared with other available methods.

CONCLUSION

ctDNA assessment for early risk stratification, therapy monitoring, and early relapse detection in bladder cancer is feasible and provides a basis for clinical studies that evaluate early therapeutic interventions.

Abstract P1-15-16: Pathological complete response rates with the addition of carboplatin to standard neoadjuvant chemotherapy in a cohort of real–world patients with triple negative breast cancer

Objectives: Addition of carboplatin to standard neoadjuvant chemotherapy (NACT) for triple negative breast cancer (TNBC) remains controversial. There are several randomized trials showing that carboplatin increases the likelihood of achieving pathological complete response (pCR) in TNBC. Patients with TNBC who achieve pCR has been shown to have better disease-free and overall survival. The aim of this study was to asses the impact of adding carboplatin to standard NACT in TNBC in terms of pCR rates and toxicity. Methods:In this cross-sectional study, 252 consecutive patients with primary TNBC who were submitted to neoadjuvant chemotherapy between 2013 and 2018, in a single center, were selected. Patients with biopsy-confirmed TNBC, previously untreated, with clinical stages I-III were included (n=179). Clinical pathological features, pathological response, treatment protocol, and toxicities were analyzed and considered for statistical analysis. Eighty patients treated from 2013 to 2015 received doxorubicin plus cyclophosphamide once every 3 weeks (AC) for four cycles, followed by 12 weeks (wP) or every 3 weeks (P) paclitaxel(AC-T group). Ninety-nine patients, treated from 2015 to 2018 had four cycles of AC followed by wP plus weekly carboplatin (Cb) area under curve (AUC) 1.5-2.0 (AC-TCb group). Pathologic response was determined locally, and pCR was defined as the absence of residual invasive disease with or without ductal carcinoma in situ in the breast and axilla. Results: Data from 179 patients were included in the analysis (AC-T: n=80; AC-TCb: n=99). Patients in AC-TCb group had a median age of 51.7 years vs. 47.4 years in AC-T group, p=0.01. In AC-TCb group 61.6% of patients were postmenopausal vs 43.7% in AC-T group, p=0.03. The distribution of clinical stage in groups AC-TCb and AC-T were as follows: stage I 6.0% vs 0%; stage II 42.4% vs 43.7%; stage III 51.6% vs 56.3%, respectively (p=0.02). In AC-TCbgroup, 34 patients (35.0%) had pCR in comparison to 20 patients (25.0%) on AC-T group (p=0.22). Pathological stage distribution in groups AC-TCb and AC-T were: stage I 24.7% vs 33.7%; stage II 23.7% vs 26.3%; stage III 16.4% vs 15%, respectively (p=0.42). More than 85.0% of patients in AC-TCb group received at least 9 weeks of carboplatin and less than 20.0% required dose reduction due to toxicity.Conclusions: An improved pathological complete response for TNBC patients submitted to standard NACT plus carboplatin was observed. The results are in accordance with previous studies demonstrating that the addition of carboplatin to NACT improves pCR rate in TNBC with a favorable risk to benefit profile. Therefore carboplatin might be a potential component of NACT and should be considered in this context.

Distribution of patients with TNBC submitted to NACT with AC-T and AC-TCb according clinical–pathological characteristicsClinical pathological characteristicsAC-T n= 80AC-TCb n=99pMenopausal  0.03yes3561 no4538 Clinical stage  0.02I06 II3542 III4551 Histologic type  0.25IDC8096 others03 Histologic grade  0.86101 22932 35164 Pathological stage  0.42O2034 I2724 II2123 III1216 pCR  0.22yes2034 no6063 

Citation Format: Ramalho S, Natal RdA, Cardoso Filho C, Xavier MB, da Silva AER, Silva LR, Vasconcelos V, Reinert T, Coelho GP, Silva GRdP, dos Santos CC. Pathological complete response rates with the addition of carboplatin to standard neoadjuvant chemotherapy in a cohort of real–world patients with triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-15-16.

Abstract P1-08-27: Advanced stage at diagnosis and worse clinicopathologic features in young woman with breast cancer. A sub-analysis of Brazilian population through the AMAZONA III study (GBECAM 0115)

BACKGROUND: Breast cancer (BC) in young women is uncommon and often more aggressive. There are disparities in terms of screening coverage, diagnostic features and access to optimal treatment among young BC patients worldwide. To better understand this scenario through real world data we performed a sub-analysis of AMAZONA III study. METHODS: The AMAZONA III study (GBECAM 0115) is a prospective registry that included 2950 women newly diagnosed with invasive BC in Brazil during the period of January 2016 to March 2018 within 22 sites. Of them, 2888 patients had valid data regarding age at diagnosis and complete baseline information. For the purpose of comparisons of epidemiologic and clinicopathologic features at the time of diagnosis of BC, patients were divided in two groups: women aged ≤40 years (Group 1) and &gt;40 years (Group 2). Quantitative variables were expressed with mean, while categorical variables were described as their count and percentage and compared using the chi-square test. RESULTS: Of 2888 women, 486 (17%) were ≤40 years of age. No differences were found between ethnicity, performance status, body mass index, personal income, health insurance and family history of cancer between the two groups. Young women had higher educational level (p&lt;0.001), were more involved into a labor activity (p&lt;0.001) and were more frequently married (p&lt;0.001). There were also significant differences regarding nulliparity (p&lt;0.001) and previous use of oral contraceptives (p&lt;0.001). Mode of detection of BC was symptomatic in 73.4% of young group versus 64.5% in older group and screen-detected was only 26.6% vs. 35.5% respectively (p&lt;0.001). Table 1 describes clinicopathological characteristics of the two groups. Young women presented more frequently with stage III,T3/T4, Grade 3 tumors and HER-2 positive, Luminal B and triple negative subtypes. Women older than 40 years had more stage I, Luminal A and Grade 1/2 tumors. CONCLUSION: Brazilian women under the age of 40 have unfavorable clinicopathological features of BC at diagnosis with more aggressive subtypes and advanced stage compared with older women. No differences in socioeconomic and ethnical aspects were found but a higher percentage of young women had symptomatic detection of BC which could explain the later stage of disease at diagnosis. Young women were economically active and the majority married which highlights the socioeconomic impact of this disease in Brazil.

Breast cancer features by age groups at diagnosis in Brazilian women.InformationGroup 1 (≤40 years)Group 2 (&gt; 40 years)p-valueN: 2888486 (16.83%)2402 (83.17%) Stage at diagnosis  p&lt; 0.001I76 (19.2%)541 (27.8%) II156 (39.4%)816 (41.9%) III146 (36.8%)489 (25.1%) IV19 (4.6%)101 (5.2%) Tumor size  p&lt; 0.001T1114 (27.1%)749 (36.9%) T2141 (33.6%)764 (37.6%) T3101 (24.1%)282 (13.9%) T464 (15.2%)235 (11.6%) Tumor grade  p &lt; 0.001Grade 146 (10.7%)381 (17.9%) Grade 2198 (46.2%)1150 (52.0%) Grade 3185 (43.1%)641 (30.1%) Molecular Subtype  p &lt; 0.001Luminal A106 (30.6%)957 (51.3%) Luminal B - HER 2 negative55 (15.8%)212 (11.4%) Luminal B- HER 2 positive79 (22.8%)298 (16.0%) HER 2 positive27 (7.8%)135 (7.2%) Triple negative80 (23.0%)264 (14.1%) 

Citation Format: Franzoi MA, Rosa D, Barrios C, Bines J, Cronemberger E, Queiroz G, Cordeiro de Lima VC, Junior R, Couto J, Emerenciano K, Resende H, Crocamo S, Reinert T, Van Evyl B, Neron Y, Dybal V, Lazaretti N, Costamilan RdC, de Andrade D, Mathias C, Zerwes Vacaro G, Borges G, Silva K, Werutsky G, Morelle A, Sampaio Filho CA, Mano M, Zaffaroni F, Simon S, Liedke PE. Advanced stage at diagnosis and worse clinicopathologic features in young woman with breast cancer. A sub-analysis of Brazilian population through the AMAZONA III study (GBECAM 0115) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-08-27.

Abstract P4-12-01: Not presented

This abstract was not presented at the conference.

Citation Format: Werutsky G, Villareal-Garza C, Moreno HG, Cartagena AA, Campos-Gomez S, Reyes RO, Lence JJ, Liedke P, Reinert T, Binotto M, Dybal V, Martinez-Mesa J, Freitas RD, Nunes Filho PR, Zaffaroni F, Barrios CH. Not presented [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-12-01.

Abstract P1-08-29: Current status of clinical and pathological characteristics of breast cancer patients in Brazil: Results of the AMAZONA III study (GBECAM 0115)

BACKGROUND

Breast cancer (BC) is the most common tumor in women in Brazil with about 60 thousand new cases estimated per year. In low and middle-income countries, patients with BC are diagnosed with more advanced stages as compared with high-income countries. In Brazil, disparities in access to new therapies are recognized; previous data suggests worse survival of BC patients treated in the public system. The aim of AMAZONA III study (GBECAM 0115) is to describe the current status of BC care in Brazil. Here we report patients data at baseline.

METHODS

The AMAZONA III is a prospective BC registry that included women 18 years or older with newly diagnosed stage I to IV BC from 22 sites in Brazil in the period of January 2016 to March 2018. All patients provided written informed consent; data was collected from interview and medical charts, comprising clinical-demographic variables, initial treatment and a planned follow-up for 5 years. BC subtypes were defined by hormone receptor (HR) expression, HER2 status and grade according to von Minckwitz G. et al 2012. Here we present a descriptive analysis of the patients' baseline characteristics. Continuous variables are shown as mean (standard-deviation) and categorical variables by its absolute and relative frequencies. The study is registered in clinicaltrials.gov NCT02663973.

RESULTS

A total of 2950 patients were included in the study. Median age at diagnosis was 53 years old (8.4% &lt;= 35 years, 34.8% 36-50 years, 56.8% &gt; 50 years), 58.6% were white, 34.4% had brown skin-color, 83% had children before BC diagnosis (median of 1 child/patient) and 63.1% had public health insurance. In terms of method of detection 34% were screen-detected whereas 66% were symptomatic, the last was even higher (70%) in patients in younger than 50 years. The distribution of BC stage at diagnosis was I (26.4%), II (41.6%), III (27%) and IV (5%). The most common histologies were ductal (80.9%) and lobular carcinoma (6.9%). The pathological characteristics were HR positive in 78.0%, HER-2 positive in 23.4% and grade 2 in 51%. BC subtypes were as follows: Luminal A 48%, Luminal B 12%, Luminal HER2 positive 17%, Non-luminal HER2 positive 7.3% and Triple negative 15.5%.

DISCUSSION

Breast cancer is diagnosed at an earlier age among Brazilian patients. The majority of patients were detected through symptomatic BC and therefore a significant proportion is still diagnosed in stages III and IV. Among other factors, these findings could have a significant impact in treatment outcomes. Further analysis of this large cohort of patients will help to identify other important elements and direct future strategies for breast cancer control.

TRIAL REGISTRY: NCT02663973

KEYWORDS: Breast Cancer; Epidemiology; Treatment; Brazil

Citation Format: Rosa D, Barrios C, Bines J, Werustky G, Cronemberger E, Queiroz GS, Lima VC, Freitas-Júnior R, Couto J, Emerenciano K, Resende H, Crocamo S, Reinert T, Van Eyil B, Néron Y, Dybal V, Lazaretti N, Costamilan RC, Andrade DA, Mathias C, Vacaro GZ, Borges G, Torres KL, Morelle A, Sampaio Filho CA, Mano M, Zaffaroni F, Simon S. Current status of clinical and pathological characteristics of breast cancer patients in Brazil: Results of the AMAZONA III study (GBECAM 0115) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-08-29.

Abstract 1590: Personalized circulating tumor DNA analysis to monitor colorectal cancer

Early detection of disease recurrence has shown to improve survival in patients with early-stage colorectal cancer (CRC) (Pita-Fernandez et al., 2015). Detection of circulating tumor DNA (ctDNA) postoperatively in patients with stage II colon cancer provides direct evidence of residual disease and identifies patients at high risk of recurrence (Tie et al., 2016). Previous studies have performed ctDNA analysis to monitor tumor burden in early-stage CRC using small gene panel sequencing or digital droplet PCR (ddPCR) assays to detect specific variants (Tie et al., 2016, Reinert et al., 2016). Building upon these previous studies, here we use a personalized multiplex ctDNA technology measuring 16 mutations specific to each patient's tumor respectively to assess minimal residual disease postoperatively and to monitor treatment response in CRC. Our study includes 130 patients diagnosed with stage I-III CRC treated with intended curative surgery. Of the 130 patients, 80 received adjuvant chemotherapy for a duration of six months. For 119 patients, one pre-operative and one post-operative plasma sample were available. In addition, longitudinally-collected plasma samples were available from 78 of 130 patients for early detection of disease recurrence and to determine their relationship with imaging and carcinoembryonic antigen (CEA) during a 3-year post-operative surveillance period.

To identify patient-specific tumor mutation signatures, whole-exome sequencing of CRC tissue and germline DNA is used. Patient specific multiplex-PCR assay panels are designed to target 16 tumor-specific single-nucleotide variants (SNVs) in plasma. Targeted sequencing is then performed on plasma samples collected pre- and post-operative and during adjuvant therapy. We then correlate ctDNA status to the clinical outcome, including CEA and radiographic imaging, for each patient. Data collection is ongoing and results will be presented at the AACR 2018 meeting.

Conclusion. This study provides a novel methodology to detect minimal residual disease postoperatively and to monitor treatment efficacy in CRC using a personalized multiplex-PCR approach. The performance of this patient-specific ctDNA technology will be compared to the current standard of care for monitoring disease burden.

References:

S. Pita-Fernàndez, et al. Ann. Oncol. 26, 644–656 (2015).

Tie J, et al. Sci Transl Med. 2016 Jul 6;8(346):346ra92.

Reinert T. Gut. 2016 Apr;65(4):625-34.

Citation Format: Thomas Reinert, Tenna V. Henriksen, Mads H. Rasmussen, Himanshu Sethi, Shruti Sharma, Hsin-Ta Wu, Dina Hafez, Prashanthi Natarajan, Scott Dashner, Mustafa Balcioglu, Ann Nguyen, Derrick Renner, Bernhard Zimmermann, Lene H- Iversen, Mogens R. Madsen, Cheng-Ho Jimmy Lin, Claus L. Andersen. Personalized circulating tumor DNA analysis to monitor colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1590.

Direct detection of early-stage cancers using circulating tumor DNA

Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction sequencing (TEC-Seq) that allows ultrasensitive direct evaluation of sequence changes in circulating cell-free DNA using massively parallel sequencing. We have used this approach to examine 58 cancer-related genes encompassing 81 kb. Analysis of plasma from 44 healthy individuals identified genomic changes related to clonal hematopoiesis in 16% of asymptomatic individuals but no alterations in driver genes related to solid cancers. Evaluation of 200 patients with colorectal, breast, lung, or ovarian cancer detected somatic mutations in the plasma of 71, 59, 59, and 68%, respectively, of patients with stage I or II disease. Analyses of mutations in the circulation revealed high concordance with alterations in the tumors of these patients. In patients with resectable colorectal cancers, higher amounts of preoperative circulating tumor DNA were associated with disease recurrence and decreased overall survival. These analyses provide a broadly applicable approach for noninvasive detection of early-stage tumors that may be useful for screening and management of patients with cancer.

Abstract P6-08-24: Reproductive status and clinical pathological characteristics of young women diagnosed with breast cancer in Latin America: LACOG 0414 study

BACKGROUND

Approximately 7% of women diagnosed with breast cancer (BC) are under 40 years old. Chemotherapy may adversely affect ovarian function therefore fertility is an issue to be addressed for these patients. Patients with cancer in Latin America have limited access to fertility preservation. However age at first birth in women from Latin America is lower than in developed country and the needs of fertility preservation may be different from developed countries. The aim of the present study was to describe the reproductive status and clinical pathological features of young women diagnosed with BC in Latin America.

METHODS

LACOG 0414 is a prospective registry in Latin America which included young patients with &lt; 40 years old with diagnosis of BC and indication of (neo) adjuvant chemotherapy. Demographic data, reproductive status and clinical pathological information were retrieved from patients` medical charts. This study was approved by local ethics committees and regulatory authorities.

RESULTS

A total of 343 patients (pts) from 19 different sites distributed in 4 Latin American countries were included: Brasil (N=132 pts), Mexico (N=112 pts), Peru (N=83 pts) and Cuba (N=16 pts). The mean age at BC diagnosis was 34.02 (±4.17) years (14% had &lt; 30 years, 41% had 30-35 years and 44% had 36-40 years). From all included patients, 245 (71.42%) already had children at the time of BC diagnosis. From those the median number of children per women was 2 (range 1–6). The probability of having children at the time of diagnosis was significantly higher with increased age, being as high as 80% in those aged between 36 and 40 years old. There was no difference in terms of having a child at BC diagnosis within the 4 countries, by stage at diagnosis or per breast cancer subtypes.

In terms of educational level, approximately 8% of patients were Illiterate and only 40% had university degree. Stages at BC diagnosis were the following: 12% stage I, 49% stage II, 35% stage III and 3% stage IV. The distribution of BC subtypes was: luminal 48%, HER2-positive 29% and triple negative 23%.

CONCLUSION

To our knowledge, this is the first study describing reproductive status of young patients diagnosed with BC in Latin America. Despite the lack of access to fertility preservation programs in the region, we found that a high number of patients had children at diagnosis of BC. Considering the high prevalence of advanced disease and aggressive subtypes the socioeconomic impact of young BC patients in Latin America needs to be addressed.

Citation Format: Werutsky G, Villarreal-Garza C, Morante Cruz ZD, Debiasi M, Zaffaroni F, Fonseca A, Castro-Sánchez A, Platas A, Gómez Moreno H, Bretel D, Ortiz RM, Reinert T, Dybal V, Liedke P, Barrios C. Reproductive status and clinical pathological characteristics of young women diagnosed with breast cancer in Latin America: LACOG 0414 study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-08-24.

Abstract P4-12-04: Cost-effectiveness analysis of locally advanced estrogen receptor-positive, HER-2 negative breast cancer care using a tailored treatment approach in Brazil

Introduction: Breast cancer is the most common cancer in women worldwide, and 70% of breast cancer deaths occur in women from low-income and middle-income countries. In Brazil there were 14388 deaths due to this disease in 2013 and an estimate of over 58000 new cases in 2016. Neoadjuvant endocrine therapy (NET) is an attractive alternative to Neoadjuvant chemotherapy (NAC) for Hormone Receptor-positive tumors and could be a resources-saving strategy of treatment.

Methods: We built a decision analysis model of breast cancer treatment to compare a NET schema, with response based on the evaluation of Ki-67, against the surgery followed by adjuvant chemotherapy (AC) and radiation therapy (RT) standard-of-care as two competing approaches to breast cancer management. Our objective is to determine whether tailoring chemotherapy treatment based on response to neoadjuvant endocrine therapy is a cost-effective approach. The NET schema is based on the ACOSOG Z1031B trial, in which post-menopausal women with estrogen receptor-positive, HER-2 negative disease would receive 4 weeks of NET followed by a core-needle biopsy for Ki-67 evaluation. If Ki-67 were lower than 10%, patients would continue in NET for 16-18 weeks followed by surgery and RT according to international guidelines. The indication of AC in these patients would be based on the preoperative endocrine prognostic index (PEPI). Patients with a PEPI score equal to zero would be spared from AC. If Ki-67&gt;10%, patients would be triaged to NAC or surgery. The cost-effectiveness analysis was conducted using a Markov model from the provider's perspective, in this case the Brazilian Health ministry. Healthcare costs, in the form of charges from the hospitals to the health ministry, were obtained from cost tables available at the federal government's webpage. In the Markov model, possible health states were disease-free, local relapse, metastatic disease and death.Transition probabilities and mortality rates were extracted from randomized studies. Our assumptions were that both treatment strategies have similar clinical outcomes and that Ki-67 is a reliable method to triage patients to NAC or surgery. We performed one-way sensitivity analysis to assess the impact of the failure of the Ki-67 test on cost-effectiveness.

Results: Our model shows that the NET schema dominates the standard-of-care strategy. Costs were R$ 47799.89 per patient for the NET strategy and R$79809.24 for the standard-of-care strategy. There was an incremental cost saving of R$32009.36 per patient for the NET strategy compared to the standard-of-care strategy. Cost-effectiveness of the NET strategy was R$2612.63 and R$4369.11 for the standard-of-care. Considering the willingness-to-pay of R$ 85494.00, defined by the World Health Organization as three times the gross domestic product per capita, the standard-of-care strategy would only be more cost-effective in the scenario of a Ki-67 test that misclassifies patients more than 9.1% of the time.

Conclusion: The use of response to neoadjuvant endocrine treatment based on Ki-67 analysis as a way to tailor locally advanced breast cancer treatment is a cost-saving strategy in the presence of robust biomarkers.

Citation Format: Goncalves R, Reinert T, Ellis MJ, Sarian LO, Filassi JR. Cost-effectiveness analysis of locally advanced estrogen receptor-positive, HER-2 negative breast cancer care using a tailored treatment approach in Brazil [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-12-04.

Trends in progression-free survival (PFS) and time to progression (TTP) over time within first-line aromatase inhibitors trials in hormone receptor-positive advanced breast cancer

BACKGROUND

Over the last 20 years, aromatase inhibitors (AI) have been tested in clinical trials as first-line therapy for hormone receptor-positive (HR-positive) advanced breast cancer (ABC), firstly as experimental arms, when they proved to be effective, and recently as control arms. This analysis aims to evaluate trends in progression-free survival (PFS) and time to progression (TTP) over time.

PATIENTS AND METHODS

A literature review was conducted using the MEDLINE database to identify randomized controlled phase II or III trials which reported PFS or TTP of at least one arm using first-line AI HR-positive ABC patients. A linear correlation was used to access the association between the year of the first patient enrolled and the observed PFS/TTP.

RESULTS

The search retrieved 19 trials, accounting for 4552 postmenopausal patients divided into 21 separate AI treatment arms. The PFS/TTP increased from 6 to 9 months in the earlier trials to 13-16 months in the current era, representing an absolute gain of approximately 7 months, without the addition of any other drug. Our analysis showed a positive correlation between the year of the first patient enrolled in these trials and median PFS/TTP reported (R ² = 0.34; p < 0.01). No correlation was found between the year of the first patient included in these trials and other potential prognostic factors such as visceral metastasis at baseline (R ² = 0.26; p = 0.20) or exposure to adjuvant therapy (R ² = 0.05; p = 0.18).

CONCLUSION

Patients treated with first-line AIs in the more recently conducted trials have longer PFS/TTP when compared to their counterparts treated with the same drugs in older studies. These findings have important implications for the estimation of sample size and follow-up periods for the planning of future trials as well as in the translation of the results into clinical practice decisions.

Abstract LB-246: Detection of circulating tumor DNA in early stage cancers

Early detection is a major goal for reducing mortality of human cancer. However, non-invasive detection of early stage tumors has remained a challenge. We have developed an approach called Targeted Error Correction Sequencing (TEC-Seq) for ultra-sensitive analyses of circulating cell-free tumor DNA (ctDNA). This methodology involves in-solution targeted capture of multiple regions of the genome and deep sequencing (~30,000x) of cell-free DNA fragments. Laboratory and bioinformatic methods were optimized to enrich for rare ctDNA molecules and to reduce potential amplification, sequencing, and contamination errors. We have used this approach to examine 58 cancer related genes, and demonstrated a limit of detection of mutant to wild-type DNA of 0.05% and a specificity &gt;99.999% across targeted regions of interest. We applied this method to analyze plasma from healthy individuals as well as over 200 individuals with breast, lung, colorectal and ovarian cancers. Analysis of plasma from 44 healthy individuals revealed no tumor-related somatic mutations and identified alterations in genes related to myelodysplasia in a subset of cases. Among patients with cancer, we detected measurable ctDNA in 56%, 71%, 57%, and 56% of patients with early stage (I and II) breast, colorectal, lung and ovarian cancer. Over three quarters of patients with late stage (III and IV) disease had detectable ctDNA among all cases analyzed. Analyses of mutations in the circulation revealed a high concordance with alterations in the independently analyzed tumors of these patients. These analyses provide a widely applicable, ultra-sensitive, and non-invasive method for detection of ctDNA, and have important implications for detection of early stage disease and management of patients with cancer.

Citation Format: Jillian A. Phallen, Mark Sausen, Vilmos Adleff, Alessandro Leal, Jacob Fiksel, Carolyn Hruban, Savannah Speir, Eniko Papp, Valsamo Anagnostou, Mai-Britt W. Orntoft, Thomas Reinert, Brian D. Woodward, Derek Murphy, Sonya Parpart-Li, David Riley, Monica Nesselbush, Naomi Sengamalay, Andrew Georgiadis, Rob Scharpf, Qing K. Li, Sian Jones, Samuel Angiuoli, Joost Huiskens, Cornelis Punt, Nicole van Grieken, Remond Fijneman, Gerrit Meijer, Hatim Husain, Luis Diaz, Torben Ørntoft, Hans J. Nielsen, Claus L. Anderson, Victor E. Velculescu. Detection of circulating tumor DNA in early stage cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-246. doi:10.1158/1538-7445.AM2017-LB-246

Clinical Implications of Monitoring Circulating Tumor DNA in Patients with Colorectal Cancer

Purpose: We investigated whether detection of ctDNA after resection of colorectal cancer identifies the patients with the highest risk of relapse and, furthermore, whether longitudinal ctDNA analysis allows early detection of relapse and informs about response to intervention.Experimental Design: In this longitudinal cohort study, we used massively parallel sequencing to identify somatic mutations and used these as ctDNA markers to detect minimal residual disease and to monitor changes in tumor burden during a 3-year follow-up period.Results: A total of 45 patients and 371 plasma samples were included. Longitudinal samples from 27 patients revealed ctDNA postoperatively in all relapsing patients (n = 14), but not in any of the nonrelapsing patients. ctDNA detected relapse with an average lead time of 9.4 months compared with CT imaging. Of 21 patients treated for localized disease, six had ctDNA detected within 3 months after surgery. All six later relapsed compared with four of the remaining patients [HR, 37.7; 95% confidence interval (CI), 4.2-335.5; P < 0.001]. The ability of a 3-month ctDNA analysis to predict relapse was confirmed in 23 liver metastasis patients (HR 4.9; 95% CI, 1.5-15.7; P = 0.007). Changes in ctDNA levels induced by relapse intervention (n = 19) showed good agreement with changes in tumor volume (κ = 0.41; Spearman ρ = 0.4).Conclusions: Postoperative ctDNA detection provides evidence of residual disease and identifies patients at very high risk of relapse. Longitudinal surveillance enables early detection of relapse and informs about response to intervention. These observations have implications for the postoperative management of colorectal cancer patients. Clin Cancer Res; 23(18); 5437-45. ©2017 AACR.

Comprehensive Transcriptional Analysis of Early-Stage Urothelial Carcinoma

Non-muscle-invasive bladder cancer (NMIBC) is a heterogeneous disease with widely different outcomes. We performed a comprehensive transcriptional analysis of 460 early-stage urothelial carcinomas and showed that NMIBC can be subgrouped into three major classes with basal- and luminal-like characteristics and different clinical outcomes. Large differences in biological processes such as the cell cycle, epithelial-mesenchymal transition, and differentiation were observed. Analysis of transcript variants revealed frequent mutations in genes encoding proteins involved in chromatin organization and cytoskeletal functions. Furthermore, mutations in well-known cancer driver genes (e.g., TP53 and ERBB2) were primarily found in high-risk tumors, together with APOBEC-related mutational signatures. The identification of subclasses in NMIBC may offer better prognostication and treatment selection based on subclass assignment.

Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery

OBJECTIVE

To develop an affordable and robust pipeline for selection of patient-specific somatic structural variants (SSVs) being informative about radicality of the primary resection, response to adjuvant therapy, incipient recurrence and response to treatment performed in relation to diagnosis of recurrence.

DESIGN

We have established efficient procedures for identification of SSVs by next-generation sequencing and subsequent quantification of 3-6 SSVs in plasma. The consequence of intratumour heterogeneity on our approach was assessed. The level of circulating tumour DNA (ctDNA) was quantified in 151 serial plasma samples from six relapsing and five non-relapsing colorectal cancer (CRC) patients by droplet digital PCR, and correlated to clinical findings.

RESULTS

Up to six personalised assays were designed for each patient. Our approach enabled efficient temporal assessment of disease status, response to surgical and oncological intervention, and early detection of incipient recurrence. Our approach provided 2-15 (mean 10) months' lead time on detection of metastatic recurrence compared to conventional follow-up. The sensitivity and specificity of the SSVs in terms of detecting postsurgery relapse were 100%.

CONCLUSIONS

We show that assessment of ctDNA is a non-invasive, exquisitely specific and highly sensitive approach for monitoring disease load, which has the potential to provide clinically relevant lead times compared with conventional methods. Furthermore, we provide a low-coverage protocol optimised for identifying SSVs with excellent correlation between SSVs identified in tumours and matched metastases. Application of ctDNA analysis has the potential to change clinical practice in the management of CRC.

Genomic Alterations in Liquid Biopsies from Patients with Bladder Cancer

BACKGROUND

At least half of the patients diagnosed with non-muscle-invasive bladder cancer (NMIBC) experience recurrence and approximately 15% will develop progression to muscle invasive or metastatic disease. Biomarkers for disease surveillance are urgently needed.

OBJECTIVE

Development of assays for surveillance using genomic variants in cell-free tumour DNA from plasma and urine.

DESIGN, SETTING, AND PARTICIPANTS

Retrospective pilot study of 377 samples from 12 patients with recurrent or progressive/metastatic disease. Three next-generation sequencing methods were applied and somatic variants in DNA from tumour, plasma, and urine were subsequently monitored by personalised assays using droplet digital polymerase chain reaction (ddPCR). Samples were collected from 1994 to 2015, with up to 20 yr of follow-up.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Progression to muscle-invasive or metastatic bladder cancer; t test for ddPCR data.

RESULTS AND LIMITATIONS

We developed from one to six personalised assays per patient. Patients with progressive disease showed significantly higher levels of tumour DNA in plasma and urine before disease progression, compared with patients with recurrent disease (p=0.032 and 1.3×10(-6), respectively). Interestingly, tumour DNA was detected in plasma and urine in patients with noninvasive disease, being no longer detectable in disease-free patients. A significant level of heterogeneity was observed for each patient; this could be due to tumour heterogeneity or assay performance.

CONCLUSIONS

Cell-free tumour DNA can be detected in plasma and urine, even in patients with noninvasive disease, with high levels of tumour DNA detectable before progression, especially in urine samples. Personalised assays of genomic variants may be useful for disease monitoring.

PATIENT SUMMARY

Tumour DNA can be detected in blood and urine in early and advanced stages of bladder cancer. Measurement of these highly tumour-specific biomarkers may represent a novel diagnostic tool to indicate the presence of residual disease or to discover aggressive forms of bladder cancer early in the disease course.

Abstract 5245: Identification and quantification of somatic structural variations in tumor, urine and plasma from bladder cancer patients

Bladder tumors can be divided into two clinically divergent groups, non-muscle invasive (NMIBC) and muscle invasive bladder tumors (MIBC). NMIBCs have a recurrence rate of 50-70%, while MIBCs often develop metastases. No molecular biomarkers are yet available to directly guide treatment and follow-up regimes for patients with BC.

Aim of this study was to identify tumor specific, large somatic structural variations (SSV) in DNA from tumors and quantify SSVs in DNA from urine and in circulating free DNA (cfDNA) in plasma from successive visits during treatment and follow-up.

Methods: Whole genome paired-end (WGS) or mate-pair (MPS) sequencing on HiSeq2000 and Nextseq sequencers. SSVs called by algorithms “CREST” or “Breakdancer”. cfDNA was extracted from 1-3 ml plasma. Quantification of SSVs was done by droplet digital PCR (ddPCR) using probes covering the breakpoint.

We selected six patients with progressive/metastatic disease, followed for 4 to 19 years with consecutive sampling of tumors, urine and plasma samples (4 to 27 visits). WGS was carried out on DNA from germ-line and tumors from four patients (57x and 45x read depth). CREST identified 20-226 SSVs per tumor. PCR assays (n = 170, 21-64 per patient) showed validation rates of 60-75% (CTX), 75-90% (ITX), 88-100% (INS) and 50% (INV) among the eight tumors. MPS was carried out on DNA from two patients (22-30x physical read depth). Breakdancer identified 82 and 120 SSVs, 24 and 13 were potential somatic with a validation rate of 69% and 79%. For each patient, 3-5 fluorescent probes covering the breakpoint were used to quantify the level of tumor specific by ddPCR. SSVs were quantified in tumor DNA from several visits. Their frequency varied considerably (0.08-0.54) between the individual tumors, indicating a large inter-tumor heterogeneity. SSVs detected in DNA from urine pellets were correlated to the presence of tumor and treatment for some cases. Inter-individual cfDNA level ranged from 600-3500 genomic equivalents (GEs) per ml plasma. SSVs were identified in plasma. The level of ctDNA ranged between 5-300 GEs/ml plasma and an increase in ctDNA was already detectable up to 21 months before progression to muscle invasive disease. For metastasized disease, a 42-fold increase of the ctDNA level was observed compared to localized disease. No SSVs were detected in cfDNA from patients cured from BC (3 and 7 years post-recurrence and 5 years post-cystectomy).

Conclusions: Tumor derived SSVs were identified and quantified in cfDNA from plasma of patients with progressive and metastatic BC. Detection of SSVs in cfDNA was possible at early time points before progression and metastasis of the disease were discovered by cystoscopy or image diagnostic. The tumor specific and highly sensitive detection and quantification of SSVs in cfDNA from plasma may offer a unique tool to monitor disease course, residual tumor burden, disease progression and treatment response in BC.

Citation Format: Karin Birkenkamp-Demtröder, Iver Nordentoft, Emil Christensen, Søren Hoyer, Thomas Reinert, Søren Vang, Jørgen Bjerggaard Jensen, Torben F. Ørntoft, Lars Dyrskjøt. Identification and quantification of somatic structural variations in tumor, urine and plasma from bladder cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5245. doi:10.1158/1538-7445.AM2015-5245

Mutational context and diverse clonal development in early and late bladder cancer

Bladder cancer (or urothelial cell carcinoma [UCC]) is characterized by field disease (malignant alterations in surrounding mucosa) and frequent recurrences. Whole-genome, exome, and transcriptome sequencing of 38 tumors, including four metachronous tumor pairs and 20 superficial tumors, identified an APOBEC mutational signature in one-third. This was biased toward the sense strand, correlated with mean expression level, and clustered near breakpoints. A>G mutations were up to eight times more frequent on the sense strand (p<0.002) in [ACG]AT contexts. The patient-specific APOBEC signature was negatively correlated to repair-gene expression and was not related to clinicopathological parameters. Mutations in gene families and single genes were related to tumor stage, and expression of chromatin modifiers correlated with survival. Evolutionary and subclonal analyses of early/late tumor pairs showed a unitary origin, and discrete tumor clones contained mutated cancer genes. The ancestral clones contained Pik3ca/Kdm6a mutations and may reflect the field-disease mutations shared among later tumors.

Abstract 3153: Whole genome and transcriptome analysis reveals novel genomic alterations in bladder cancer

Bladder cancer (BC) is a common malignancy with the highest incidence rates found in Europe and United

States where it rates as the fifth and fourth most common malignancy, respectively. There are two clinically distinct groups of BC, non-muscle invasive (NMIBC) and muscle invasive bladder tumors (MIBC) accounting at diagnosis for 75% and 25%, respectively, and demanding very different treatments. NMIBC have the highest cancer recurrence rate observed (50-70%) and often necessitates lifelong surveillance, however the prognosis is relatively good. MIBC in contrast often progresses and develop systemic disease. To improve the treatment of BC it is essential to understand the disease biology and to be able to predict disease progression. In this study we applied the advance of next generation sequencing technology to annotate genomic mutations and genomic rearrangements to base pair resolution in four metachronous BC cases (&gt;90% tumor cells) progressing from

Ta to T1 or T2, and matching blood. Furthermore, we explored clonal relationship among the initial tumor and the progressing tumor. Each sample was sequenced to 40-50 x whole genome coverage, 200 x targeted Exome sequencing, and 65 million paired end reads of whole transcriptome RNA-seq. Eight normal urothelium biopsies from BPH patients were used as reference for the RNA-seq. Notably we identified genetic high impact alterations in KDMA6A, PIK3CA, ZNF233, FGFR3, UBE3C, TMEM128, HOXA11,

HOXA2, ELF3, TP53, KAT2B and DYRK3 (corrected for background mutation rate). We annotated a total of 559 unique deletions, translocations, insertions and inversions. In total, 120 of these DNA breaks were selected for validation with

PCR and Sanger sequencing (80% validation rate). Ingenuity pathway analysis identified 19 canonical pathways significantly affected in four out of 8 samples. Currently we are validating the SNV findings in 50 BC samples using

Exome-Seq and RNA-seq. Furthermore, protein expression of selected genes are validated by immunohistochemistry on FFPE tissue sections from the discovery samples and on a tissue microarray containing 290 cores from Ta and T1 tumors in order to correlate protein expression to disease specific survival. All sequencing was performed on the Illumina HiSeq platform. The results reveal promising descriptive and potentially predictive knowledge that may help determine the genomic fingerprint facilitating progression of NMIBC to MIBC.

Citation Format: Iver K. Nordentoft, Karin Birkenkamp-Demtroder, Philippe Lamy, Thomas Reinert, Niels Fristrup, Jakob Skou Pedersen, Søren Vang, Jakob Hedegaard, Kasper Thorsen, Michael Borre, Lars Dyrskjøt, Torben Falck Ørntoft. Whole genome and transcriptome analysis reveals novel genomic alterations in bladder cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3153. doi:10.1158/1538-7445.AM2013-3153

Combinations of urinary biomarkers for surveillance of patients with incident nonmuscle invasive bladder cancer: the European FP7 UROMOL project

PURPOSE

We determined a combination of markers with optimal sensitivity to detect recurrence in voided urine after resection of an incident low grade, nonmuscle invasive bladder tumor.

MATERIALS AND METHODS

A total of 136 patients with G1/G2 nonmuscle invasive bladder tumor were included in the study at transurethral resection of the incident tumor. At least 3 followup urine samples were required for patient selection. DNA was extracted from the incident tumor and cell pellets of subsequently collected urine samples. We performed FGFR3, PIK3CA and RAS mutation analysis, and microsatellite and methylation analysis on tissue and urine DNA samples.

RESULTS

We obtained 716 urine samples. The 136 patients experienced a total of 552 recurrences during a median 3-year followup. Sensitivity for detecting a recurrent tumor varied between 66% and 68% for the molecular tests after patient stratification based on tumor DNA analysis. A combination of markers increased sensitivity but decreased the number of patients eligible for a certain test combination. Combining urine cytology with FGFR3 analysis without stratifying for FGFR3 status of the incident tumor increased sensitivity from 56% to 76%.

CONCLUSIONS

A combination of markers increased the percentage of patients eligible for urine based followup and the sensitivity of recurrence detection. Adding FGFR3 analysis to urine cytology could be valuable for noninvasive followup of patients with nonmuscle invasive bladder cancer.

Diagnosis of bladder cancer recurrence based on urinary levels of EOMES, HOXA9, POU4F2, TWIST1, VIM, and ZNF154 hypermethylation

Background

Non muscle invasive bladder cancer (NMIBC) has the highest recurrence rate of any malignancy and as many as 70% of patients experience relapse. Aberrant DNA methylation is present in all bladder tumors and can be detected in urine specimens. Previous studies have identified DNA methylation markers that showed significant diagnostic value. We evaluated the significance of the biomarkers for early detection of tumor recurrence in urine.

Methodology/Principal Findings

The methylation levels of EOMES, HOXA9, POU4F2, TWIST1, VIM, and ZNF154 in urine specimens were measured by real-time PCR (MethyLight). We analyzed 390 urine sediments from 184 patients diagnosed with NMIBC. Urine from 35 age-matched control individuals was used to determine the methylation baseline levels. Recurrence was diagnosed by cystoscopy and verified by histology. Initially, we compared urine from bladder cancer patients and healthy individuals and detected significant hypermethylation of all six markers (P<0.0001) achieving sensitivity in the range 82%–89% and specificity in the range 94%–100%. Following, we validated the urinary hypermethylation for use in recurrence surveillance and found sensitivities of 88–94% and specificities of 43–67%. EOMES, POU4F2, VIM and ZNF154 were more frequently methylated in urine from patients with higher grade tumors (P≤0.08). Univariate Cox regression analysis showed that five markers were significantly associated with disease recurrence; HOXA9 (HR = 7.8, P = 0.006), POU4F2 (HR = 8.5, P = 0.001), TWIST1 (HR = 12.0, P = 0.015), VIM (HR = 8.0, P = 0.001), and ZNF154 (HR = 13.9, P<0.001). Interestingly, for one group of patients (n = 15) we found that hypermethylation was consistently present in the urine samples despite the lack of tumor recurrences, indicating the presence of a field defect.

Conclusion/Significance

Methylation levels of EOMES, HOXA9, POU4F2, TWIST1, VIM, and ZNF154 in urine specimens are promising diagnostic biomarkers for bladder cancer recurrence surveillance.

Analysis of molecular intra-patient variation and delineation of a prognostic 12-gene signature in non-muscle invasive bladder cancer; technology transfer from microarrays to PCR

Background:

Multiple clinical risk factors and genetic profiles have been demonstrated to predict progression of non-muscle invasive bladder cancer; however, no easily clinical applicable gene signature has been developed to predict disease progression independent of disease stage and grade.

Methods:

We measured the intra-patient variation of an 88-gene progression signature using 39 metachronous tumours from 17 patients. For delineation of the optimal quantitative reverse transcriptase PCR panel of markers, we used 115 tumour samples from patients in Denmark, Sweden, UK and Spain.

Results:

Analysis of intra-patient variation of the molecular markers showed 71% similar classification results. A final panel of 12 genes was selected, showing significant correlation with outcome. In multivariate Cox regression analysis, we found that the 12-gene signature was an independent prognostic factor (hazard ratio=7.4 (95% confidence interval: 3.4–15.9), P<0.001) when adjusting for stage, grade and treatment. Independent validation of the 12-gene panel and the determined cut-off values is needed and ongoing.

Conclusion:

Intra-patient marker variation in metachronous tumours is present. Therefore, to increase test sensitivity, it may be necessary to test several metachronous tumours from a patient’s disease course. A PCR-based 12-gene signature significantly predicts disease progression in patients with non-muscle invasive bladder cancer.

Expression of MAGE-A3, NY-ESO-1, LAGE-1 and PRAME in urothelial carcinoma

BACKGROUND

The potential for cancer-testis (CT) antigens as targets for immunotherapy in cancer patients has been heavily investigated, and currently cancer vaccine trials based on the CT antigens, MAGE-A3 and NY-ESO-1, are being carried out.

METHODS

We used specific q-RT-PCR assays to analyse the expression of the CT genes MAGE-A3, NY-ESO-1 (CTAG1B), LAGE-1 (CTAG2) and PRAME in a panel of bladder tumours from 350 patients with long-term follow-up and detailed treatment information.

RESULTS

Overall, 43% of the tumours expressed MAGE-A3, 35% expressed NY-ESO-1, 27% expressed LAGE-1 and 20% expressed PRAME. In all, 56% of the tumours expressed at least one of the CT genes analysed. Univariate Cox regression analysis of CT gene expression in non-muscle-invasive tumours showed that expression of MAGE-A3 (P=0.026), LAGE-1 (P=0.001) and NY-ESO-1 (P=0.040) was significantly associated with a shorter progression-free survival. In addition, we found that patients with tumours expressing PRAME responded poorly to chemotherapy (P=0.02, χ(2)-test).

CONCLUSION

Cancer-testis genes are frequently expressed in bladder cancer and especially in tumours of high stage and grade. In addition, the CT gene expression may have both prognostic and predictive value. Development of specific immunotherapy against the CT antigens in bladder cancer may ultimately increase patient survival.

Abstract 3109: Correlation between genomic aberrations and the DNA damage response in bladder cancer

Carcinogenesis is paralleled by ongoing insults to tumor genome integrity, commonly sensed and reacted to by the DNA damage response (DDR). The DDR is thought to act as an inducible barrier against early tumor development, but, if compromised, may allow tumor progression and rampant genomic instability. However, the interplay between the DDR, genomic integrity, and tumor development is still poorly understood. To extend current knowledge of these issues, we analyzed 45 human bladder tumors from 22 patients using a combination of Affymetrix Genome-Wide Human SNP Arrays 6.0 and immunohistochemistry (IHC). This allowed us to characterize genomic aberrations at high resolution, and determine the tissue expression patterns of several DDR components in the context of the underlying genomic complexity. The complexity of individual SNP-profiles varied considerably and widespread aberrations included novel features such as 151 copy neutral loss of heterozygosity (LOH) regions. Some of these were of potential functional relevance because they spanned mutated FGFR3 and PIK3CA alleles, in addition to a homozygous deletion involving the p16 tumor suppressor locus at chr9p22. In fact, most (34/60) homozygous deletions identified were confined to this region. The SNP-profiles also showed that metachronous tumors generally had several aberrations in common, thus suggesting a clonal relationship. We partitioned tumor-derived SNP-profiles into three groups of increasing complexity, likely to reflect histories of varying genomic instability, and compared these to IHC results. DDR tissue staining patterns using phospho-specific antibodies against p53, γH2AX, ATR, and ATM, indicative of an activated DDR, were not correlated to the total sum of accumulated DNA damage. Rather, the most complex tumor genomes were associated with absence of p16 expression, a high Ki67-proliferation index, and abundant expression of the multifunctional DDR protein Timeless. Tipin, an important interaction partner of Timeless, was expressed without any association to Timeless staining patterns and genomic integrity. Interestingly, in a large cohort of more than 250 non-muscle invasive bladder tumors, Timeless expression was associated with risk of progression to muscle-invasive disease (p&lt;0.001; HR, 2.4; 95% CI, 1.6-3.8). In conclusion, we generated a high-resolution analysis of bladder tumor genomes and identified novel regions of potential functional relevance, including several copy neutral LOH regions. Moreover, we showed that the overall complexity of tumor genomes is not closely associated to common phosphorylation events within the DDR but instead involves p16 loss, high Ki67 index, and abundant Timeless expression. Finally, evaluation of Timeless expression by IHC may improve current approaches to estimate risk of progression in non-muscle invasive bladder tumors based on established histopathological variables.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3109. doi:1538-7445.AM2012-3109

Comprehensive genome methylation analysis in bladder cancer: identification and validation of novel methylated genes and application of these as urinary tumor markers

PURPOSE

Epigenetic alterations are common and can now be addressed in a parallel fashion. We investigated the methylation in bladder cancer with respect to location in genome, consistency, variation in metachronous tumors, impact on transcripts, chromosomal location, and usefulness as urinary markers.

EXPERIMENTAL DESIGN

A microarray assay was utilized to analyze methylation in 56 samples. Independent validation was conducted in 63 samples by a PCR-based method and bisulfite sequencing. The methylation levels in 174 urine specimens were quantified. Transcript levels were analyzed using expression microarrays and pathways were analyzed using dedicated software.

RESULTS

Global methylation patterns were established within and outside CpG islands. We validated methylation of the eight tumor markers genes ZNF154 (P < 0.0001), HOXA9 (P < 0.0001), POU4F2 (P < 0.0001), EOMES (P = 0.0005), ACOT11 (P = 0.0001), PCDHGA12 (P = 0.0001), CA3 (P = 0.0002), and PTGDR (P = 0.0110), the candidate marker of disease progression TBX4 (P < 0.04), and other genes with stage-specific methylation. The methylation of metachronous tumors was stable and targeted to certain pathways. The correlation to expression was not stringent. Chromosome 21 showed most differential methylation (P < 0.0001) and specifically hypomethylation of keratins, which together with keratin-like proteins were epigenetically regulated. In DNA from voided urine, we detected differential methylation of ZNF154 (P < 0.0001), POU4F2 (P < 0.0001), HOXA9 (P < 0.0001), and EOMES (P < 0.0001), achieving 84% sensitivity and 96% specificity.

CONCLUSIONS

We initiated a detailed mapping of the methylome in metachronous bladder cancer. Novel genes with tumor, chromosome, as well as pathway-specific differential methylation in bladder cancer were identified. The methylated genes were promising cancer markers for early detection of bladder cancer.

Abstract 4801: Comprehensive genome methylation analysis in bladder cancer; identification and validation of novel methylated genes and application of these as urinary tumor markers

Cancer of the urinary bladder is one of the major cancers being the fifth most common neoplasm in the industrialised countries. Urothelial carcinomas account for more than 90% of all bladder cancers. The majority of bladder cancers are non-muscle invasive cancers characterized by frequent recurrences after resection and up to 25% will develop an aggressive phenotype. We investigated the methylation in bladder cancer with respect to location in genome, consistency, variation in metachronous tumors, impact on transcripts, chromosomal location, and usefulness as urinary markers of bladder cancer.

In this study, a microarray assay with more than 27.000 CpG sites was utilized to analyze methylation in 56 samples. Independent validations were performed in 63 samples by methylation-sensitive high-resolution melting (MS-HRM) and bisulfite sequencing. Transcript levels were analyzed using expression microarrays, and pathways using dedicated software. DNA from 40 urinary specimens was analyzed by MS-HRM.

Our results show that global methylation patterns were established within and outside CpG-islands. Differential methylation (p&lt;0.0001 to p&lt;0.05) was identified in 1588 genes between normals and cancers, in 1019 genes with stage specific methylation, and in 149 genes as progression markers. We validated methylation of eight genes, the tumor markers ZNF154 (p&lt;0.0001), HOXA9 (p&lt;0.0001), and POU4F2 (p&lt;0.0001) and the progression marker TBX4 (p&lt;0.002). The methylation of metachronous tumors was relatively stable and targeted to certain pathways. The correlation to expression was not stringent. Chromosome 21 showed most differential methylation (p&lt;0.0001) and specifically hypomethylation of keratins, which together with keratin like proteins were epigenetically regulated. In DNA from voided urine we detected differential methylation of ZNF154 (p&lt;0.0001), POU4F2 (p&lt;0.0001), and HOXA9 (p&lt;0.0044), achieving 94% sensitivity and 100% specificity.

Our results suggest that both hypo- and hyper methylation is stage dependent, over-represented at chromosome 21, and has a restricted influence on transcript levels in general, but clearly on keratins. The methylated genes are highly promising urinary cancer markers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4801. doi:10.1158/1538-7445.AM2011-4801

New Routes to Silicic Acid Containing Inorganic-Organic Hybrid Precursors and Polymers

In view of the outstanding role that silicic acids (sa.) play in inorganic materials a survey will be presented regarding the possibilities of the integration of sa. in organic matrices via chemical reactions. The objective is to combine the advantageous properties of the silicic acid with those of the organic compounds in order to generate novel materials. The reactions of silicic acids with organic molecules, as studied by 29Si NMR spectroscopy, are described using the silicic acid H8Si8O20 with a defined double four-ring structure as an example. By silylation of the hydrophilic H8Si8O20 its functional organophilic derivatives were synthesized. The s.a. derivatives with epoxy-, alkoxy-, HSi-, ketoester or unsaturated groups are capable of condensation, polymerization, complexation or additive reactions leading to reactive inorganic-organic precursors or polymers with the defined silicic acid unit. The synthesis and structure of the following s.a. containing precursors and polymers will be reported, (a) inorganic-organic polymers with a high content of silanol groups, (b) microporous polymers free of silanol groups and (c) metal (Al, Zr) alkoxide complexes attached to defined silicic acid units. The model reactions of the double four-ring silicic acid derivatives can be transferred to technical silicic acid solutions prepared from water glass. The presented reaction pathways are a basis for the preparation of a great variety of new inorganic-organic compounds with tailor-made structures and properties which can be used for highly homogeneous and stoichiometric materials.

Development of chloride-mediated inhibition in neurons of the anteroventral cochlear nucleus of gerbil (Meriones unguiculatus)

At the initial stages in neuronal development, GABAergic and glycinergic neurotransmission exert depolarizing responses, assumed to be of importance for maturation, which in turn shift to hyperpolarizing in early postnatal life due to development of the chloride homeostasis system. Spherical bushy cells (SBC) of the mammalian cochlear nucleus integrate excitatory glutamatergic inputs with inhibitory (GABAergic and glycinergic) inputs to compute signals that contribute to sound localization based on interaural time differences. To provide a fundamental understanding of the properties of GABAergic neurotransmission in mammalian cochlear nucleus, we investigated the reversal potential of the GABA-evoked currents (E GABA) by means of gramicidin-perforated-patch recordings in developing SBC. The action of GABA switches from depolarizing to hyperpolarizing by the postnatal day 7 due to the negative shift in E GABA. Furthermore, we studied the expression pattern of the K+-Cl(-)-extruding cotransporter KCC2, previously shown to induce a switch from neonatal Cl(-) efflux to the mature Cl(-) influx in various neuron types, thereby causing a shift from depolarizing to hyperpolarizing GABA action. The KCC2 protein is expressed in SBC already at birth, yet its activity is attained toward the end of the first postnatal week as indicated by pharmacological inhibition. Interruption of the Cl(-) extrusion by [(dihydroindenyl)oxy] alkanoic acid or furosemide gradually shifted E(GABA) in positive direction with increasing maturity, suggesting that KCC2 could be involved in maintaining low [Cl(-)]i after the postnatal day 7 thereby providing the hyperpolarizing Cl(-)-mediated inhibition in SBC.

Treatment of alcohol withdrawal syndrome with a combination of tiapride/carbamazepine: results of a pooled analysis in 540 patients

This was a retrospective study to examine the efficacy, practicability and medical safety of a combination of tiapride and unretarded (fast acting formula) carbamazepine in the treatment of alcohol withdrawal syndrome. In five hospitals using this combination for treatment of alcohol withdrawal, 540 patients who had been treated with this combination were identified. An intensive evaluation of patients files and charts was performed. Details of alcohol history and comorbid disorders were extracted from patient files. Severity of alcohol withdrawal had been assessed using the CIWA-A-Score. Gender differences and differences between patients in their first and at least second withdrawal were computed by means of variance analyses (GLM). At baseline (day 1) mean dosage given was 796 for tiapride and 543 mg for carbamazepine. A pooled analysis of the results showed that, in general, medication was well tolerated. Withdrawal symptomatology as indicated by CIWA-A scores clearly decreased over time. Although a significant number of patients had a history of alcohol withdrawal delirium (103) and epileptic seizures (151), few patients suffered from them during treatment (8 and 5, respectively). Only 24 (4.4%) patients dropped out because of lack of efficacy or change of medication, 15 (2.8%) because of side effects. No case of malignant neuroleptic syndrome was recorded. Data analysis showed gender differences and differences between patients in their first and at least second withdrawal for side effects, complications, and in some CIWA-A-scores. In general, severe complications of withdrawal syndrome were more frequent in men compared to women and in patients with repeated inpatient treatment. In line with previous research, the results from this study give further evidence that a combination of the anticonvulsant carbamazepine and tiapride is an effective and safe treatment for alcohol withdrawal treatment.