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Plots showing percentage changes in total cfDNA concentration for each patient at weeks 4 and 8 of treatment, compared to same-patient baseline value. The left plot includes non-responding patients and the right plot includes patients who responded to olaparib in the clinical trial. Below, Mann-Whitney test comparing these changes at each time point for responders and non-responder patients.

Consort diagram describing samples disposition in the study.

Supplementary figure and table legends

Supplementary Data 6: Monitoring of somatic genomic alterations in plasma during targeted therapy. Allele frequencies (AF) of identified mutations are represented on the left Y-axis while the sum of the target lesions on the CT scan, are represented on the right Y-axis.

Additional Information on molecular analyses determining CHD1 and SPOP status

Supplementary Data 1: Primers and probes for ddPCR assay Supplementary Data 2: Consort Diagram Supplementary Data 3: List of drugs Supplementary Data 4: Cross validation of PGM sequencing assay with ddPCR Supplementary Data 5: To test intra-run assay performance, 3 different libraries were prepared using the same plasma cfDNA from a single patient Supplementary Data 6: See figure 6 below. Supplementary Data 7: Time to progression for patients having a 30% decrease in plasma mutation AF, following targeted drug administration, and association with time to progression by RECIST evaluation.

Sample overview

Figure S1. Flowchart of study selection process with ICIs treatment. Figure S2. Flowchart of study selection process with TAs treatment. Figure S3. Overall Survival comparing HPD with non-HPD in patients with progression disease as best response in the ICIs and TAs cohorts ( RECIST 1.1 progression disease Landmark Analysis). Figure S4. Overall Survival in second line (a) and third (b) setting HPD vs non-HPD progressors by RECIST criteria in ICIs cohort. Figure S5. Concordance between RECIST and TGR criteria in ICIs cohort. Table S1. Computed tomography (CT) acquisition protocol parameters. Table S2. Clinical variables in patients treated with TAs. Table S3. Multivariate model in patients with progression disease as best response in ICIs group (using TGR).

SPOP mutation identified in this cohort.

Purpose: CHD1 deletions and SPOP mutations frequently cooccur in prostate cancer with lower frequencies reported in castration-resistant prostate cancer (CRPC). We monitored CHD1 expression during disease progression and assessed the molecular and clinical characteristics of CHD1-deleted/SPOP-mutated metastatic CRPC (mCRPC).Experimental Design: We identified 89 patients with mCRPC who had hormone-naive and castration-resistant tumor samples available: These were analyzed for CHD1, PTEN, and ERG expression by IHC. SPOP status was determined by targeted next-generation sequencing (NGS). We studied the correlations between these biomarkers and (i) overall survival from diagnosis; (ii) overall survival from CRPC; (iii) duration of abiraterone treatment; and (iv) response to abiraterone. Relationship with outcome was analyzed using Cox regression and log-rank analyses.Results: CHD1 protein loss was detected in 11 (15%) and 13 (17%) of hormone-sensitive prostate cancer (HSPC) and CRPC biopsies, respectively. Comparison of CHD1 expression was feasible in 56 matched, same patient HSPC and CRPC biopsies. CHD1 protein status in HSPC and CRPC correlated in 55 of 56 cases (98%). We identified 22 patients with somatic SPOP mutations, with six of these mutations not reported previously in prostate cancer. SPOP mutations and/or CHD1 loss was associated with a higher response rate to abiraterone (SPOP: OR, 14.50 P = 0.001; CHD1: OR, 7.30, P = 0.08) and a longer time on abiraterone (SPOP: HR, 0.37, P = 0.002, CHD1: HR, 0.50, P = 0.06).Conclusions: SPOP-mutated mCRPCs are strongly enriched for CHD1 loss. These tumors appear highly sensitive to abiraterone treatment. Clin Cancer Res; 24(22); 5585–93. ©2018 AACR.

Purpose:Most hyperprogression disease (HPD) definitions are based on tumor growth rate (TGR). However, there is still no consensus on how to evaluate this phenomenon.Patients and Methods:We investigated two independent cohorts of patients with advanced solid tumors treated in phase I trials with (i) programmed cell death 1 (PD-1)/PD-L1 antibodies in monotherapy or combination and (ii) targeted agents (TA) in unapproved indications. A Response Evaluation Criteria in Solid Tumors (RECIST) 1.1–based definition of hyperprogression was developed. The primary endpoint was the assessment of the rate of HPD in patients treated with ICIs or TAs using both criteria (RECIST and TGR) and the impact on overall survival (OS) in patients who achieved PD as best response.Results:Among 270 evaluable patients treated with PD-1/PD-L1 inhibitors, 29 PD-1/PD-L1–treated patients (10.7%) had HPD by RECIST definition. This group had a significantly lower OS (median of 5.23 months; 95% CI, 3.97–6.45) when compared with the non-HPD progressor group (median, 7.33 months; 95% CI, 4.53–10.12; HR = 1.73, 95% CI, 1.05–2.85; P = 0.04). In a subset of 221 evaluable patients, 14 (6.3%) were categorized as HPD using TGR criteria, differences in median OS (mOS) between this group (mOS 4.2 months; 95% IC, 2.07–6.33) and non-HPD progressors (n = 44) by TGR criteria (mOS 6.27 months; 95% CI, 3.88–8.67) were not statistically significant (HR 1.4, 95% IC, 0.70–2.77; P = 0.346). Among 239 evaluable patients treated with TAs, 26 (10.9%) were classified as having HPD by RECIST and 14 using TGR criteria in a subset of patients. No differences in OS were observed between HPD and non-HPD progressors treated with TAs.Conclusions:HPD measured by TGR or by RECIST was observed in both cohorts of patients; however, in our series, there was an impact on survival only in the immune-checkpoint inhibitor cohort when evaluated by RECIST. We propose a new way to capture HPD using RECIST criteria that is intuitive and easy to use in daily clinical practice.

Combined SPOP/ CHD1 status and time/ response to abiraterone.

Background: Mucinous colorectal carcinoma (CRC) is found in 10-20% of patients and is associated with worse prognosis and treatment resistance. The early identification of mucinous tumor component at baseline and monitoring resistant clones at follow-up is challenging in clinical practice, which hinders appropriate and timely treatment selection. At CT, being routinely acquired in clinical practice, mucinous tumors can be characterized by semantic features, such as hypoattenuation and more heterogeneous enhancement than the non-mucinous tumors (Wnorowski et al 2019). However, the diagnostic accuracy of such CT findings reaches at most 62% (Young et al 2007). This can be substantially improved by utilizing robust feature quantification using state-of-art machine learning and neural network techniques. Materials and Methods: 7 mucinous and 7 non-mucinous CRC CTs were included in the model development (80% training and 20% validation) and 2 mucinous and 2 non-mucinous independent patients were used to test the model performance. Multiple lesions (primary and metastatic) were semi-automatically segmented in 3D Slicer (N=32 development and N=12 test). Three different classification models were generated using CT images: (1) a logistic regression model based on a newly developed hypodense tissue connectivity (HTC) metric, (2) a logistic regression model using a set of automatically selected radiomics (RAD) features (shape, 1st order and 2nd order) and (3) a convolutional neural network model (CNN) based on the ResNet architecture and automatically selected features. HTC was computed as a ratio between the volume of the connected hypodense tissue (0 Citation Format: Kinga Bernatowicz, Raquel Perez Lopez, Hector Garcia Palmer, Elena Elez Fernandez, Jose Fernandez Navarro, Marta Ligero Hernandez, Alonso Garcia Ruiz, Manuel Escobar Amores. Humans cannot accurately detect mucinous colorectal carcinoma from CT images, can AI help? [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-021.

Purpose: We evaluated whether next-generation sequencing (NGS) of circulating cell-free DNA (cfDNA) could be used for patient selection and as a tumor clone response biomarker in patients with advanced cancers participating in early-phase clinical trials of targeted drugs. Experimental Design: Plasma samples from patients with known tumor mutations who completed at least two courses of investigational targeted therapy were collected monthly, until disease progression. NGS was performed sequentially on the Ion Torrent PGM platform. Results: cfDNA was extracted from 39 patients with various tumor types. Treatments administered targeted mainly the PI3K–AKT–mTOR pathway (n = 28) or MEK (n = 7). Overall, 159 plasma samples were sequenced with a mean sequencing coverage achieved of 1,685X across experiments. At trial initiation (C1D1), 23 of 39 (59%) patients had at least one mutation identified in cfDNA (mean 2, range 1–5). Out of the 44 mutations identified at C1D1, TP53, PIK3CA and KRAS were the top 3 mutated genes identified, with 18 (41%), 9 (20%), 8 (18%) different mutations, respectively. Out of these 23 patients, 13 received a targeted drug matching their tumor profile. For the 23 patients with cfDNA mutation at C1D1, the monitoring of mutation allele frequency (AF) in consecutive plasma samples during treatment with targeted drugs demonstrated potential treatment associated clonal responses. Longitudinal monitoring of cfDNA samples with multiple mutations indicated the presence of separate clones behaving discordantly. Molecular changes at cfDNA mutation level were associated with time to disease progression by RECIST criteria. Conclusions: Targeted NGS of cfDNA has potential clinical utility to monitor the delivery of targeted therapies. Clin Cancer Res; 21(20); 4586–96. ©2015 AACR.

INTRODUCTION: Response assessment of bone metastases (BM) remains a challenge for drug development in metastatic castration resistant prostate cancer (mCRPC) as standard imaging techniques, computed tomography and bone scintigraphy, fail to characterize BM. Diffusion-weighted imaging (DWI) is a functional MRI technique that studies the motion of water molecules within a tissue informing on cellularity. We hypothesized that changes in whole body (WB) DWI informs on BM response to treatment in mCRPC. METHODS: We conducted a phase II trial of the PARP inhibitor olaparib in mCRPC (TOPARP-A; CRUK/11/029); the primary endpoint was response rate defined using RECIST 1.1, PSA falls of ≥50% and conversion of circulating tumour cell (CTC) counts from ≥5 to RESULTS: Overall, 33/42 pt consented to the WB-DWI substudy of whom 21 had WB-DWI at baseline and at 12w. Of these 29% (6/21) were classified as responders to olaparib as per the primary endpoint definition and had not progressed prior to 12w. At baseline, median CTC count was 46 CTC/7.5ml blood and median PSA was 411 ng/ml for this cohort. When assessing all the areas of DWI signal abnormality, median volume of BM per patient was 445ml and mADC was 782 x10-6 mm2/s. Baseline CTC counts and PSA were significantly associated with volume of BM (ρ = 0.59, p = 0.005; ρ = 0.64, p = 0.002 respectively). All pts who responded to olaparib showed a decrease in volume of BM (median -41.1%, range -58.8%, -6.3%), whilst in non-responders a decrease was not observed in any pt (median 20.7%, range 0.0%, 76.9%); the difference between responders and non-responders was statistically significant (p = 0.001). Increases in mADC after 12 weeks of treatment were associated with increased odds of response (Odds Ratio: 1.08, 95% CI 1.00, 1.15, p = 0.04). Additionally, we detected a significant positive association between changes in volume of BM estimated by DWI and best percentage change in PSA and CTC (ρ = 0.63, p = 0.002 and ρ = 0.77, p CONCLUSION: Decrease in volume and increase in mADC of BM assessed by WB-DWI are indicators of response to olaparib in BM from mCRPC. These data require validation but support the use of WB-DWI for assessing BM during treatment. Citation Format: Raquel Perez-Lopez, Matthew D. Blackledge, Helen Mossop, Joaquin Mateo, David Collins, Veronica A. Morgan, Alison McDonald, Shahneen Sandhu, Aurelius Omlin, Diletta Bianchini, Zafeiris Zafeiriou, Pasquale Rescigno, Michael Kolinsky, Daniel Nava Rodrigues, Penny Flohr, Berni Ebbs, Gemma Fowler, Nuria Porta, Emma Hall, Martin Leach, Johann S. de Bono, Dow-Mu Koh, Nina Tunariu. Diffusion-weighted imaging of bone metastases as treatment response biomarker in prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3973.

Background: ATR mediates the homologous recombination DNA repair pathway and cellular response to replication stress. VX-970 is a potent and selective inhibitor of ATR (Ki Methods: Pts with advanced solid tumors enrolled in 2 sequential parts. Part A: pts received IV VX-970 mono weekly in single-pt cohorts, with 3+3 cohorts initiated if grade (G) ≥2 VX-970-related adverse events (AEs) were observed. Part B: pts received CP on day 1 and VX-970 on days 2 and 9 of a 21-day cycle in a 3+3 dose-escalation design. Paired VX-970 tumor biopsies were obtained in selected CP treated pts pre- and post-VX-970, and pS345 Chk1 levels assessed by IHC. Results: 25 pts were treated; M/F 10/15; median age 67 yr (range 49-76 yr); ECOG PS 0/1: 11/14. In Part A, 11 pts (colorectal [CRC; n = 2]; mesothelioma [n = 2]; other [n = 7]; median prior lines of therapy = 3) received VX-970 at 60 mg/m2 (n = 1), 120 mg/m2 (n = 2), 240 mg/m2 (n = 1) and 480 mg/m2 (n = 7). In Part B, 14 pts (CRC [n = 6]; ovarian [n = 2]; other [n = 6]; median prior lines of therapy = 3) received VX-970 240 mg/m2 + CP AUC5 (n = 3; dose level 1 [DL1]), VX-970 120 mg/m2 + CP AUC5 (n = 3; DL2), VX-970 120 mg/m2 + CP AUC4 (n = 3; DL3) and VX-970 90 mg/m2 + CP AUC5 (n = 5; DL4). In Part A, no dose-limiting toxicities (DLT) or drug-related G3-4 AEs were seen. In Part B, 2 pts had DLT: G4 neutropenia and fever (n = 1; DL1) and G3 hypersensitivity (n = 1; DL2). Non-DLT G3-4 AEs were neutropenia (n = 4; DL1-2) and thrombocytopenia (n = 1; DL2) requiring dose delays. No G3-4 AEs were seen at DL3-4. RP2D cohort expansion is ongoing at DL4. VX-970 displayed linear AUC and Cmax at all DLs; median half-life was 16h with no accumulation. Based on preclinical models, efficacious exposures were achieved. When combined with CP, DL1 and DL2 showed similar VX-970 exposure, suggesting no apparent drug interactions. Decreased Chk1 phosphorylation was seen in 2/2 paired tumor biopsies (74% at DL4; 94% at DL2). An advanced CRC pt (serosal disease and abdominal lymphadenopathy; 3 prior lines of chemotherapy) with complete ATM loss by IHC achieved RECIST complete response to VX-970 mono at 60 mg/m2 and remains on trial at 59+ wks. RECIST stable disease (SD) was seen with VX-970 mono in 4 pts (median duration of SD = 11 wks [11-17.4 wks]) and VX-970 + CP in 7 pts, who were still ongoing (duration of SD = 5+ to 20+ wks), including several pts who had progressed on prior platinum therapy. Conclusion: VX-970 is well tolerated as monotherapy and in combination with CP, with preliminary evidence of target modulation and antitumor activity. VX-970 will be further explored in early phase II studies; in multiple tumor types, including triple-negative breast cancer and non-small cell lung cancer; and in patients with DDR aberrations. Citation Format: Timothy A. Yap, Maria J. de Miguel Luken, Brent O'Carrigan, Desam Roda, Dionysis Papadatos-Pastos, David Lorente, Nina Tunariu, Raquel Perez Lopez, Sasha Gayle, Ruth Riisnaes, Ines Figueiredo, Susana Miranda, Suzanne Carreira, Fang Yang, Sharon Karan, Marina Penney, John Pollard, L. Rhoda Molife, Udai Banerji, Mohammed Asmal, Scott Z. Fields, Johann S. de Bono. Phase I trial of first-in-class ataxia telangiectasia-mutated and Rad3-related (ATR) inhibitor VX-970 as monotherapy (mono) or in combination with carboplatin (CP) in advanced cancer patients (pts) with preliminary evidence of target modulation and antitumor activity. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr PR14.

Introduction: Next generation sequencing (NGS) has identified genomic aberrations causing DNA repair defects in sporadic metastatic castration resistant prostate cancer (mCRPC). We hypothesized that single agent olaparib would have antitumor activity in a sub-population of mCRPC patients (pts) and that exome and transcriptome studies would identify this population. Methods: TOPARP is an open-label, investigator-initiated phase II trial with a novel multi-step adaptive design (CRUK/11/029). The first part of the study (TOPARP-A) has a two-stage design evaluating the antitumor activity of single agent olaparib in unselected mCRPC pts (p0 = 0.05; p1 = 0.20; α = 0.02; β = 0.10) with a preplanned analysis to identify a biomarker defined sensitive subgroup. Primary endpoint, response rate (RR), was defined as objective response by RECIST 1.1 and/or PSA fall ≥50% and/or confirmed circulating tumor cell (CTC) count falls from ≥5 to Results: Fifty pts were enrolled from 7 UK centers; all had had prior docetaxel, 48 (96%) prior abiraterone and 29 (58%) prior cabazitaxel. Overall, 16 of 49 evaluable pts experienced a response (RR 32.7%, 95% CI: 20.0 to 47.5), with 11 and 4 pts having been on treatment for >6 and >12 months respectively at data cut-off. NGS identified homozygous deletions and/or putatively deleterious mutations in DNA repair genes in 15/49 (30.6%) evaluable pts. While a majority of these genomic aberrations occurred in BRCA2 and ATM, biallelic loss of other relevant genes, including members of the Fanconi Anemia complementation group and CHEK2, were also observed. Among these fifteen pts, 13 (86.7%) responded to olaparib. All seven pts with BRCA2 loss (somatic [4/7] or germline [3/7]) and 4/5 pts with ATM truncating mutations responded to olaparib. The specificity of the biomarker suite was 94% in this population. Conversely, PTEN loss and ERG rearrangements were not associated with response. Finally, consistent with previous studies of olaparib, anemia (10/50, 20%) and fatigue (6/50, 12%) were the most common grade>3 adverse events, with 13 (26%) pts requiring a dose reduction. Conclusions: Olaparib has durable antitumor activity in heavily pre-treated pts with sporadic mCRPC with a 32.7% overall response rate. Genomic defects in DNA repair genes associate with olaparib sensitivity in sporadic mCRPC, offering a possibility for the very first molecular treatment stratification of advanced prostate cancer. Citation Format: Joaquin Mateo, Shahneen Sandhu, Susana Miranda, Suzanne Carreira, Suneil Jain, Christy Ralph, Andrew Protheroe, Syed Hussain, Robert Jones, Tony Elliot, Ursula McGovern, Alexa Gillman, Claire Paulding, Helen Mossop, Nuria Porta, Diletta Bianchini, Zafeiris Zafeiriou, Gunther Boysen, Daniel Nava Rodrigues, Penelope Flohr, George Seed, Jane Goodall, Ines Figueiredo, Raquel Perez-Lopez, Nina Tunariu, Aurelius Omlin, Roberta Ferraldeschi, Lakshmi P. Kunju, Rosalind Eeles, Gerhardt Attard, Dan Robinson, Arul Chinnaiyan, Emma Hall, Johann S. de Bono. DNA repair defects and antitumor activity with PARP inhibition: TOPARP, a phase II trial of olaparib in metastatic castration resistant prostate cancer. [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 CT322. doi:10.1158/1538-7445.AM2015-CT322