1
|
Rolfo CD, Madison RW, Pasquina LW, Brown DW, Huang Y, Hughes JD, Graf RP, Oxnard GR, Husain H. Measurement of ctDNA Tumor Fraction Identifies Informative Negative Liquid Biopsy Results and Informs Value of Tissue Confirmation. Clin Cancer Res 2024:741992. [PMID: 38526394 DOI: 10.1158/1078-0432.ccr-23-3321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/23/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
PURPOSE Liquid biopsy (LBx) for tumor profiling is increasingly used, but concerns remain regarding negative results. A lack of results may truly reflect tumor genomics, or it may be a false negative that would be clarified by tissue testing. A method of distinguishing between these scenarios could help clarify when follow-on tissue testing is valuable. EXPERIMENTAL DESIGN Here we evaluate circulating tumor DNA (ctDNA) tumor fraction (TF), a quantification of ctDNA in LBx samples, for utility in identifying true negative results.We assessed concordance between LBx and tissue-based results, stratified by ctDNA TF, in a real-world genomic data set of paired samples across multiple disease types. We also evaluated the frequency of tissue results identifying driver alterations in lung cancer patients after negative LBx in a real-world clinicogenomic database. RESULTS The positive percent agreement and negative predictive value between liquid and tissue samples for driver alterations increased from 63% and 66% for all samples to 98% and 97% in samples with ctDNA TF ≥1%. Among 505 lung cancer patients with no targetable driver alterations found by LBx who had subsequent tissue-based profiling, 37% had a driver, all of which had ctDNA TF <1%. CONCLUSIONS Lung cancer patients with negative LBx and ctDNA TF ≥1% are unlikely to have a driver detected on confirmatory tissue testing; such informative negative results may benefit instead from prompt treatment initiation. Conversely, negative LBx with ctDNA TF <1% will commonly have a driver identified by follow-on tissue testing and should be prioritized for reflex testing.
Collapse
Affiliation(s)
- Christian D Rolfo
- Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | | | | | | | - Yanmei Huang
- Foundation Medicine, Inc, Boston, MA, United States
| | | | - Ryon P Graf
- Foundation Medicine, San Diego, CA, United States
| | | | - Hatim Husain
- University of California, San Diego, San Diego, CA, United States
| |
Collapse
|
2
|
Rotow JK, Lee JK, Madison RW, Oxnard GR, Jänne PA, Schrock AB. Real-World Genomic Profile of EGFR Second-Site Mutations and Other Osimertinib Resistance Mechanisms and Clinical Landscape of NSCLC Post-Osimertinib. J Thorac Oncol 2024; 19:227-239. [PMID: 37806383 DOI: 10.1016/j.jtho.2023.09.1453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION The emergence of osimertinib as standard of care for EGFR-mutant NSCLC has renewed the need to understand and overcome drug resistance. We sought to understand the genomics and real-world treatment landscape of NSCLC with EGFR C797S and other on- and off-target resistance mechanisms. METHODS Comprehensive genomic profiling (CGP) results from tissue or blood samples from 93,065 patients with NSCLC were queried for osimertinib EGFR second-site resistance mutations (ssEGFRms; C797, L718, G724, G796, L792). A real-world electronic health record-derived deidentified clinicogenomic database of patients with NSCLC undergoing CGP from approximately 280 U.S. cancer clinics was queried to assess post-osimertinib resistance and clinical treatment outcomes. RESULTS A ssEGFRm was identified in 239 of 8845 (2.7%) EGFR-driven (L858R or exon 19 deletion) NSCLCs, most frequently C797 (71%), L718 (15%), and G724 (9.5%). ssEGFRms were not equally distributed across drivers; C797 and G724 changes strongly favored exon 19 deletion and L718, G796 and L792 favored L858R. Post-osimertinib CGP detected ssEGFRm in 19% of the cases (39 of 205); in paired pre-/post-osimertinib samples, on- and off-target resistance was largely mutually exclusive and observed in 24% and 27% of the cases, respectively. Of 391 patients with post-osimertinib treatment data, 62% received a chemotherapy-based regimen, whereas 25% received a targeted therapy or clinical study drug. Median real-world overall survival was 11.4 months from osimertinib progression. CONCLUSIONS The osimertinib resistance landscape is diverse with on-target ssEGFRm and off-target resistance detected in tissue and liquid biopsy. Post-osimertinib, patients are receiving primarily chemotherapy-based regimens with poor outcomes, and CGP at resistance may offer an opportunity to inform therapeutic development and improve treatment selection.
Collapse
Affiliation(s)
- Julia K Rotow
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jessica K Lee
- Department of Clinical Development, Foundation Medicine, Inc., Boston, Massachusetts
| | - Russell W Madison
- Department of Clinical Development, Foundation Medicine, Inc., Boston, Massachusetts
| | - Geoffrey R Oxnard
- Department of Clinical Development, Foundation Medicine, Inc., Boston, Massachusetts
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alexa B Schrock
- Department of Clinical Development, Foundation Medicine, Inc., Boston, Massachusetts.
| |
Collapse
|
3
|
Russo A, Lee JK, Pasquina LW, Del Re M, Dilks HH, Murugesan K, Madison RW, Lee Y, Schrock AB, Comment L, Dietrich M, Oxnard GR, Rolfo C. Liquid Biopsy of Lung Cancer Before Pathological Diagnosis Is Associated With Shorter Time to Treatment. JCO Precis Oncol 2024; 8:e2300535. [PMID: 38295321 PMCID: PMC10843270 DOI: 10.1200/po.23.00535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024] Open
Abstract
PURPOSE Studies have investigated the early use of liquid biopsy (LBx) during the diagnostic workup of patients presenting with clinical evidence of advanced lung cancer, but real-world adoption and impact has not been characterized. The aim of this study was to determine whether the use of LBx before diagnosis (Dx; LBx-Dx) enables timely comprehensive genomic profiling (CGP) and shortens time until treatment initiation for advanced non-small-cell lung cancer (aNSCLC). MATERIALS AND METHODS This study used the Flatiron Health-Foundation Medicine electronic health record-derived deidentified clinicogenomic database of patients with aNSCLC from approximately 280 US cancer clinics. RESULTS Of 1,076 patients with LBx CGP ordered within 30 days prediagnosis/postdiagnosis, we focused on 56 (5.2%) patients who ordered LBx before diagnosis date (median 8 days between order and diagnosis, range, 1-28). Compared with 1,020 patients who ordered LBx after diagnosis (Dx-LBx), LBx-Dx patients had similar stage and ctDNA tumor fraction (TF). LBx-Dx patients received CGP results a median of 1 day after Dx versus 25 days for Dx-LBx patients. Forty-three percent of LBx-Dx were positive for an National Comprehensive Cancer Network driver, and 32% had ctDNA TF >1% but were driver negative (presumed true negatives). In 748 patients with previously untreated aNSCLC, median time from Dx to therapy was shorter in the LBx-Dx versus Dx-LBx group (21 v 35 days; P < .001). CONCLUSION Early LBx in anticipation of pathologic diagnosis of aNSCLC was uncommon in this real-world cohort, yet this emerging paradigm was associated with an abbreviated time to CGP results and faster therapy initiation. Forthcoming prospective studies will clarify the utility of LBx in parallel with biopsy for diagnostic confirmation for patients presenting with suspected advanced lung cancer.
Collapse
Affiliation(s)
- Alessandro Russo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Onco-hematology, Papardo Hospital, Messina, Italy
| | | | | | - Marzia Del Re
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | | | | | - Yi Lee
- Trinity Health Oakland, Pontiac, MI
- Wayne State University School of Medicine, Detroit, MI
| | | | | | - Martin Dietrich
- Florida Cancer Specialists & Research Institute, Lake Mary, FL
| | | | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
4
|
Pellini B, Madison RW, Childress MA, Miller ST, Gjoerup O, Cheng J, Huang RS, Krainock M, Gupta P, Zou W, Shames DS, Moshkevich S, Ballinger M, Liu MC, Young A, Srivastava MK, Oxnard GR, Socinski MA. Circulating Tumor DNA Monitoring on Chemo-immunotherapy for Risk Stratification in Advanced Non-Small Cell Lung Cancer. Clin Cancer Res 2023; 29:4596-4605. [PMID: 37702716 PMCID: PMC10643998 DOI: 10.1158/1078-0432.ccr-23-1578] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/21/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
PURPOSE Chemoimmunotherapy (chemoIO) is a prevalent first-line treatment for advanced driver-negative non-small cell lung cancer (NSCLC), with maintenance therapy given after induction. However, there is significant clinical variability in the duration, dosing, and timing of maintenance therapy after induction chemoIO. We used circulating tumor DNA (ctDNA) monitoring to inform outcomes in patients with advanced NSCLC receiving chemoIO. EXPERIMENTAL DESIGN This retrospective study included 221 patients from a phase III trial of atezolizumab+carboplatin+nab-paclitaxel versus carboplatin+nab-paclitaxel in squamous NSCLC (IMpower131). ctDNA monitoring used the FoundationOne Tracker involving comprehensive genomic profiling of pretreatment tumor tissue, variant selection using an algorithm to exclude nontumor variants, and multiplex PCR of up to 16 variants to detect and quantify ctDNA. RESULTS ctDNA was detected (ctDNA+) in 96% of pretreatment samples (median, 93 mean tumor molecules/mL), and similar ctDNA dynamics were noted across treatment arms during chemoIO. ctDNA decrease from baseline to C4D1 was associated with improved outcomes across multiple cutoffs for patients treated with chemoIO. When including patients with missing plasma or ctDNA- at baseline, patients with ctDNA- at C4D1 (clearance), had more favorable progression-free survival (median 8.8 vs. 3.5 months; HR, 0.32;0.20-0.52) and OS (median not reached vs. 8.9 months; HR, 0.22; 0.12-0.39) from C4D1 than ctDNA+ patients. CONCLUSIONS ctDNA monitoring during induction chemoIO can inform treatment outcomes in patients with advanced NSCLC. Importantly, monitoring remains feasible and informative for patients missing baseline ctDNA. ctDNA testing during induction chemoIO identifies patients at higher risk for disease progression and may inform patient selection for novel personalized maintenance or second-line treatment strategies.
Collapse
Affiliation(s)
- Bruna Pellini
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | | | | | | | - Ole Gjoerup
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | - Jason Cheng
- Genentech, Inc., South San Francisco, California
| | | | | | | | - Wei Zou
- Genentech, Inc., South San Francisco, California
| | | | | | | | | | - Amanda Young
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | | | | |
Collapse
|
5
|
Batalini F, Madison RW, Sokol ES, Jin DX, Chen KT, Decker B, Pavlick DC, Frampton GM, Wulf GM, Garber JE, Oxnard G, Schrock AB, Tung NM. Homologous Recombination Deficiency Landscape of Breast Cancers and Real-World Effectiveness of Poly ADP-Ribose Polymerase Inhibitors in Patients With Somatic BRCA1/ 2, Germline PALB2, or Homologous Recombination Deficiency Signature. JCO Precis Oncol 2023; 7:e2300091. [PMID: 37992259 PMCID: PMC10681426 DOI: 10.1200/po.23.00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 09/05/2023] [Accepted: 10/13/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE Poly ADP-ribose polymerase inhibitors (PARPi) are approved for patients with human epidermal growth factor receptor 2-negative metastatic breast cancer (mBC) and germline pathogenic/likely pathogenic variant (hereafter mutation) in the BRCA1/2 genes (gBRCA); however, clinical benefit has also been demonstrated in mBC with somatic BRCA1/2 mutations (sBRCA) or germline PALB2 mutations (gPALB2). This study aims to describe the genomic landscape of homologous recombination repair (HRR) gene alterations in mBC and assess PARPi treatment outcomes for patients with gBRCA compared with other HRR genes and by status of a novel homologous recombination deficiency signature (HRDsig). METHODS A real-world (RW) clinico-genomic database (CGDB) of comprehensive genomic profiling (CGP) linked to deidentified, electronic health record-derived clinical data was used. CGP was analyzed for HRR genes and HRDsig. The CGDB enabled cohort characterization and outcomes analyses of 177 patients exposed to PARPi. RW progression-free survival (rwPFS) and RW overall survival (rwOS) were compared. RESULTS Of 28,920 patients with mBC, gBRCA was detected in 3.4%, whereas the population with any BRCA alteration or gPALB2 increased to 9.5%. HRDsig+ represented 21% of patients with mBC. BRCA and gPALB2 had higher levels of biallelic loss and HRDsig+ than other HRR alterations. Outcomes on PARPi were assessed for 177 patients, and gBRCA and sBRCA/gPALB2 cohorts were similar: gBRCA versus sBRCA/gPALB2 rwPFS was 6.3 versus 5.4 months (hazard ratio [HR], 1.37 [0.77-2.43]); rwOS was 16.2 versus 21.2 months (HR, 1.45 [0.74-2.86]). Additionally, patients with HRDsig+ versus HRDsig- had longer rwPFS (6.3 v 2.8 months; HR, 0.62 [0.42-0.92]) and numerically longer rwOS (17.8 v 13.0 months; HR, 0.72 [0.46-1.14]). CONCLUSION Patients with sBRCA and gPALB2 derive similar benefit from PARPi as those with gBRCA alterations. In combination, HRDsig+, sBRCA, and gPALB2 represent an additional 19% of mBC that can potentially benefit from PARPi. Randomized trials exploring a more inclusive biomarker such as HRDsig are warranted.
Collapse
|
6
|
Powles T, Young A, Nimeiri H, Madison RW, Fine A, Zollinger DR, Huang Y, Xu C, Gjoerup OV, Aushev VN, Wu HT, Aleshin A, Carter C, Davarpanah N, Degaonkar V, Gupta P, Mariathasan S, Schleifman E, Assaf ZJ, Oxnard G, Hegde PS. Molecular residual disease detection in resected, muscle-invasive urothelial cancer with a tissue-based comprehensive genomic profiling-informed personalized monitoring assay. Front Oncol 2023; 13:1221718. [PMID: 37601688 PMCID: PMC10433150 DOI: 10.3389/fonc.2023.1221718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Circulating tumor DNA (ctDNA) detection postoperatively may identify patients with urothelial cancer at a high risk of relapse. Pragmatic tools building off clinical tumor next-generation sequencing (NGS) platforms could have the potential to increase assay accessibility. Methods We evaluated the widely available Foundation Medicine comprehensive genomic profiling (CGP) platform as a source of variants for tracking of ctDNA when analyzing residual samples from IMvigor010 (ClinicalTrials.gov identifier NCT02450331), a randomized adjuvant study comparing atezolizumab with observation after bladder cancer surgery. Current methods often involve germline sampling, which is not always feasible or practical. Rather than performing white blood cell sequencing to filter germline and clonal hematopoiesis (CH) variants, we applied a bioinformatic approach to select tumor (non-germline/CH) variants for molecular residual disease detection. Tissue-informed personalized multiplex polymerase chain reaction-NGS assay was used to detect ctDNA postsurgically (Natera). Results Across 396 analyzed patients, prevalence of potentially actionable alterations was comparable with the expected prevalence in advanced disease (13% FGFR2/3, 20% PIK3CA, 13% ERBB2, and 37% with elevated tumor mutational burden ≥10 mutations/megabase). In the observation arm, 66 of the 184 (36%) ctDNA-positive patients had shorter disease-free survival [DFS; hazard ratio (HR) = 5.77; 95% confidence interval (CI), 3.84-8.67; P < 0.0001] and overall survival (OS; HR = 5.81; 95% CI, 3.41-9.91; P < 0.0001) compared with ctDNA-negative patients. ctDNA-positive patients had improved DFS and OS with atezolizumab compared with those in observation (DFS HR = 0.56; 95% CI, 0.38-0.83; P = 0.003; OS HR = 0.66; 95% CI, 0.42-1.05). Clinical sensitivity and specificity for detection of postsurgical recurrence were 58% (60/103) and 93% (75/81), respectively. Conclusion We present a personalized ctDNA monitoring assay utilizing tissue-based FoundationOne® CDx CGP, which is a pragmatic and potentially clinically scalable method that can detect low levels of residual ctDNA in patients with resected, muscle-invasive bladder cancer without germline sampling.
Collapse
Affiliation(s)
- Thomas Powles
- Barts Experimental Cancer Medicine Centre, Barts Cancer Institute, Queen Mary University of London ECMC, Barts Health, London, United Kingdom
| | - Amanda Young
- Foundation Medicine, Cambridge, MA, United States
| | | | | | | | | | - Yanmei Huang
- Foundation Medicine, Cambridge, MA, United States
| | - Chang Xu
- Foundation Medicine, Cambridge, MA, United States
| | | | | | | | | | - Corey Carter
- Roche/Genentech, South San Francisco, CA, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Sokol ES, Madison RW, Jin DX, Chen KT, Fleischmann Z, Newberg J, Shrock A, Fabrizio D, He J, Bhardwaj N, Lin KK, McNeish IA, Swisher EM. Abstract 966: Exploration of a novel HRD signature (HRDsig) as a biomarker for rucaparib benefit in ARIEL2. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: The ARIEL2 (Parts 1 and 2) all-comers study tested the effectiveness of the PARP inhibitor rucaparib in patients (pts) with platinum-sensitive or resistant/refractory relapsed high-grade ovarian cancer. Pre-specified analyses identified associations of BRCA1/2 mutation status and genomic LOH (gLOH) with prolonged PFS. Recently, a novel scar-based measure of HRD was described [HRDsig; AACR #1249], and we retrospectively examined its predictive value in the ARIEL2 study.
Methods: ARIEL2 (CO-338-017; NCT01891344) was an international multicenter, two-part, phase 2 open-label study conducted across 64 sites. Tumor tissues were profiled with comprehensive genomic profiling for all classes of alterations in at least 287 genes (FoundationOne®). HRDsig was called using a machine learning based algorithm with a broad set of genome-wide copy number and short variant features, independent of gLOH (AACR 2022 #1249). Survival analysis was limited to samples where both gLOH and HRDsig could be evaluated (n=394). Hazard ratios were estimated using a univariate Cox proportional hazards model and objective response rates (ORR) were compared using Fisher’s exact test. gLOH high was defined using a cutoff of 16%, based on ARIEL2 and subsequently FDA approved as a complementary diagnostic. BRCA1 promoter methylation was quantified by digital droplet PCR.
Results: HRDsig(+) was identified in 56% (251/449) of cases, including 92% (108/117) of those with deleterious BRCA1/2 alterations and 43% (143/332) of BRCAwt. In the intention to treat (ITT) and in pts with platinum sensitive (plat-sen) disease, HRDsig(+) was predictive of PFS benefit on rucaparib (ITT HR = 0.63 [0.50-0.80], p<0.001; plat-sen HR = 0.44 [0.32-0.60]; p<0.001), similar to gLOH-high (ITT HR = 0.70 [0.56-0.87], p=0.0016; plat-sen HR 0.55 [0.41-0.74], p<0.001). In BRCAwt pts with plat-sen disease (n=179), HRDsig was predictive of objective response and PFS on rucaparib, (ORR 28% in HRDsig(+) vs 10% in HRDsig(-), p=0.002; PFS HR = 0.66 [0.48-0.91]; p=0.012). Tumors with RAD51C/D alterations (5/5; 100%) were identified as HRDsig(+). Most other HRR alterations showed little association with HRDsig, including ATM (0/5 HRDsig(+)), and CHEK2 (0/4 HRDsig(+)). Additionally, 33 BRCAwt pts were identified as BRCA1 methylation positive in the cohort, with 32/33 (97%) identified as HRDsig(+), similar to gLOH-high (30/33; 91%).
Conclusions: HRDsig(+) was associated with rucaparib benefit overall and in BRCAwt pts with platinum-sensitive ovarian cancer in this study. HRDsig(+) status exhibited strong association with deficiency caused by both epigenetic (BRCA1 methylation) and genetic (HRR mutation) mechanisms. Additional studies should further explore the utility of this biomarker for pt selection in ovarian cancer and other relevant cancer types to inform the use of PARP inhibitors or other DNA damaging agents.
Citation Format: Ethan S. Sokol, Russell W. Madison, Dexter X. Jin, Kuei Ting Chen, Zoe Fleischmann, Justin Newberg, Alexa Shrock, David Fabrizio, Jie He, Neeru Bhardwaj, Kevin K. Lin, Iain A. McNeish, Elizabeth M. Swisher. Exploration of a novel HRD signature (HRDsig) as a biomarker for rucaparib benefit in ARIEL2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 966.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Jie He
- 1Foundation Medicine, Inc., Cambridge, MA
| | | | | | | | | |
Collapse
|
8
|
Rugo HS, Raskina K, Schrock AB, Madison RW, Graf RP, Sokol ES, Sivakumar S, Lee JK, Fisher V, Oxnard GR, Tukachinsky H. Biology and Targetability of the Extended Spectrum of PIK3CA Mutations Detected in Breast Carcinoma. Clin Cancer Res 2023; 29:1056-1067. [PMID: 36321996 PMCID: PMC10011882 DOI: 10.1158/1078-0432.ccr-22-2115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/16/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
PURPOSE Alpelisib is a PI3K alpha (PI3Kα)-selective inhibitor approved for the treatment of hormone receptor-positive/HER2-negative (HR+/HER2-) PIK3CA-mutated advanced breast cancer (ABC) based on the SOLAR-1 trial, which defined 11 substitutions in exons 7, 9, and 20 in PIK3CA (SOLAR1m). We report alpelisib effectiveness for ABC harboring SOLAR1m, as well as other pathogenic PIK3CA mutations (OTHERm) using comprehensive genomic profiling (CGP). EXPERIMENTAL DESIGN A total of 33,977 tissue and 1,587 liquid biopsies were analyzed using hybrid capture-based CGP covering the entire coding sequence of PIK3CA. Clinical characteristics and treatment history were available for 10,750 patients with ABC in the deidentified Flatiron Health-Foundation Medicine clinico-genomic database (FH-FMI CGDB). RESULTS PIK3CAm were detected in 11,767/33,977 (35%) of tissue biopsies, including 2,300 (7%) samples with OTHERm and no SOLAR1m. Liquid biopsy had 77% sensitivity detecting PIK3CAm, increasing to 95% with circulating tumor DNA fraction ≥2%. In patients with HR+/HER2- ABC and PIK3CAm receiving alpelisib/fulvestrant (ALP+FUL; n = 182) or fulvestrant alone (FUL; n = 119), median real-world progression-free survival (rwPFS) was 5.9 months on ALP+FUL [95% confidence interval (CI): 5.1-7.4] versus 3.1 months on FUL (95% CI: 2.7-3.7; P < 0.0001). In patients with OTHERm, median rwPFS was 4.0 months on ALP+FUL (95% CI: 2.8-10.1) versus 2.5 months on FUL (95% CI: 2.2-3.7; P = 0.0054). CONCLUSIONS CGP detects diverse PIK3CAm in a greater number of patients with ABC than PCR hotspot testing; 20% of patients with PIK3CAm do not have SOLAR1m. These patients may derive benefit from alpelisib. See related commentary by Tau and Miller, p. 989.
Collapse
Affiliation(s)
- Hope S. Rugo
- University of California, San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Kira Raskina
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | | | - Ryon P. Graf
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | | | | | | | | | | |
Collapse
|
9
|
Reichert ZR, Morgan TM, Li G, Castellanos E, Snow T, Dall'Olio FG, Madison RW, Fine AD, Oxnard GR, Graf RP, Stover DG. Prognostic value of plasma circulating tumor DNA fraction across four common cancer types: a real-world outcomes study. Ann Oncol 2023; 34:111-120. [PMID: 36208697 PMCID: PMC9805517 DOI: 10.1016/j.annonc.2022.09.163] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Genomic analysis of circulating tumor DNA (ctDNA) is increasingly incorporated into the clinical management of patients with advanced cancer. Beyond tumor profiling, ctDNA analysis also can enable calculation of circulating tumor fraction (TF), which has previously been found to be prognostic. While most prognostic models in metastatic cancer are tumor type specific and require significant patient-level data, quantification of TF in ctDNA has the potential to serve as a pragmatic, tumor-agnostic prognostic tool. PATIENTS AND METHODS This study utilized a cohort of patients in a nationwide de-identified clinico-genomic database with metastatic castration-resistant prostate cancer (mCRPC), metastatic breast cancer (mBC), advanced non-small-cell lung cancer (aNSCLC), or metastatic colorectal cancer (mCRC) undergoing liquid biopsy testing as part of routine care. TF was calculated based on single-nucleotide polymorphism aneuploidy across the genome. Clinical, disease, laboratory, and treatment data were captured from the electronic health record. Overall survival (OS) was evaluated by TF level while controlling for relevant covariables. RESULTS A total of 1725 patients were included: 198 mCRPC, 402 mBC, 902 aNSCLC, and 223 mCRC. TF ≥10% was highly correlated with OS in univariable analyses for all cancer types: mCRPC [hazard ratio (HR) 3.3, 95% confidence interval (CI) 2.04-5.34, P < 0.001], mBC (HR 2.4, 95% CI 1.71-3.37, P < 0.001), aNSCLC (HR 1.68, 95% CI 1.34-2.1, P < 0.001), and mCRC (HR 2.11, 95% CI 1.39-3.2, P < 0.001). Multivariable assessments of TF had similar point estimates and CIs, suggesting a consistent and independent association with survival. Exploratory analysis showed that TF remained consistently prognostic across a wide range of cutpoints. CONCLUSIONS Plasma ctDNA TF is a pragmatic, independent prognostic biomarker across four advanced cancers with potential to guide clinical conversations around expected treatment outcomes. With further prospective validation, ctDNA TF could be incorporated into care paradigms to enable precision escalation and de-escalation of cancer therapy based on patient-level tumor biology.
Collapse
Affiliation(s)
| | | | - G Li
- Foundation Medicine, Cambridge, USA
| | | | - T Snow
- Flatiron Health, New York, USA
| | - F G Dall'Olio
- Gustave Roussy, Villejuif, France; University of Bologna, Bologna, Italy
| | | | - A D Fine
- Foundation Medicine, Cambridge, USA
| | | | - R P Graf
- Foundation Medicine, Cambridge, USA
| | - D G Stover
- The Ohio State University, Columbus, USA.
| |
Collapse
|
10
|
Kansara M, Bhardwaj N, Thavaneswaran S, Xu C, Lee JK, Chang L, Madison RW, Lin F, Hsu E, Patel VK, Aleshin A, Oxnard GR, Simes J, Nimeiri H, Thomas DM. Early circulating tumor DNA dynamics as a pan-tumor biomarker for long-term clinical outcome in patients treated with durvalumab and tremelimumab. Mol Oncol 2022; 17:298-311. [PMID: 36426653 PMCID: PMC9892824 DOI: 10.1002/1878-0261.13349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
There is an urgent need to identify biomarkers of early response that can accurately predict the benefit of immune checkpoint inhibitors (ICI). Patients receiving durvalumab/tremelimumab had tumor samples sequenced before treatment (baseline) to identify variants for the design of a personalized circulating tumor (ctDNA) assay. ctDNA was assessed at baseline and at 4 and/or 8 weeks into treatment. Correlations between ctDNA changes to radiographic response and overall survival (OS) were made to assess potential clinical benefit. 35/40 patients (87.5%) had personalized ctDNA assays designed, and 29/35 (82.9%) had plasma available for baseline analysis, representing 16 unique solid tumor histologies. As early as 4 weeks after treatment, decline in ctDNA from baseline predicted improved OS (P = 0.0144; HR = 9.98) and ctDNA changes on treatment-supported and refined radiographic response calls. ctDNA clearance at any time through week 8 identified complete responders by a median lead time of 11.5 months ahead of radiographic imaging. ctDNA response monitoring is emerging as a dynamic, personalized biomarker method that may predict survival outcomes in patients with diverse solid tumor histologies, complementing and sometimes preceding standard-of-care imaging assessments.
Collapse
Affiliation(s)
- Maya Kansara
- The Kinghorn Cancer CentreGarvan Institute of Medical ResearchDarlinghurstNSWAustralia,Faculty of Medicine, St. Vincent's Clinical SchoolUNSW SydneyKensingtonNSWAustralia
| | | | - Subotheni Thavaneswaran
- The Kinghorn Cancer CentreGarvan Institute of Medical ResearchDarlinghurstNSWAustralia,Faculty of Medicine, St. Vincent's Clinical SchoolUNSW SydneyKensingtonNSWAustralia,National Health and Medical Research Council Clinical Trials CentreUniversity of SydneyNSWAustralia
| | - Chang Xu
- Foundation Medicine, Inc.CambridgeMAUSA
| | | | | | | | - Frank Lin
- The Kinghorn Cancer CentreGarvan Institute of Medical ResearchDarlinghurstNSWAustralia,Faculty of Medicine, St. Vincent's Clinical SchoolUNSW SydneyKensingtonNSWAustralia,National Health and Medical Research Council Clinical Trials CentreUniversity of SydneyNSWAustralia
| | - Eugene Hsu
- Radiology DepartmentSt Vincent's HospitalSydneyNSWAustralia
| | | | | | | | - John Simes
- National Health and Medical Research Council Clinical Trials CentreUniversity of SydneyNSWAustralia
| | | | - David M. Thomas
- The Kinghorn Cancer CentreGarvan Institute of Medical ResearchDarlinghurstNSWAustralia,Faculty of Medicine, St. Vincent's Clinical SchoolUNSW SydneyKensingtonNSWAustralia
| |
Collapse
|
11
|
Husain H, Pavlick DC, Fendler BJ, Madison RW, Decker B, Gjoerup O, Parachoniak CA, McLaughlin-Drubin M, Erlich RL, Schrock AB, Frampton GM, Das Thakur M, Oxnard GR, Tukachinsky H. Tumor Fraction Correlates With Detection of Actionable Variants Across > 23,000 Circulating Tumor DNA Samples. JCO Precis Oncol 2022; 6:e2200261. [PMID: 36265119 PMCID: PMC9616642 DOI: 10.1200/po.22.00261] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
PURPOSE Profiling of circulating tumor DNA (ctDNA) is increasingly adopted in the management of solid tumors, concurrent with increased availability of more comprehensive ctDNA panels. However, variable ctDNA shed can result in variable assay sensitivity. We studied the relationship between ctDNA tumor fraction (TF) and detection of actionable alterations across cancer types. METHODS A total of 23,482 liquid biopsies (LBx) submitted between September 2020 and October 2021 were sequenced using a hybrid capture panel that reports genomic alterations (GAs) and genomic biomarkers across 324 cancer-related genes. The primary end points were the prevalence of targetable GAs by cancer type and detection in relationship to ctDNA TF. Sensitivity of detection in LBx was assessed in 1,289 patients with available tissue results. RESULTS 94% (n = 22,130) of LBx had detectable ctDNA, with a median TF of 2.2%. LBx profiling detected GAs in National Comprehensive Cancer Network category 1 genes in 37% of lung, 30% of prostate, 36% of breast, and 51% of colon cancer cases. Potential germline GAs flagged on clinical reports were detected in genes including <i>BRCA1/2</i>, <i>PALB2</i>, <i>CHEK2</i>, and <i>ATM.</i> Polyclonal mutations in genes associated with resistance such as <i>AR</i>, <i>ESR1</i>, <i>RB1</i>, and <i>NF1</i> were detected. The sensitivity of LBx to detect driver alterations identified in tissue biopsy from the same patient ranged from 58% to 86% but was consistently at or near 100% in cases with TF ≥ 10%. CONCLUSION Elevated ctDNA shed is associated with both high sensitivity and negative predictive value for detection of actionable GAs. The presence of elevated TF suggests adequate tumor profiling and may reduce the value of subsequent reflex to confirmatory tissue testing in patients with negative LBx results.
Collapse
Affiliation(s)
- Hatim Husain
- University of California, San Diego, La Jolla, CA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Hanna Tukachinsky
- Foundation Medicine, Cambridge, MA,Hanna Tukachinsky, PhD, Foundation Medicine, 150 Second St, Cambridge, MA 02141; e-mail:
| |
Collapse
|
12
|
Dagogo-Jack I, Madison RW, Lennerz JK, Chen KT, Hopkins JF, Schrock AB, Ritterhouse LL, Lester A, Wharton KA, Mino-Kenudson M, Danziger N, Hung YP, Mata DA, Ross JS. Molecular Characterization of Mesothelioma: Impact of Histologic Type and Site of Origin on Molecular Landscape. JCO Precis Oncol 2022; 6:e2100422. [PMID: 35704798 DOI: 10.1200/po.21.00422] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Mesothelioma is an aggressive malignancy with heterogeneous outcomes that are partly driven by the differential efficacy of existing therapies across histologic types and sites of origin. Large-scale molecular analysis of mesothelioma and its subtypes has the potential to inform future therapeutic strategies. MATERIALS AND METHODS We analyzed 1,294 mesotheliomas {980 pleural (malignant pleural mesothelioma [MPM]) and 314 peritoneal (malignant peritoneal mesothelioma [MPeM])} using next-generation sequencing, determined programmed death ligand-1 (PD-L1) expression and histology in a subset of cases, and assessed MTAP/CDKN2A copy-number status by fluorescence in situ hybridization and T-cell infiltration in an independent cohort. RESULTS The molecular landscape of MPM was characterized by inactivating alterations in CDKN2A (49%), BAP1 (44%), CDKN2B (42%), MTAP (34%), and NF2 (33%). Compared with epithelioid MPM, nonepithelioid (ie, biphasic and sarcomatoid) MPM had identical tumor mutational burden (median 1.25 mut/Mb, P = .63), more commonly expressed PD-L1 (74% v 51%, P = .02), and was more likely to harbor MTAP, CDKN2A, and CDKN2B copy loss (P < .05). Fluorescence in situ hybridization confirmed that homozygous MTAP loss was enriched in nonepithelioid MPM. Relative to MPM, MPeM had comparable tumor mutational burden and PD-L1 expression. The molecular profile of MPeM was similar to MPM, with the distinction that PBRM1 alterations occurred at higher frequency (16% v 7%, P < .01). ALK rearrangements were only observed in MPeM. CONCLUSION Regardless of histology and location, the molecular landscape of mesothelioma primarily consists of inactivating alterations in tumor suppressor genes, with enrichment of certain alterations in distinct subsets (eg, MTAP loss in nonepithelioid tumors). Given the limited efficacy of current therapies for this disease, novel approaches targeting recurring alterations should be explored.
Collapse
Affiliation(s)
- Ibiayi Dagogo-Jack
- Department of Medicine, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA
| | | | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | | | | | | | - Lauren L Ritterhouse
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | | | | | | | | | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | - Jeffrey S Ross
- Foundation Medicine Inc, Cambridge, MA.,Departments of Pathology, Urology and Oncology, Upstate Medical University, Syracuse, NY
| |
Collapse
|
13
|
Madison RW, Hu X, Ramanan V, Xu Z, Huang RSP, Sokol ES, Frampton GM, Schrock AB, Ali SM, Ganesan S, De S. Clustered 8-Oxo-Guanine Mutations and Oncogenic Gene Fusions in Microsatellite-Unstable Colorectal Cancer. JCO Precis Oncol 2022; 6:e2100477. [PMID: 35584350 PMCID: PMC9200390 DOI: 10.1200/po.21.00477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Colorectal carcinomas (CRCs) with microsatellite-instability (MSI) are enriched for oncogenic kinase fusions (KFs), including NTRK1, RET, and BRAF, but the mechanism underlying this finding is unclear. Clustered 8-oxo-guanine mutations promote oncogenic fusions in MSI colorectal tumor![]()
Collapse
Affiliation(s)
| | - Xiaoju Hu
- Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ
| | | | - Zhuxuan Xu
- Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ
| | | | | | | | | | | | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ
| |
Collapse
|
14
|
Myer PA, Lee JK, Madison RW, Pradhan K, Newberg JY, Isasi CR, Klempner SJ, Frampton GM, Ross JS, Venstrom JM, Schrock AB, Das S, Augenlicht L, Verma A, Greally JM, Raj SM, Goel S, Ali SM. The Genomics of Colorectal Cancer in Populations with African and European Ancestry. Cancer Discov 2022; 12:1282-1293. [PMID: 35176763 DOI: 10.1158/2159-8290.cd-21-0813] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/28/2021] [Accepted: 02/11/2022] [Indexed: 11/16/2022]
Abstract
Blacks have a higher incidence of colorectal cancer (CRC) and worse survival rates when compared to Whites. Comprehensive genomic profiling was performed in 46,140 colorectal adenocarcinoma cases. Ancestry-informative markers identified 5,301 patients of African descent (AFR) and 33,770 patients of European descent (EUR). AFR were younger, had fewer MSI-H tumors, and had significantly more frequent alterations in KRAS, APC, and PIK3CA. AFR had increased frequency of KRAS mutations specifically KRAS G12D and KRAS G13. There were no differences in rates of actionable kinase driver alterations (HER2, MET, NTRK, ALK, ROS1, RET). In patients with young onset CRC (<50 years), AFR and EUR had similar frequency of MSI-H and TMB-H tumors, and strikingly different trends in APC mutations by age, as well as differences in MAPK pathway alterations. These findings inform treatment decisions, impact prognosis, and underscore the need for model systems representative of our diverse US population.
Collapse
Affiliation(s)
| | | | | | - Kith Pradhan
- Albert Einstein College of Medicine, bronx, United States
| | | | | | | | | | | | - Jeffrey M Venstrom
- University of California, San Francisco, San Francisco, CA, United States
| | | | - Sudipto Das
- Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York, United States
| | - John M Greally
- Albert Einstein College of Medicine, Bronx, United States
| | | | - Sanjay Goel
- Montefiore Medical Center, and Albert Einstein College of Medicine, Bronx, NY, United States
| | | |
Collapse
|
15
|
Lee JK, Hazar-Rethinam M, Decker B, Gjoerup O, Madison RW, Lieber DS, Chung JH, Schrock AB, Creeden J, Venstrom J, Alexander B, Oxnard GR. The Pan-Tumor Landscape of Targetable Kinase Fusions in Circulating Tumor DNA. Clin Cancer Res 2022; 28:728-737. [PMID: 34753780 PMCID: PMC9377769 DOI: 10.1158/1078-0432.ccr-21-2136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/15/2021] [Accepted: 11/05/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Oncogenic kinase fusions are targetable with approved and investigational therapies and can also mediate acquired resistance (AR) to targeted therapy. We aimed to understand the clinical validity of liquid biopsy comprehensive genomic profiling (CGP) to detect kinase fusions pan tumor. EXPERIMENTAL DESIGN CGP was performed on plasma and tissue samples during clinical care. All exons plus selected introns of 16 kinases involved in oncogenic fusions (ALK, BRAF, EGFR, ERBB2, FGFR1/2/3, MET, NTRK1/2/3, PDGFRA/B, RAF1, RET, and ROS1) were sequenced to capture fusions, including well-characterized and novel breakpoints. Plasma circulating tumor DNA (ctDNA) fraction was estimated to inform sensitivity. RESULTS Of 36,916 plasma cases, 32,492 (88%) had detectable ctDNA. Kinase fusions were detected in 1.8% of ctDNA-positive cases (571/32,492) and were most prevalent in patients with cholangiocarcinoma (4.2%), bladder cancer (3.6%), and non-small cell lung cancer (NSCLC; 3.1%). Of the 63 paired patient samples that had tissue and ctDNA specimens collected within 1 year and with estimated plasma ctDNA fraction >1%, fusions were detected in 47 of 51 (92%) liquid specimens with a fusion in the tissue sample. In 32 patients with fusions detected in liquid but not in tissue, 21 (66%) had evidence of putative acquired resistance. CONCLUSIONS Targetable kinase fusions are identified in ctDNA across cancer types. In pairs with tissue-identified fusions, fusion detection in ctDNA is reliable with elevated ctDNA fraction. These data support the validity of CGP to enable ctDNA-based fusion detection for informing clinical care in patients with advanced cancer.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Geoffrey R. Oxnard
- Corresponding Author: Geoffrey R. Oxnard, Clinical Development, Foundation Medicine, Cambridge, MA 02141. Phone: 617-418-2200; E-mail:
| |
Collapse
|
16
|
Graf RP, Fisher V, Mateo J, Gjoerup OV, Madison RW, Raskina K, Tukachinsky H, Creeden J, Cunningham R, Huang RSP, Mata DA, Ross JS, Oxnard GR, Venstrom JM, Zurita AJ. Predictive Genomic Biomarkers of Hormonal Therapy Versus Chemotherapy Benefit in Metastatic Castration-resistant Prostate Cancer. Eur Urol 2021; 81:37-47. [PMID: 34716049 DOI: 10.1016/j.eururo.2021.09.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/29/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Biomarkers predicting second-generation novel hormonal therapy (NHT) benefit relative to taxanes are critical for optimized treatment decisions for metastatic castration-resistant prostate cancer (mCRPC) patients. These associations have not been reported simultaneously for common mCRPC genomic biomarkers. OBJECTIVE To evaluate predictive associations of common genomic aberrations in mCRPC using an established comprehensive genomic profiling (CGP) system. DESIGN, SETTING, AND PARTICIPANTS A retrospective cohort study used data from a deidentified US-based clinicogenomic database comprising patients treated in routine clinical practice between 2011 and 2020, evaluated with Foundation Medicine CGP in tissue biopsies obtained around the time of treatment decision. The main cohort included 180 NHT and 179 taxane lines of therapy (LOTs) from 308 unique patients. The sequential cohort comprised a subset of the main cohort NHT LOTs immediately followed by taxane from 55 unique patients. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Prostate-specific antigen (PSA) response, time to next treatment (TTNT), and overall survival (OS) were assessed. Main cohort analyses were adjusted for known treatment assignment biases via inverse probability of treatment weighting (IPTW) in treatment interaction models. RESULTS AND LIMITATIONS In the main cohort, patients with AR amplification (ARamp) or PTEN aberrations (PTENalt) had worse relative PSA response on NHT versus taxanes compared with patients without. Patients with ARamp, PTENalt, or RB1 aberrations (RB1alt) also had worse relative TTNT and OS on NHT but not on taxanes. In multivariable models for TTNT and OS adjusted via IPTW, ARamp, PTENalt, and RB1alt were shown as poor prognostic factors overall and demonstrated significant treatment interactions, indicating reduced hazards of therapy switch and death on taxanes versus NHT. Consistent associations favoring increased benefit from subsequent taxane despite prior NHT treatment line were observed only for ARamp in the sequential cohort, in which very few patients had RB1alt for assessment. CONCLUSIONS ARamp status is a candidate biomarker to predict poor effectiveness of NHT relative to taxanes in mCRPC in scenarios where both options are considered. PATIENT SUMMARY Specific alterations in the DNA of tumors may assist in choosing between novel oral hormonal therapies and standard chemotherapy in advanced prostate cancer patients.
Collapse
Affiliation(s)
| | | | - Joaquin Mateo
- Vall d'Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | - Amado J Zurita
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
17
|
Necchi A, Cucchiara V, Grivas P, Bratslavsky G, Jacob J, Spiess PE, Sokol ES, Killian JK, Lin D, Ramkissoon S, Huang RSP, Madison RW, Venstrom JM, Schrock AB, Danziger N, Decker B, Gjoerup O, Graf RP, Oxnard GR, Tukachinsky H, Ross JS. Contrasting genomic profiles from metastatic sites, primary tumors, and liquid biopsies of advanced prostate cancer. Cancer 2021; 127:4557-4564. [PMID: 34379803 DOI: 10.1002/cncr.33865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND This study assessed the contrasting genomic profiles from the primary tumors (PTs), metastatic (MET) sites, and circulating tumor DNA (ctDNA) of patients with prostate cancer (PC). METHODS A total of 1294 PC tissue specimens and 2462 ctDNA specimens underwent hybrid capture-based comprehensive genomic profiling (CGP). Specimens included tissue from PTs; MET biopsies from bone, liver (LIV), lung (LU), brain (BN), lymph node, and soft tissue sites; and ctDNA. RESULTS Differences in alteration frequencies between PT, MET, and ctDNA specimens for selected genes were observed. TMPRSS2:ERG fusion frequencies were similar between PTs and MET sites (35% vs 33%) but varied among MET sites. Genomic alterations (GAs) in AR were lowest in PTs (2%) and highest in MET sites (from 24% in LU to 50% in LIV). BN had the highest genomic alterations/tumor (8) and enrichment for PTEN GAs. The BRCA2 GA frequency varied from 0% in BN to 15% in LIV. ERBB2 amplification was increased in MET sites in comparison with PTs. RB1 GAs were increased in LIV. Biomarkers potentially associated with an anti-PD(L)1 response included CDK12 GAs (16% in LU) and a microsatellite instability-high status (29% in BN). Analyses of ctDNA featured a broad spectrum of GAs similar to those detected across MET sites. CONCLUSIONS CGP of PTs, MET sites, and ctDNA in PC exhibited differences most likely associated with tumor progression, clonal evolution, and exposure to systemic therapies; ctDNA can also capture a broad range of potential therapeutic opportunities for patients with PC.
Collapse
Affiliation(s)
- Andrea Necchi
- IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Vito Cucchiara
- IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy
| | - Petros Grivas
- Fred Hutchinson Cancer Research Center, Seattle Cancer Care Alliance, University of Washington, Seattle, Washington
| | - Gennady Bratslavsky
- Upstate Medical University, State University of New York, Syracuse, New York
| | - Joseph Jacob
- Upstate Medical University, State University of New York, Syracuse, New York
| | | | | | | | - Douglas Lin
- Foundation Medicine, Inc, Cambridge, Massachusetts
| | | | | | | | | | | | | | | | - Ole Gjoerup
- Foundation Medicine, Inc, Cambridge, Massachusetts
| | - Ryon P Graf
- Foundation Medicine, Inc, Cambridge, Massachusetts
| | | | | | - Jeffrey S Ross
- Upstate Medical University, State University of New York, Syracuse, New York.,Foundation Medicine, Inc, Cambridge, Massachusetts
| |
Collapse
|
18
|
Tukachinsky H, Madison RW, Chung JH, Gjoerup OV, Severson EA, Dennis L, Fendler BJ, Morley S, Zhong L, Graf RP, Ross JS, Alexander BM, Abida W, Chowdhury S, Ryan CJ, Fizazi K, Golsorkhi T, Watkins SP, Simmons A, Loehr A, Venstrom JM, Oxnard GR. Genomic Analysis of Circulating Tumor DNA in 3,334 Patients with Advanced Prostate Cancer Identifies Targetable BRCA Alterations and AR Resistance Mechanisms. Clin Cancer Res 2021; 27:3094-3105. [PMID: 33558422 PMCID: PMC9295199 DOI: 10.1158/1078-0432.ccr-20-4805] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/13/2021] [Accepted: 02/03/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE Comprehensive genomic profiling (CGP) is of increasing value for patients with metastatic castration-resistant prostate cancer (mCRPC). mCRPC tends to metastasize to bone, making tissue biopsies challenging to obtain. We hypothesized CGP of cell-free circulating tumor DNA (ctDNA) could offer a minimally invasive alternative to detect targetable genomic alterations (GA) that inform clinical care. EXPERIMENTAL DESIGN Using plasma from 3,334 patients with mCRPC (including 1,674 screening samples from TRITON2/3), we evaluated the landscape of GAs detected in ctDNA and assessed concordance with tissue-based CGP. RESULTS A total of 3,129 patients (94%) had detectable ctDNA with a median ctDNA fraction of 7.5%; BRCA1/2 was mutated in 295 (8.8%). In concordance analysis, 72 of 837 patients had BRCA1/2 mutations detected in tissue, 67 (93%) of which were also identified using ctDNA, including 100% of predicted germline variants. ctDNA harbored some BRCA1/2 alterations not identified by tissue testing, and ctDNA was enriched in therapy resistance alterations, as well as possible clonal hematopoiesis mutations (e.g., in ATM and CHEK2). Potential androgen receptor resistance alterations were detected in 940 of 2,213 patients (42%), including amplifications, polyclonal and compound mutations, rearrangements, and novel deletions in exon 8. CONCLUSIONS Genomic analysis of ctDNA from patients with mCRPC recapitulates the genomic landscape detected in tissue biopsies, with a high level of agreement in detection of BRCA1/2 mutations, but more acquired resistance alterations detected in ctDNA. CGP of ctDNA is a compelling clinical complement to tissue CGP, with reflex to tissue CGP if negative for actionable variants.See related commentary by Hawkey and Armstrong, p. 2961.
Collapse
Affiliation(s)
| | | | - Jon H Chung
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | | | - Lucas Dennis
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | | | - Lei Zhong
- Foundation Medicine Inc., Cambridge, Massachusetts
| | - Ryon P Graf
- Foundation Medicine Inc., Cambridge, Massachusetts
| | - Jeffrey S Ross
- Foundation Medicine Inc., Cambridge, Massachusetts
- Upstate Medical University, Syracuse, New York
| | | | - Wassim Abida
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Simon Chowdhury
- Guy's, King's, and St. Thomas' Hospital, London, England, United Kingdom
| | - Charles J Ryan
- University of Minnesota Medical School, Minneapolis, Minnesota
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Madison RW, Gupta SV, Elamin YY, Lin DI, Pal SK, Necchi A, Miller VA, Ross JS, Chung JH, Alexander BM, Schrock AB, Heymach JV, Reddy P, Ali SM. Urothelial cancer harbours EGFR and HER2 amplifications and exon 20 insertions. BJU Int 2020; 125:739-746. [PMID: 31985116 DOI: 10.1111/bju.15006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 12/25/2022]
Abstract
OBJECTIVE To review the genomic landscape of advanced urothelial carcinoma (UC) to assess the frequencies of EGFR and ERBB2 (HER2) alterations. MATERIALS AND METHODS Tumour specimens from 3753 patients with advanced UC were assayed with hybrid capture-based comprehensive genomic profiling of 180-395 genes. Tumour mutational burden (TMB) was assessed on 0.8 or 1.1 Mb of DNA, and is reported as mutations per megabase. RESULTS In 3753 cases of UC, EGFR alterations were detected in 4.1% (154) and were most commonly amplifications (64%; 99/154), while exon 20 insertions (EGFRexon20ins ) were the second most common alteration (18%; 27/154). Alterations in ERBB2 were observed in 15% (552/3753) of cases and, similarly, ERBB2 amplification was the most commonly observed alteration (278/552; 50%); ERBB2exon20ins occurred in 3.6% (20/552) of cases. EGFRexon20ins and ERBB2exon20ins occurred in younger patients (median age 62 vs 69 years, P = 2.6E-2 and 60 vs 68 years, P = 7.8E-4), and these cases had significantly lower TMB (median 3.6 vs 7.2, P = 2.7E-4 and 2.5 vs 10, P = 1.2E-7) and less frequent TP53 alterations (3.7% vs 83%, P = 4.3E-14 and 20% vs 68%, P = 9.8E-4) compared to cases with other EGFR or ERBB2 alterations. CONCLUSION EGFR and ERBB2 alterations occur in 4% and 15% of UC, respectively. EGFRexon20ins and ERBB2exon20ins were present in 0.7% and 0.5% of UC overall and collectively define a small, but distinct, subset of UC with infrequent co-occurrence of other drivers and low TMB. Given recent promising clinical studies of inhibitors with activity against exon 20 insertions in non-small cell lung cancer, consideration should be given to developing a trial inclusive of patients with UC harbouring these alterations.
Collapse
Affiliation(s)
| | | | | | | | | | - Andrea Necchi
- Fondazione IRCCS - Instituto Nazionale dei Tumori, Milan, IT, USA
| | | | - Jeffrey S Ross
- Foundation Medicine, Cambridge, MA, USA.,Upstate Medical Center, Syracuse, NY, USA
| | | | | | | | | | | | | |
Collapse
|