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C.P. Paweletz
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MA 07 - ALK, ROS and HER2 (ID 673)
- Event: WCLC 2017
- Type: Mini Oral
- Track: Advanced NSCLC
- Presentations: 1
- Moderators:Robert C. Doebele, J.C. Ho
- Coordinates: 10/17/2017, 15:45 - 17:30, Room 316
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MA 07.12 - Short-Term Culture of Patient Derived Tumor Organoids Identify Neratinib/Trastuzumab as an Effective Combination in HER2 Mutant Lung Cancer (ID 10119)
17:00 - 17:05 | Author(s): C.P. Paweletz
- Abstract
- Presentation
Background:
There are currently no effective targeted therapies for HER2 mutant lung cancer. Both neratinib alone or in combination with temsirolimus both have low response rates. One challenge is the lack of patient derived HER2 mutant cell line models and a platform in which to identify the most effective therapeutic strategy. Patient derived xenografts (PDXs) are emerging as an alternative tool to screen for drug efficacy, but can take months to generate and are impractical for screening of large sets of drug combinations. Here we report on a novel 3D microfluidic platform that allows for evaluating ex vivo responses to targeted therapies or targeted therapy combinations from patient derived tumor spheroids (xDOTS).
Method:
We generated xDOTS from DFCI 359, a PDX derived from a HER2 mutant (InsYVMA) NSCLC patient under an IRB approved protocol. Tumor organoids (<100 μm and >40μm) were treated with: HER2 covalent inhibitors (neratinib, afatinib); an EGFR inhibitor (gefitinib), and combinations of HER2 inhibitors and other compounds (neratinib/trastuzumab or neratinib/temsirolimus) at known peak plasma concentrations for 3 days in our 3D microfluidic cell culture device. Live/death quantification was performed by dual labeling de-convolution fluorescence microscopy using acridine orange for live and propidium iodide for dead cells. Cell type characterization was performed by immunofluorescence. The most effective combination was used to treat the DFCI 359 PDX and a HER2 InsYVMA genetically engineered mouse model (GEMM).
Result:
Both neratinib alone and afatinib alone, but not gefitinib, induced high degree of cell death in the DFCI 359 xDOTS. The combinations of neratinib/trastuzumab, and neratinib/temsirolimus enhanced the therapeutic benefit compared to neratinib alone, with the former combination being more effective than the latter. Using fluorescence microscopy we demonstrate that the effects are specific to the tumor cells, rather than the stromal component. We then went on to confirm these findings in a concomitant in-vivo efficacy experiment using the DFCI 359 PDX and the HER2 InsYVMA GEMM. In both in vivo models, the neratinib/trastuzumab combination led to significant tumor regressions and was superior to either single agents or the neratinib/temsirolimus combination.
Conclusion:
Our findings demonstrate the ability to use a 3-D in vivo microfluidic system to identify combination therapies for HER2 mutant NSCLC. Based on our studies, neratinib/trastuzumab is a promising combination for a clinical trial for HER2 mutant lung cancer.
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MA 20 - Recent Advances in Pulmonology/Endoscopy (ID 685)
- Event: WCLC 2017
- Type: Mini Oral
- Track: Pulmonology/Endoscopy
- Presentations: 1
- Moderators:C. Lee, S. Sasada
- Coordinates: 10/18/2017, 14:30 - 16:15, F205 + F206 (Annex Hall)
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MA 20.14 - Genotyping of Lung Cancer Using Cell-Free DNA (cfDNA) from Cytologic Supernatant (CSN) (ID 9057)
15:55 - 16:00 | Author(s): C.P. Paweletz
- Abstract
- Presentation
Background:
Tumor genotyping is transforming lung cancer care but increasingly requires more tumor tissue. Advances in minimally invasive bronchoscopic techniques increase access to small lesions, but often result in smaller samples. With the advent of new cfDNA (“liquid biopsy”) genotyping technologies, we hypothesized that CSN might increase the yield from small FNAs, facilitating cancer genotyping.
Method:
We studied patients with known or suspected lung cancer undergoing FNAs. CSN, which is usually discarded, was collected under IRB approval. cfDNA was extracted after a hard spin (1600 Gs) and tested by both ddPCR (EGFR, KRAS mutations) and targeted next-generation sequencing (NGS).
Result:
14 patients with suspected or known lung cancer were studied at time of analysis (final diagnosis: 2 non-malignant, 9 adenocarcinomas, 1 small-cell carcinoma, 2 squamous cell carcinomas), including 12 EBUS-TBNAs and 2 CT-guided FNAs. Among 6 known KRAS and EGFR mutations, all could be detected with ddPCR of CSN, with allelic fraction (AF) ranging from 1%-46% (median 8.5%). No ddPCR false positives were seen across 9 cases. NGS analysis was piloted on 7 specimens; 5 failed due to insufficient residual DNA. In one specimen, an EGFR exon 19 deletion was detected at 6% AF (2% AF ddPCR). In the other, a BRAF V600E, PIK3CA E784D and TP53 V274F mutations were detected at 48% (46% AF ddPCR), 18% and 86% AF, respectively.
Conclusion:
Cytology supernatant, usually discarded, may be a rich source of fresh tumor DNA, increasing the yield from FNAs. This widely available biospecimen has potential for aiding resistance genotyping, reducing turnaround time of cancer genotyping, and possibly a future role in clarifying the malignant potential of non-diagnostic biopsies. Enrollment continues in order to optimize this biospecimen for NGS. Figure 1
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OA 09 - EGFR TKI Resistance (ID 663)
- Event: WCLC 2017
- Type: Oral
- Track: Advanced NSCLC
- Presentations: 1
- Moderators:Thanyanan Reungwetwattana, Lecia V Sequist
- Coordinates: 10/17/2017, 11:00 - 12:30, Room 301 + 302
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OA 09.02 - Osimertinib Resistance Mediated by Loss of EGFR T790M Is Associated with Early Resistance and Competing Resistance Mechanisms (ID 9000)
11:10 - 11:20 | Author(s): C.P. Paweletz
- Abstract
- Presentation
Background:
Osimertinib is a third-generation EGFR tyrosine kinase inhibitor (TKI) active in EGFR-mutant NSCLC with resistance to prior TKI. Improved understanding of the clinical and molecular characteristics of acquired resistance to osimertinib is needed.
Method:
We initially studied resistance biopsies and plasma specimens from an institutional cohort of 119 patients treated with osimertinib for T790M-positive NSCLC with resistance to prior TKI. For validation, we studied plasma from 157 patients treated with osimertinib on the AURA trial (NCT01802632).
Result:
45 of 119 patients underwent a resistance biopsy and 33 had resistance tumor genotyping available. 11 patients maintained T790M at resistance: 7 acquired EGFR C797S, 1 had a PIK3CA mutation. 22 patients had loss of T790M at resistance: 14 harbored a competing resistance mechanism, including histologic transformation to SCLC, MET amplification, mutations in BRAF, PIK3CA, or KRAS, or fusions in RET or FGFR. Median time to treatment failure (TTF) on osimertinib was 3 months in patients with loss of T790M and 15 months in patients with maintained T790M. In the validation cohort, 110 of 157 patients had detectable tumor DNA in plasma and were eligible for analysis. 58 patients (53%) maintained T790M at resistance; 24 (22%) also acquired a C797S mutation. 52 patients (47%) had loss of T790M at resistance and no C797S. Median TTF was shorter in patients with loss of T790M than in those with maintained T790M at resistance (5.7 vs 12.5 months). 50 patients had both pre- and post-osimertinib plasma genotyping. Studying the relative allelic fraction (AF) of T790M compared to driver EGFR mutation, patients with T790M loss had only slightly lower relative T790M AF pretreatment (29% vs. 38% median, p = 0.06). The ability of plasma response to predict subsequent resistance was studied in 19 patients from the initial cohort with baseline and follow-up plasma genotyping after 1-3 weeks on osimertinib. Studying the difference between the relative change in plasma levels of T790M and the EGFR driver, patients with T790M loss at time of resistance consistently had a greater T790M response than driver response (median difference 16%), suggesting incomplete suppression of the driver due to competing resistance mechanisms.
Conclusion:
In patients with acquired resistance to osimertinib, repeat testing for T790M could offer key insights into disease biology. Patients with early resistance on osimertinib are at risk of T790M loss with emergence of a complex variety of competing resistance mechanisms, and represent intuitive candidates for combination approaches such as combined EGFR & MET inhibition.
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P3.02 - Biology/Pathology (ID 620)
- Event: WCLC 2017
- Type: Poster Session with Presenters Present
- Track: Biology/Pathology
- Presentations: 1
- Moderators:
- Coordinates: 10/18/2017, 09:30 - 16:00, Exhibit Hall (Hall B + C)
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P3.02-014 - Amplicon-Based Next-Generation Sequencing (NGS) of Plasma Cell-Free DNA (cfDNA) for Detection of Driver and Resistance Mutations in NSCLC (ID 10551)
09:30 - 09:30 | Author(s): C.P. Paweletz
- Abstract
Background:
While several studies have evaluated hybrid-capture NGS for cfDNA genotyping, amplicon-based NGS is an attractive alternative with the potential to be faster and less expensive. We performed a blinded evaluation of this approach for the characterization and monitoring of the molecular profile of advanced NSCLC during genotype-directed therapy.
Method:
Plasma samples from patients with advanced NSCLC and a known targetable genotype (EGFR, BRAF, MET, HER2 mutations; ALK, ROS1 rearrangements) were collected and analyzed, blinded to tumor genotype, with IRB approval. Up to 4 specimens were collected for each patient: baseline, initial 2 follow-ups, and progression. Plasma NGS was performed using enhanced tagged amplicon sequencing of hotspots and coding regions from 36 genes. A novel approach was used to detect ALK/ROS1 fusions using amplicon sequencing in cfDNA. Diagnostic accuracy was compared to plasma ddPCR and tumor genotype (including NGS when available).
Result:
A total of 146 specimens from 49 patients were studied. Testing was completed for 115 specimens at the time of analysis. Matched plasma NGS and ddPCR were available across 95 samples and revealed high concordance of allelic fraction (AF). At baseline, sensitivity of plasma NGS for the detection of the driver was 100% (26/26) for EGFR (88.5% ddPCR sensitivity). Sensitivity for the detection of ALK/ROS1 fusions was 89% (6/7 ALK, 2/2 ROS1). Rare instances of plasma NGS-positive/tissue NGS-negative discordance were seen across 13 cases with match tumor NGS (3/442 genes sequenced) and appear related to resistance heterogeneity, clonal hematopoiesis, and low tumor content of biopsy. Among patients with acquired T790M and available specimens at osimertinib resistance (n=21), 11 resistance mechanisms could be detected including tertiary EGFR mutations (e.g. C797S), mutations in BRAF, PIK3CA, or KRAS, and amplification of MET, HER2, or FGFR1. 4 were detected pre-osimertinib.
Conclusion:
This blinded analysis demonstrates for the first time the ability of amplicon-based plasma NGS to detect a full range of targetable genotypes in NSCLC. This approach has attractive sensitivity and specificity and deserves further study as an alternative to better-established hybrid capture approaches. Serial plasma NGS can detect competing resistance mutations in patients with TKIs resistance, highlighting the pitfalls of PCR-based plasma assays in patients with heterogeneous resistance and paving the way towards combination therapies.
