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N. Pham
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MINI 14 - Pre-Clinical Therapy (ID 119)
- Event: WCLC 2015
- Type: Mini Oral
- Track: Biology, Pathology, and Molecular Testing
- Presentations: 1
- Moderators:L. Fernandez-Cuesta, A.F. Gazdar
- Coordinates: 9/08/2015, 10:45 - 12:15, Mile High Ballroom 2c-3c
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MINI14.12 - Genomic Profiling of Patient-Derived Xenografts Identify Passenger Aberrations Associated with Better Prognosis in Non-Small Cell Lung Cancer (ID 1735)
11:50 - 11:55 | Author(s): N. Pham
- Abstract
Background:
Patient-derived tumor xenografts (PDXs) increasingly are being used as preclinical models to study human cancers, test novel therapeutics, and identify potential biomarkers, as they more accurately model human cancers than established tumor cell line cultures. However, uncertainty remains as to how well the genomic characteristics of patient non-small cell lung cancer (NSCLC) are recapitulated in these PDX models.
Methods:
PDXs were established by implantation of surgically resected NSCLC patient tumors into the subcutaneous or sub-renal capsule of non-obese diabetic severe combined immune deficient (NOD-SCID mice. Comprehensive genomic profiling including exome, gene copy number, DNA methylation and mRNA expression were conducted on 36 independent PDX models, their matched patient tumors and normal lung tissue. Publicly available cell line and TCGA data were used for comparison. Integrative analysis was performed to identify genomic alterations in PDXs that are associated with significant clinical outcomes in patients.
Results:
From 441 resected NSCLC tumors, 127 serially transplantable and stable PDX models were established. Among 264 NSCLC patients with at least 3-years follow-up, patients whose tumor formed stable PDXs (versus those who did not) showed significantly worse disease free (HR=3.12, 95% CI =2.02-4.83, P<0.0001) and overall survival (HR=4.08, 95% CI =2.16-7.73, P<0.0001), after multivariable adjustment for clinical pathological factors. Genomic and transcriptomic profiling of 36 PDXs showed greater similarity in somatic alterations between PDX and primary tumors than with published cell line data. In addition to known mutations, we found at least 16 non-synonymous somatic mutations in known oncogenes and tumor suppressors that have never been reported. All these mutations had higher observed variant allele frequency in PDXs compared to their matched patient tumors, suggesting that these were tumor sub-clones selected or enriched for growth in the PDXs. Tumor models characterized by a higher number of somatic alterations among 865 frequently altered genes were associated with better overall patient survival (HR=0.15, p=0.00015) compared to patients with corresponding PDXs characterized by higher alteration number; this was validated in the TCGA lung cancer dataset patients (HR=0.28, p=0.000022). These 865 genes were enriched for those encoding for proteins involved in cell adhesion and interactions with the extracellular matrix, and a quarter of the genomic alterations would putatively form neo-antigens implicating a potential role of immune response in the observed improved patient survival.
Conclusion:
PDXs are close preclinical models of patient tumors. Further investigations of passenger mutations may clarify their clinical impact on interactions between tumor cells, stroma, immune microenvironment and patient prognosis.
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ORAL 21 - Biology - Moving Beyond the Oncogene to Oncogene-Modifying Genes (ID 118)
- Event: WCLC 2015
- Type: Oral Session
- Track: Biology, Pathology, and Molecular Testing
- Presentations: 1
- Moderators:A. Katz, M.S. Tsao
- Coordinates: 9/08/2015, 10:45 - 12:15, Mile High Ballroom 4a-4f
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ORAL21.05 - p53/KRAS Mutation Status Does Not Predict Sensitivity to Chemotherapy in NSCLC PDXs (ID 2459)
11:28 - 11:39 | Author(s): N. Pham
- Abstract
- Presentation
Background:
The LACE-Bio group assessed the prognostic and predictive values of KRAS and p53 mutations in 1543 completely resected non-small cell lung cancer (NSCLC) tumors. The predictive value of combined KRAS/p53 mutations for survival benefit from adjuvant chemotherapy was evaluated on 49 patients and chemotherapy was deleterious in this group compared to observation (HR 2.49 CI 95% [1.10 – 5.66], p=0.03). Patients with tumors harboring combined KRAS/p53 mutations had a worse outcome when treated with adjuvant chemotherapy compared patient with double wild type (WT) tumors (HR 3.03 (95% CI [1.29 – 7.15], p=0.01, interaction p=0.06). We have compared the chemo-sensitivity of patient derived xenografts (PDXs) with double p53/KRAS mutations, single p53, single KRAS mutation or double WT. 0
Methods:
Surgically resected early stage lung adenocarcinomas (ADC) were implanted into non-obese diabetic severe combined immune deficient (NOD-SCID) mice. Fourteen lung ADC PDXs with various p53/KRAS status were revived and implanted: 11 engrafted and were expanded for comparison of treatment vs control. For each model, 6 replicates were included in treatment and control arms. Chemotherapy (cisplatin 3 mg/kg and vinorelbine 7 mg/kg intraperitoneally weekly) was initiated in the PDXs at tumor volumes of 150 mm[3].
Results:
Four models were p53/KRAS double mutant, 4 p53 mutant, 2 KRAS mutant and 1 double WT. The 4 double mutant PDXs responded to chemotherapy, 2 with reduced (SD) and 2 inhibited (PR) growth. Among the 4 PDXs with p53 mutation only, 2 responded (1 PR and 1 SD) and 2 were resistant. Among the 2 PDXs with KRAS mutation only, 1 had a complete response, but relapsed at treatment arrest and 1 achieved PR. The double WT PDX was highly sensitive to chemotherapy (PR) but also relapsed at treatment arrest.
Conclusion:
Among these 11 PDXs, the p53/KRAS mutation status did not predict chemo-sensitivity to cisplatin/vinorelbine, one of the most active adjuvant chemotherapy regimens in NSCLC. As these PDXs were molecularly profiled, we currently are investigating other biomarkers that might predict their sensitivity or resistance to chemotherapy.
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P2.04 - Poster Session/ Biology, Pathology, and Molecular Testing (ID 234)
- Event: WCLC 2015
- Type: Poster
- Track: Biology, Pathology, and Molecular Testing
- Presentations: 2
- Moderators:
- Coordinates: 9/08/2015, 09:30 - 17:00, Exhibit Hall (Hall B+C)
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P2.04-026 - Second Generation EGFR TKIs Inhibit Tumor Growth in a Chemo-Resistant Squamous Cell Lung Cancer Patient Derived Xenograft Model (ID 1265)
09:30 - 09:30 | Author(s): N. Pham
- Abstract
Background:
In clinical trials testing the efficacy of first generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), occasional responses were observed in patients with lung squamous cell carcinomas (LSCC) (Shepherd FA, et al. New Engl J Med 2005) and survival benefit was confirmed for erlotinib in a subset analysis of male, ever-smokers with LSCC (Clark GM, et al. Clin Lung Cancer 2006). Currently, the LUX-Lung 8 phase III clinical trial is comparing afatinib versus erlotinib in the second-line setting for LSCC after cisplatin-based chemotherapy (Goss GD, et al. ESMO 2014). Preclinical data indicate that high EGFR protein expression may be predictive of response to erlotinib in EGFR wild type LSCC (Cranston et al, AACR 2013). Herein we assessed and compared the anti-tumor efficacy of different EGFR inhibitors in chemo-resistant squamous cell lung cancer patient derived xenograft (PDX) models with high EGFR expression and EGFR amplification.
Methods:
The cryopreserved PDX model established from a resected early stage LSCC was revived in non-obese diabetic severe combined immunodeficient mice (NOD SCID), expanded and subsequently treated with chemotherapy (cisplatin 3 mg/kg and vinorelbine 7 mg/kg intraperitoneally [IP]), cetuximab 20 mg/kg IP, and daily oral schedules were followed for erlotinib 50 mg/kg, afatinib 20 mg/kg, dacomitinib 3 mg/kg. For each model, 6 mice were used in each of the different treatment and the control arms. Treatment was initiated in the PDXs at a tumor average volume of 150 mm[3].
Results:
The PDX was derived from a 57 year old male, smoker, following right pneumonectomy for a stage IIIB (T4N1M0) LSCC. This patient received adjuvant cisplatin/vinorelbine, but relapsed three weeks after the end of cycle 4 and died a week later. The tumor had a high EGFR expression by immunohistochemistry (H score = 300) and EGFR amplification (clusters) by fluorescent in situ hybridization. The PDX was EGFR wild type by Illumina exome sequencing and OncoCarta[TM ]MassArray mutation screen (Sequenom), also was refractory to cisplatin/vinorelbine. Reduced growth rate (stable disease, SD) was obtained with erlotinib and cetuximab. Treatment with afatinib and dacomitinib resulted in tumor growth inhibition (partial response, PR). The PDX developed resistance to dacomitinib after 100 days of treatment, but continued to be inhibited by afatinib after 215 days of treatment.
Conclusion:
This study shows the efficacy of second generation especially afatinib irreversible EGFR TKIs in a chemoresistant LSCC PDX, with high wild type EGFR expression and EGFR amplification. Our results lend further support to the LUX-Lung 8 trial, and also the use of PDX to model therapeutic responses in lung cancer.
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P2.04-053 - Patient-Derived Xenograft Studies Suggest FGFR1 Amplification Is Insufficient to Predict Response to FGFR Inhibitors in Lung SqCC (ID 3067)
09:30 - 09:30 | Author(s): N. Pham
- Abstract
Background:
FGFR1 amplification has been reported in 16%-20% of lung squamous cell carcinoma (SqCC). Early phase clinical trials with anti-FGFR small molecule inhibitors are in progress. It remains unclear whether genomic changes involving FGFR1 is associated with a dependency in FGFR-driven oncogenic activity that could be inhibited with pharmacologic agents. We evaluated a pan-FGFR inhibitor (BGJ398) in four SqCC patient-derived xenograft (PDX) models with amplification of the FGFR1 gene.
Methods:
FGFR1 gene copy changes were assessed by fluorescence in-situ hybridization. PDX models were established by implanting surgical resected tumor fragments into the subcutaneous tissue of non-obese diabetic severe combined immune deficient (NOD-SCID) mice. Protein and mRNA expression levels were assessed by immunohistochemistry/western blot and RT-qPCR, respectively.
Results:
FGFR1 amplification was observed in 13 of 60 (22%) SqCC patient tumors, with all amplified tumors forming PDX. PDX models with FGFR1 gene amplification displayed higher levels of mRNA and protein compared to non-amplified tumor, excluding polysomy cases. One model demonstrated an average of 50% decrease in tumor volume in the BGJ398 treated group compared to control group, 21 days post-treatment. This model also expressed high FGFR1 and high cMYC protein. BGJ398-resistant PDX models included one model with high FGFR1 but low cMYC protein levels, and two models with low FGFR1 and high cMYC protein levels.
Conclusion:
The lack of growth arrest to a pan-FGFR small molecule inhibitor in the 4 PDX models evaluated suggests that FGFR1 amplification alone was not a sufficient predictive marker for pan-FGFR1 inhibitor activity. FGFR1 protein and MYC protein are putative markers.
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P3.04 - Poster Session/ Biology, Pathology, and Molecular Testing (ID 235)
- Event: WCLC 2015
- Type: Poster
- Track: Biology, Pathology, and Molecular Testing
- Presentations: 1
- Moderators:
- Coordinates: 9/09/2015, 09:30 - 17:00, Exhibit Hall (Hall B+C)
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P3.04-099 - Proteome Signatures with Prognostic Impact Distinguish Non-Small Cell Lung Cancer Histology Subtypes and Metabolic States (ID 1009)
09:30 - 09:30 | Author(s): N. Pham
- Abstract
Background:
We showed that the ability to establish a primary tumorderived xenograft (PDX) is an independent predictor of shorter disease-free survival in early stage non-small cell lung carcinoma (NSCLC). Hence, NSCLC engraftment may select for critical, aggressive aspects of the cancer phenotype linked to disease progression. More recently we reported dramatic remodeling of NSCLC proteomes not predicted by genomics analyses, and which distinguish between the major histological subtypes of NSCLC. Herein we report details on NSCLC proteome remodeling as a major determinant of the expression of the metabolism proteome, engraftment, and related to patient outcome.
Methods:
Omics platforms were used to comprehensively characterize the genomes and proteomes of non-engrafting, engrafting, and derived PDX tumors associated with NSCLC. To facilitate proteome quantification by mass spectrometry, tumor samples were spiked with stable-isotope-labeled proteomes from a mixture of representative NSCLC cell lines as an internal standard.
Results:
Proteome remodeling in NSCLC is extensive and largely unpredicted by gene copy number variation, and not highly correlated with mRNA-based expression. Analysis of the proteomes of cognate engrafting primary and PDX tumor pairs revealed signatures comprising sets of metabolism proteins that distinguished between the major histological subtypes, and which were particularly highly recapitulated in PDX tumors. Interrogation of The Cancer Genome Atlas showed that the genes encoding the highly recapitulated metabolism protein signatures are for the most part not highly mutated in cancers. However, when the signature-encoding genes are considered as a singular polygene, then patients with mutations are recognized as having significantly different overall survival compared to patients without mutations. The proteomes of non-engrafting NSCLC tumors were generally more similar to normal lung than were engrafting tumor proteomes. Hence, proteome remodeling affects metabolic states associated with NSCLC outcome.
Conclusion:
NSCLC is characterized by significant proteome remodeling that is invisible to genomics platforms. The proteomes of engrafting and non-engrafting NSCLC primary tumors are different, suggesting the potential to develop proteome signatures as prognostic biomarkers. Moreover, proteome signatures associated with PDX engraftment and poor outcome may be a source of new drivers and targets in NSCLC.
