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J.N. Weinstein



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    Best of Posters - IASLC Selection - Part 2 (ID 263)

    • Event: WCLC 2013
    • Type: Exhibit Showcase Session
    • Track:
    • Presentations: 1
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      P2.06-032 - SMO mutations occur in non-small cell lung cancer (NSCLC) and may respond to hedgehog inhibitors (ID 2483)

      10:05 - 10:10  |  Author(s): J.N. Weinstein

      • Abstract
      • Slides

      Background
      Smoothened (SMO) is a 7-membrane spanning receptor involved in the hedgehog signaling pathway. In the absence of Patched inhibition, SMO accumulates and inhibits proteolytic cleavage of transcription factors. We previously identified a lung cancer patient with SMO mutation (Patient A, Table 1) and successfully treated him with erivedge, a hedgehog inhibitor. We therefore sought to determine the incidence of SMO mutations in The Cancer Genome Atlas (TCGA) lung cohorts, identify additional NSCLC patients with SMO mutations, and initiate therapy with hedgehog inhibition as proof-of-concept.

      Methods
      TCGA databases for lung adenocarcinoma (n=230) and squamous cell carcinoma (n=178) were interrogated for SMO mutations and hedgehog pathway dyregulation. Mutations were determined by whole exome sequencing. Copy number was assessed by GISTIC 2.0 (scores of 2 considered high level amplification). The lung SMO mutation patients were undergoing treatment at M.D. Anderson Cancer Center Thoracic Clinic for metastatic/refractory disease. Mutations in hotspot regions of 46 cancer-related genes including SMO was performed as part of their clinical diagnostic evaluation (Ion AmpliSeq Cancer Panel; Life Technologies, CA).

      Results
      In TCGA lung adenocarcinomas, alterations in SMO (mutation, amplification, mRNA overexpression) were observed in 12.2% of tumors. The incidence of SMO mutations was 2.6% and SMO gene amplifications 5%. SMO mutations and amplifications strongly correlated with sonic hedgehog gene dysregulation (p<0.0001). In TCGA squamous cell, SMO was altered in 10.1% of tumors, primarily via mRNA upregulation. Only 1 SMO missense mutation was identified in the Lung SCC cohort (D209Y). We identified 3 NSCLC patients with SMO mutations (Table 1) by the 46-gene panel. Patient A was treated with erivedge as he had a concomitant localized basal cell carcinoma (BCC) with a significant reduction in tumor burden. He continues to respond to therapy after 14 weeks. It is possible that Patient A’s NSCLC-SCC was misidentified and that this was metastatic BCC or that this is a germline variant. Germ-line mutation analysis is underway. However, the precise SMO mutation in Patient A was also identified in a lung adenocarcinoma Patient C (Table 1). Two additional SMO-mutated patients have just initiated erivedge and updates on their status will be provided at WLCC.

      Table 1
      Patient Biopsy site SMO mutation Reported Histology Duration of Erivedge Therapy Response to Erivedge
      A Lung Codon 641, exon 11 (CCT to GCT) p. Pro641Ala NSCLC SCC 14 weeks PR
      A Skin lesion Codon 641, exon 11 (CCT to GCT) p. Pro641Ala BCC 14 weeks CR
      B AP window lymph node Codon 525, exon 9 (ATG to TTG) p.Met525Leu NSCLC Adenoca pending pending
      C Axillary lymph node Codon 641, exon 11 (CCT to GCT) p.Pro241Ala NSCLC Adenoca pending pending

      Conclusion
      SMO mutations and pathway alterations occur in NSCLC and may be an actionable target with hedgehog inhibitors; a clinical trial is under development. Screening lung SCC tumors for SMO mutations is recommended to prevent misdiagnosis of metastatic BCC. Additional analysis of hedgehog signaling pathway alterations is underway and will subsequently be reported.

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    MO15 - Novel Genes and Pathways (ID 89)

    • Event: WCLC 2013
    • Type: Mini Oral Abstract Session
    • Track: Biology
    • Presentations: 1
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      MO15.02 - Impact of co-occurring genetic events on the signaling landscape of KRAS-mutant lung adenocarcinoma. (ID 2936)

      16:20 - 16:25  |  Author(s): J.N. Weinstein

      • Abstract
      • Presentation
      • Slides

      Background
      Personalized medicine frameworks centered on identification and therapeutic targeting of dominant oncogenic driver mutations are rapidly becoming a standard of care in the clinical management of patients with lung adenocarcinoma. However, little is currently known about the nature and impact of co-occurring genetic events on signaling output downstream of initiating oncogenes. This lacuna in our understanding is particularly pertinent for the subgroup of KRAS-driven tumors, where mounting data point towards considerable heterogeneity in pathway activation and clinical response to targeted therapies. Here, we report a comprehensive analysis of genetic events that co-occur with or are mutually exclusive of mutant KRAS in a cohort of 230 lung adenocarcinomas and assess the impact of individual co-mutations on signaling streams using data derived from state of the art transcriptomic and (phospho)proteomic profiling of primary tumors.

      Methods
      An integrated analysis of 230 lung adenocarcinomas from The Cancer Genome Atlas (TCGA) consortium was performed using mutation (whole exome sequencing), transcriptomic (RNASeq), and proteomic (reverse phase protein array) datasets. Fischer’s exact test was applied to identify secondary mutations that occurred more frequently in either KRAS-mutant (n=68) or KRAS-wild-type (n=162) tumors and (phospho)protein markers that associated with each co-mutation. Genes with a mutation rate of ≥3% in the overall cohort were included in the analysis.

      Results
      Mutations in 18 genes were associated with KRAS mutational status in patient tumors (p≤0.01). Mutations in EGFR (p=0.0001), NF1 (p=0.001), and TP53 (p=0.001) were negatively correlated with the KRAS mutation. On the other hand, mutations in STK11 were significantly more frequent in the KRAS-mutant cohort (p=0.004), as were mutations in ATM (p=0.023) and MTOR (p=0.045). The most significant positive association involved mutations in ARHGEF11, a gene that encodes a Rho guanine nucleotide exchange factor (p=0.0004). Mutations in STK11 (29.4%) and TP53 (29.4%), the two most highly prevalent genetic events within the KRAS-mutant cohort were mutually exclusive. Unsupervised hierarchical clustering of transcriptomic and quantitative (phospho)proteomic profiles revealed separation of STK11-mutant tumors at the first branch of the cluster dendrogram, indicating activation of distinct signaling pathways downstream of this key tumor suppressor gene. Several less frequent genetic events had prominent and consistent effects on signaling output. We focused our attention on signaling via the MAPK pathway which may impact clinical sensitivity to MEK inhibitors, one of the most promising classes of targeted agents currently in clinical development for KRAS-mutant tumors. Preliminary analysis suggests that mutations in 3 individual genes can identify a subgroup of tumors (19% of the cohort) with profoundly suppressed MAPK signaling flux.

      Conclusion
      Analysis of recurrent secondary genetic events may define distinct and clinically relevant subsets of KRAS-mutant lung adenocarcinoma. Efforts to refine the sub-classification further and assess the impact of co-mutations on sensitivity to molecularly targeted agents are underway and updated results will be presented at the meeting.

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    P1.01 - Poster Session 1 - Cancer Biology (ID 143)

    • Event: WCLC 2013
    • Type: Poster Session
    • Track: Biology
    • Presentations: 1
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      P1.01-003 - Targeting EMT in lung cancer: An integrated analysis of Axl and other mesenchymal targets in The Cancer Genome Atlas (TCGA) (ID 1991)

      09:58 - 10:12  |  Author(s): J.N. Weinstein

      • Abstract

      Background
      We previously developed a 76-gene signature of epithelial-to-mesenchymal transition (EMT) that predicted resistance to EGFR and PI3K inhibition in non-small cell lung cancer (NSCLC). This analysis also identified Axl, a receptor tyrosine kinase, as a novel target for mesenchymal lung cancers. Here, we conducted an integrated molecular analysis of EMT in resected, treatment-naïve tumors from three clinical cohorts, including the Cancer Genome Atlas (TCGA) lung adenocarcinomas (LUAD) and squamous cell carcinomas (LUSC), with particular focus on Axl as a potential target in mesenchymal NSCLC.

      Methods
      Using our 76-gene EMT signature, TCGA patient tumors (230 LUAD, 178 LUSC) and a large MDACC cohort of resected tumors (n=279) were assigned an “EMT score.” Expression of >160 total and phosphoproteins were measured in the tumors by reverse phase protein array (RPPA). Proteomic profiles and other molecular markers (including mutation status, miRNA expression, and copy number) were correlated with EMT scores and Axl expression levels.

      Results
      The EMT score, derived from our EMT signature, identified NSCLC tumors with mesenchymal gene expression signatures (average 23% of tumors across all cohorts, range 14-34%). In both LUAD and LUSC, EMT scores were highly correlated with (1) expression levels of the miR200 family, a group of miRNAs previously known to regulate EMT (p-values <0.001 by Pearson correlation) and (2) levels of proteins central to EMT (e.g., E-cadherin, alpha-catenin, beta-catenin, claudin-7, fibronectin; p<0.001 for all). Mesenchymal tumors also had lower expression of TTF1 in LUAD (p=0.0002) and lower p63 in LUSC (p=0.003). Although pEGFR levels were higher in epithelial LUAD tumors (p=0.01), the frequency of EGFR mutations was not significantly higher in this group. EMT score was not associated with smoking status. Consistent with our previous findings in cell lines and patients with advanced NSCLC (BATTLE trial), protein expression of the receptor tyrosine kinase Axl was significantly higher in tumors with mesenchymal signatures (high EMT scores) and with low E-cadherin protein expression (p<0.005 for both). The inverse correlation between tumor E-cadherin and Axl expression was confirmed in an independent group of NSCLC cases by immunohistochemistry. Although a small number of Axl mutations were observed (<3% of tumors), few occurred in the kinase domain and their biological significance is unknown. Other potential therapeutic targets expressed at higher levels in mesenchymal lung cancers included PKC-alpha, NFKB, and FGFR1.

      Conclusion
      The EMT gene expression signature performed well in the TCGA LUAD, TCGA LUSC, and MDACC cohorts, correlating strongly with established markers of EMT on other data platforms (miRNA and protein). We observed strong protein expression of the receptor tyrosine kinase Axl (as well as other targets) among mesenchymal tumors, supporting further investigation of AXL as a potential EMT target and into the mechanism of its overexpression in NSCLC.