Novel CDK12/13 Inhibitors AU-15506 and AU-16770 Are Potent Anti-Cancer Agents in EGFR Mutant Lung Adenocarcinoma with and without Osimertinib Resistance

Osimertinib is a third-generation epidermal growth factor receptor and tyrosine kinase inhibitor (EGFR-TKI) approved for the treatment of lung adenocarcinoma patients harboring EGFR mutations. However, acquired resistance to this targeted therapy is inevitable, leading to disease relapse within a few years. Therefore, understanding the molecular mechanisms of osimertinib resistance and identifying novel targets to overcome such resistance are unmet needs of cancer patients. Here, we investigated the efficacy of two novel CDK12/13 inhibitors, AU-15506 and AU-16770, in osimertinib-resistant EGFR mutant lung adenocarcinoma cells in culture and xenograft models in vivo. We demonstrate that these drugs, either alone or in combination with osimertinib, are potent inhibitors of osimertinib-resistant as well as -sensitive lung adenocarcinoma cells in culture. Interestingly, only the CDK12/13 inhibitor in combination with osimertinib, although not as monotherapy, suppresses the growth of resistant tumors in xenograft models in vivo. Taken together, the results of this study suggest that inhibition of CDK12/13 in combination with osimertinib has the potential to overcome osimertinib resistance in EGFR mutant lung adenocarcinoma patients.

Development of highly effective anti-mesothelin hYP218 Chimeric Antigen Receptor T cells with increased tumor infiltration and persistence for treating solid tumors

Mesothelin targeting CAR T cells have limited activity in patients. In this study, we sought to determine if efficacy of anti-mesothelin CAR T cells is dependent on the mesothelin epitopes that are recognized by them. To do so, we developed hYP218 (against membrane-proximal epitope) and SS1 (against membrane-distal epitope) CAR T cells. Their efficacy was assessed in vitro using mesothelin positive tumor cell lines and in vivo in NSG mice with mesothelin expressing ovarian cancer (OVCAR-8), pancreatic cancer (KLM-1) and mesothelioma patient-derived (NCI-Meso63) tumor xenografts. Persistence and tumor infiltration of CAR T cells was determined using flow cytometry. hYP218 CAR T cells killed cancer cells more efficiently than SS1 CAR T cells, with 2-4-fold lower ET50 value (Effector to Target ratio for 50% killing of tumor cells). In mice with established tumors, single intravenous administration of hYP218 CAR T cells lead to improved tumor response and survival compared to SS1 CAR T cells, with complete regression of OVCAR-8 and NCI-Meso63 tumors. Compared to SS1 CAR T cells, there was increased peripheral blood expansion, persistence, and tumor infiltration of hYP218 CAR T cells in the KLM-1 tumor model. Persistence of hYP218 CAR T cells in treated mice led to anti-tumor immunity when rechallenged with KLM-1 tumor cells. Our results demonstrate that hYP218 CAR T cells, targeting mesothelin epitope close to cell membrane, are very effective against mesothelin positive tumors and are associated with increased persistence and tumor infiltration. These results support its clinical development to treat patients with mesothelin expressing cancers.

SCAMP3 is a mutant EGFR phosphorylation target and a tumor suppressor in lung adenocarcinoma

Mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase domain constitutively activate EGFR resulting in lung tumorigenesis. Activated EGFR modulates downstream signaling by altering phosphorylation-driven interactions that promote growth and survival. Secretory carrier membrane proteins (SCAMPs) are a family of transmembrane proteins that regulate recycling of receptor proteins, including EGFR. The potential role of SCAMPs in mutant EGFR function and tumorigenesis has not been elucidated. Using quantitative mass-spectrometry-based phosphoproteomics, we identified SCAMP3 as a target of mutant EGFRs in lung adenocarcinoma and sought to further investigate the role of SCAMP3 in the regulation of lung tumorigenesis. Here we show that activated EGFR, either directly or indirectly phosphorylates SCAMP3 at Y86 and this phosphorylation increases the interaction of SCAMP3 with both wild-type and mutant EGFRs. SCAMP3 knockdown increases lung adenocarcinoma cell survival and increases xenograft tumor growth in vivo, demonstrating a tumor suppressor role of SCAMP3 in lung tumorigenesis. The tumor suppressor function is a result of SCAMP3 promoting EGFR degradation and attenuating MAP kinase signaling pathways. SCAMP3 knockdown also increases multinucleated cells in culture, suggesting that SCAMP3 is required for efficient cytokinesis. The enhanced growth, increased colony formation, reduced EGFR degradation and multinucleation phenotype of SCAMP3-depleted cells were reversed by re-expression of wild-type SCAMP3, but not SCAMP3 Y86F, suggesting that Y86 phosphorylation is critical for SCAMP3 function. Taken together, the results of this study demonstrate that SCAMP3 functions as a novel tumor suppressor in lung cancer by modulating EGFR signaling and cytokinesis that is partly Y86 phosphorylation-dependent.

AB0641 MANAGING ANKYLOSING SPONDYLITIS (AS) WITH SHORT TERM BIOSIMILAR ADALIMUMAB REGIMEN IN A RESOURCE STRAPPED SETTING: A PROTOCOL DRIVEN COMMUNITY CLINIC ORIENTED STUDY

Background:

We were handicapped by the exorbitant cost of innovator anti-Tumour Necrosis Factor (TNF) drugs. Despite limited use, we sometimes observed long-term benefits following short term induction like use. Emboldened by advent of biosimilars, we carried out an investigational study.

Objectives:

To evaluate the effectiveness of a short regimen of biosimilar (Bs) Adalimumab in AS

Methods:

50 consenting patients (86% B27+) naïve for biologics and negative for latent TB screen were enrolled into an observational design study of one year; Baseline mean values for age, duration, ASDAS and CRP was 31 years, 98.8 months, 4.6 and 64 mg per dl respectively. During the first year, patients were begun with 40 mg Bs Adalimumab (Bs-ADL) (Exemptia™), injected fortnight, for 12-16 weeks. No patient received DMARD or steroid in the first year of study. Patients continued standard of care follow up program in the clinic. The ASAS (Assessment Spondyloarthritis International Society) improvement indices were used. Standard intention-to-treat analysis was performed; significant p <0.05.

Results:

Optimum ASAS 40 improvement was observed at week 12 (68%); substantial improvement lasted till week 36. At one year, the ASAS 40 was 38%; ASAS partial remission 22% patients. Pro-inflammatory cytokines (IL-6, TNF α and IL-17) showed conspicuous reduction; maximum drop in IL-6 at week 24 (See Figure). 11 patients withdrew in the first year. 30 patients completed two years and 22 patients completed 3 year follow up. Over time, there was substantial loss in the ASAS 20 and 40 responses but patients seemed satisfied with the on-going symptomatic relief and improved function. Admittedly, patients showed more adherences to advice on physical exercise and stress reduction. Flares were more frequent after 1 year requiring short term round the clock NSAID; only 5 patients could afford to repeat a short term Bs-ADL regimen and one patient underwent hip arthroplasty. None received steroids and 5 patients were begun on Sulfasalazine in the second year and monitored. We could not evaluate structural modification (AS). Selected outcomes over 2 and 3 years from the current study will be compared to matched control (derived from the clinic database). None developed TB or any serious drug related toxicity. 2 patients developed recurrent uveitis.

Conclusion:

This real life documented experience unravelled impressive long term benefits following a kick start short term induction regimen of Biosimilar Adalimumab in AS. Though contrary to standard practice, this seemed a practical solution in our setting. We speculate a psychological and motivational boost rather than a prolonged real time biological effect (Bs-ADL) for this phenomenon. Our study has important socioeconomic bearing and merits validation.

Acknowledgement:

This was essentially a non-commercial investigator-initiated study. Zydus Cedilla India provided a generous research grant with free of cost Bs_ADL to several patients and a large concession in the cost to the rest.

Disclosure of Interests:

Arvind Chopra Grant/research support from: Zydus Pharamceutical Ltd India, Nagnath Khadke: None declared, Manjit Saluja: None declared, Toktam Kianifard: None declared, Anuradha Venugopalan: None declared

AB0585 SINGLE CENTER EXPERIENCE OF CLINICAL PROFILE OF INFLAMMATORY MYOSITIS FROM INDIA

Background:

Clinical profile of myositis differs in respect of the setting. We present a single center experience from a community based referral center

Objectives:

STUDY CLINICAL PROFILE OF INFLAMMATORY MYOSITIS (IM)

Methods:

We present data from 114 patients of connective tissue disorders (CTD) with dominant Inflammatory Myopathy(IM) evaluated in CRD where we have patient database since 1996. Standard investigations & ELISA, immunoblot and nephlometry to assay autoantibodies (AAb) were done. Data extraction done from 2005-2017

Results:

36 and 28 patients respectively diagnosed as dominant idiopathic dematomyositis (DM) and polymyositis (PM); remaining 41 patients showed overlap (OCTD). Mean onset age range 33-40 years in each subset with women dominance. Exclusive proximal muscle involvement seen 64% DM, 67% PM and 43% OCTD. 12 of OCTD showed classical DM rash. Raynauds’s phenomenon was seen in 38% (25% DM, 10% PM, 65% OCTD). 83% OCTD showed inflammatory polyarthritis; DM 29% and PM 42%. Two patients DM also diagnosed malignancy (ovarian CA). 25% DM, nil PM and 31.7% OCTD showed CT based lung findings. Mean creatinine phosphokinase at diagnosis were DM 1580, PM 2239 & OCTD 830. EMG required in 48 patients confirmed diagnosis (DM 17, PM 16 and OCTD 15). Seven patients with diagnostic dilemma/ poor therapy response required muscle histopathology confirmation. 59% DM,69% PM and 84% OCTD were seropositive ANA positive in 71%(ENA profile available for most). All Patients received steroids. Methotrexate prescribed in (92%), Azthioprine in (28%), hydroxychloroquine in (88%) with majority showing good response. Mycophenolate prescribed in (6%) for aggressive disease, IVIG in 2 patients for acute IIM with interstitial pneumonitis. Rituximab was prescribed in 4 resistant cases; all responding favourably. Mortality data of 4 patients(severe myositis(1), interstitial pneumonitis(1), ovarian cancer(1), septic shock(1)) was available. Antesynthatase syndrome noted in 9 patients.

Conclusion:

Overlap CTD with myositis seems more common profile than DM or PM. Response to therapy was satisfactory with steroids and methotrexate being the mainstay. Rituximab is a promising biological agent in chronic resistant cases.

References:

[1]A Kumar. Idiopathic Inflammatory Myopathies. Suppliment to JAPI, JUNE 2006, VOL. 54; Pg 62-66

[2]R Porkodi et al Clinical Spectrum of Inflammatory Myositis in South India - A Ten Year Study. J Assoc Physicians India 2002;50:1255-1258

[3]Chowdhary V, Aggarwal A, Misra R. Prevalence and clinical association of myositis-specific autoantibodies in North Indian patients with idiopathic inflammatory myopathy. APLAR J Rheumatol 2 001.

Acknowledgments :

STAFF AND PATIENTS OF CENTER FOR RHEUMATIC DISEASES, PUNE

Disclosure of Interests: :

NACHIKET KULKARNI Speakers bureau: PFIZER, NOVARTIS, YANSEN, Anuradha Venugopalan: None declared, MANJIT SALUJA: None declared, Arvind Chopra Grant/research support from: Zydus Pharamceutical Ltd India

Abstract 4528: Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V

Lung cancer is the leading cause of cancer mortality. Tumor heterogeneity is a major cause of treatment failure. Intra- and inter-metastatic tumor heterogeneity has been demonstrated by next generation sequencing (NGS) studies. However, heterogeneity in the proteome and phosphoproteome has been less studied. Integrated proteogenomics is essential to understanding the intricacies of tumor heterogeneity affecting treatment response. Here, we performed integrated mass spectrometry-based proteogenomics to characterize spatial and temporal heterogeneity of an exceptional responder lung adenocarcinoma patient who survived with metastatic disease for more than 7 years while on combination treatment with HER2-targeted and chemotherapy.

We employed Super-SILAC and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and ten different metastatic progressive lymph nodes from our patient collected across a span of seven years, including at autopsy. To further interrogate the mass spectrometry data, patient-specific database was built to incorporate all the somatic variants identified by NGS. An extensive validation pipeline was built for confirmation of variant peptides. CRISPR-Cas9-mediated gene knockout, cell viability assays, and confocal microscopy were used for further validation of novel variants.

A total of 6214 and 4061 proteins were identified from Super-SILAC and TMT experiments, respectively. 3648 proteins were identified and quantified in both experiments. More than 2000 proteins had catalytic activity, including kinases, phosphatases and metabolic enzymes. We identified 78 and 23 mutant peptides from Super-SILAC and TMT experiments, respectively. Three somatic variants, CDK12-G879V, FASN-R1439Q and HNRNPF-A105T, were confirmed using our variant peptide detection pipeline. Multiple reaction monitoring in a triple quadrupole mass spectrometer successfully identified and relatively quantified two of the variant tryptic peptides harboring the mutations, CDK12-G879V and FASN-R1439Q from the lung and lymph node metastatic sites, respectively. We investigated the consequences of loss of CDK12 function, as predicted from the novel CDK12-G879V mutant, in chemotherapy sensitivity. A549 lung adenocarcinoma cells, upon knockdown of CDK12, exhibited greater chemotherapy sensitivity that was rescued by wild type CDK12, but not by CDK12-G879V mutant.

We demonstrate the importance of integrated proteogenomic analyses to identify variant peptides in mass spectrometry data and studying proteomic heterogeneity affecting treatment response. CDK12-G879V mutation results in a nonfunctional CDK12 kinase and chemotherapy susceptibility in lung metastatic sites, likely explaining the “cure” of lung metastatic sites in this patient.

Citation Format: Xu Xhang, Khoa Dang P. Nguyen, Paul Rudnick, Nitin Roper, Emily Kawaler, Tapan K. Maity, Shivangi Awasthi, Shaojian Gao, Romi Biswas, Abhilash Venugopalan, Constance Cultraro, David Fenyo, Udayan Guha. Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4528.

Quantitative Mass Spectrometry to Interrogate Proteomic Heterogeneity in Metastatic Lung Adenocarcinoma and Validate a Novel Somatic Mutation CDK12-G879V

Lung cancer is the leading cause of cancer death in both men and women. Tumor heterogeneity is an impediment to targeted treatment of all cancers, including lung cancer. Here, we sought to characterize tumor proteome and phosphoproteome changes by longitudinal, prospective collection of tumor tissue from an exceptional responder lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for over seven years while undergoing HER2-directed therapy in combination with chemotherapy. We employed "Super-SILAC" and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and eight distinct metastatic progressive lymph nodes collected during these seven years, including five lymph nodes procured at autopsy. We identified specific signaling networks enriched in lung compared with the lymph node metastatic sites. We correlated the changes in protein abundance with changes in copy number alteration (CNA) and transcript expression. ERBB2/HER2 protein expression was higher in lung, consistent with a higher degree of ERBB2 amplification in lung compared with the lymph node metastatic sites. To further interrogate the mass spectrometry data, a patient-specific database was built by incorporating all the somatic and germline variants identified by whole genome sequencing (WGS) of genomic DNA from the lung, one lymph node metastatic site and blood. An extensive validation pipeline was built to confirm variant peptides. We validated 360 spectra corresponding to 55 germline and 6 somatic variant peptides. Targeted MRM assays revealed two novel variant somatic peptides, CDK12-G879V and FASN-R1439Q, expressed in lung and lymph node metastatic sites, respectively. The CDK12-G879V mutation likely results in a nonfunctional CDK12 kinase and chemotherapy susceptibility in lung metastatic sites. Knockdown of CDK12 in lung adenocarcinoma cells increased chemotherapy sensitivity which was rescued by wild type, but not CDK12-G879V expression, consistent with the complete resolution of the lung metastatic sites in this patient.

APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors

Intratumor mutational heterogeneity has been documented in primary non-small-cell lung cancer. Here, we elucidate mechanisms of tumor evolution and heterogeneity in metastatic thoracic tumors (lung adenocarcinoma and thymic carcinoma) using whole-exome and transcriptome sequencing, SNP array for copy-number alterations (CNAs), and mass-spectrometry-based quantitative proteomics of metastases obtained by rapid autopsy. APOBEC mutagenesis, promoted by increased expression of APOBEC3 region transcripts and associated with a high-risk APOBEC3 germline variant, correlated with mutational tumor heterogeneity. TP53 mutation status was associated with APOBEC hypermutator status. Interferon pathways were enriched in tumors with high APOBEC mutagenesis and IFN-γ-induced expression of APOBEC3B in lung adenocarcinoma cells, suggesting that the immune microenvironment may promote mutational heterogeneity. CNAs occurring late in tumor evolution correlated with downstream transcriptomic and proteomic heterogeneity, although global proteomic heterogeneity was significantly greater than transcriptomic and CNA heterogeneity. These results illustrate key mechanisms underlying multi-dimensional heterogeneity in metastatic thoracic tumors.

Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response

We used next-generation sequencing to identify somatic alterations in multiple metastatic sites from an “exceptional responder” lung adenocarcinoma patient during his 7-yr course of ERBB2-directed therapies. The degree of heterogeneity was unprecedented, with ∼1% similarity between somatic alterations of the lung and lymph nodes. One novel translocation, PLAG1-ACTA2, present in both sites, up-regulated ACTA2 expression. ERBB2, the predominant driver oncogene, was amplified in both sites, more pronounced in the lung, and harbored an L869R mutation in the lymph node. Functional studies showed increased proliferation, migration, metastasis, and resistance to ERBB2-directed therapy because of L869R mutation and increased migration because of ACTA2 overexpression. Within the lung, a nonfunctional CDK12, due to a novel G879V mutation, correlated with down-regulation of DNA damage response genes, causing genomic instability, and sensitivity to chemotherapy. We propose a model whereby a subclone metastasized early from the primary site and evolved independently in lymph nodes.

Abstract 2927: Proteogenomic heterogeneity in metastatic lung adenocarcinoma revealed from rapid/warm autopsy

Introduction: Intratumor heterogeneity has been characterized among multiple cancer types. However, in lung adenocarcinoma, recent work has been limited to early stage primary tumors and intertumor heterogeneity has not been well-studied. Most importantly, an integrated tumor heterogeneity analysis at the level of somatic variants, copy number, transcript and protein expression, and the phosphoproteome is outstanding.

Methods: In order to characterize both intra-tumor and inter-tumor heterogeneity of metastatic lung adenocarcinoma, we applied whole exome sequencing, RNA-seq, CNV-seq and mass spectrometry-based proteomic analyses on 33 tumor regions from metastatic sites including lung, liver and kidney, obtained by rapid/warm autopsy from 4 patients with Stage IV lung adenocarcinoma. The autopsy procedure was initiated between 2-4 hours of death.

Results: We found considerable intertumor heterogeneity with organ-specific, branched evolution that was consistent across DNA, RNA and protein analyses. Intratumor heterogeneity differed depending on oncogene-status: oncogene-negative tumors (without RTK/RAS/RAF mutations or known fusion gene) had significantly higher genomic intratumor heterogeneity than oncogene positive tumors. The degree of heterogeneity at the genomic and proteomic level was patient-specific. The proteomic analysis complemented genomic variants-based clonal evolution analysis. High-confidence driver mutations (KRAS, EGFR, TP53, CTNNB1) uniformly occurred early in the evolution of metastatic lung adenocarcinoma consistent with the concept of these mutations as likely ‘founders’. In contrast, other known driver mutations occurred more often in later stages among specific organ branches. Notably, oncogene-negative tumors carried significantly more driver mutations than oncogene-positive tumors suggesting that genomic alterations may have a larger role in the metastatic process versus the early evolution of lung adenocarcinoma in oncogene-negative vs. oncogene-positive tumors. Among all patients, lung cancer specific focal copy number alterations frequently occurred within metastatic branch points. Single metastatic site biopsies would therefore be unlikely to capture all significant driver mutations and copy number alterations, particularly among oncogene-negative tumors.

Conclusion: Metastatic lung adenocarcinoma evolves through a branched, organ-specific, process with acquisition of significant driver mutations and copy number changes, particularly among oncogene-negative tumors. The branched evolution is ultimately influenced by proteomic and phosphoproteomic alterations affecting key signaling pathways that may not be always a result of genomic changes.

Citation Format: Nitin Roper, Tapan K. Maity, James Gao, Abhilash Venugopalan, Xu Zhang, Romi Biswas, Constance Cultraro, David Kleiner, Stephen Hewitt, Javed Khan, Guha Udayan. Proteogenomic heterogeneity in metastatic lung adenocarcinoma revealed from rapid/warm autopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2927. doi:10.1158/1538-7445.AM2017-2927

Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response

Mutations in the Epidermal growth factor receptor (EGFR) kinase domain, such as the L858R missense mutation and deletions spanning the conserved sequence ⁷⁴⁷LREA⁷⁵⁰, are sensitive to tyrosine kinase inhibitors (TKIs). The gatekeeper site residue mutation, T790M accounts for around 60% of acquired resistance to EGFR TKIs. The first generation EGFR TKIs, erlotinib and gefitinib, and the second generation inhibitor, afatinib are FDA approved for initial treatment of EGFR mutated lung adenocarcinoma. The predominant biomarker of EGFR TKI responsiveness is the presence of EGFR TKI-sensitizing mutations. However, 30-40% of patients with EGFR mutations exhibit primary resistance to these TKIs, underscoring the unmet need of identifying additional biomarkers of treatment response. Here, we sought to characterize the dynamics of tyrosine phosphorylation upon EGFR TKI treatment of mutant EGFR-driven human lung adenocarcinoma cell lines with varying sensitivity to EGFR TKIs, erlotinib and afatinib. We employed stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative mass spectrometry to identify and quantify tyrosine phosphorylated peptides. The proportion of tyrosine phosphorylated sites that had reduced phosphorylation upon erlotinib or afatinib treatment correlated with the degree of TKI-sensitivity. Afatinib, an irreversible EGFR TKI, more effectively inhibited tyrosine phosphorylation of a majority of the substrates. The phosphosites with phosphorylation SILAC ratios that correlated with the TKI-sensitivity of the cell lines include sites on kinases, such as EGFR-Y1197 and MAPK7-Y221, and adaptor proteins, such as SHC1-Y349/350, ERRFI1-Y394, GAB1-Y689, STAT5A-Y694, DLG3-Y705, and DAPP1-Y139, suggesting these are potential biomarkers of TKI sensitivity. DAPP1, is a novel target of mutant EGFR signaling and Y-139 is the major site of DAPP1 tyrosine phosphorylation. We also uncovered several off-target effects of these TKIs, such as MST1R-Y1238/Y1239 and MET-Y1252/1253. This study provides unique insight into the TKI-mediated modulation of mutant EGFR signaling, which can be applied to the development of biomarkers of EGFR TKI response.

Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics

Mutations in the epidermal growth factor receptor (EGFR) kinase domain occur in 10-30% of lung adenocarcinoma and are associated with tyrosine kinase inhibitor (TKI) sensitivity. We sought to identify the immediate direct and indirect phosphorylation targets of mutant EGFRs in lung adenocarcinoma. We undertook SILAC strategy, phosphopeptide enrichment, and quantitative MS to identify dynamic changes of phosphorylation downstream of mutant EGFRs in lung adenocarcinoma cells harboring EGFR(L858R) and EGFR(L858R/T790M) , the TKI-sensitive, and TKI-resistant mutations, respectively. Top canonical pathways that were inhibited upon erlotinib treatment in sensitive cells, but not in the resistant cells include EGFR, insulin receptor, hepatocyte growth factor, mitogen-activated protein kinase, mechanistic target of rapamycin, ribosomal protein S6 kinase beta 1, and Janus kinase/signal transducer and activator of transcription signaling. We identified phosphosites in proteins of the autophagy network, such as ULK1 (S623) that is constitutively phosphorylated in these lung adenocarcinoma cells; phosphorylation is inhibited upon erlotinib treatment in sensitive cells, but not in resistant cells. Finally, kinase-substrate prediction analysis from our data indicated that substrates of basophilic kinases from, AGC and Calcium and calmodulin-dependent kinase groups, as well as STE group kinases were significantly enriched and those of proline-directed kinases from, CMGC and Casein kinase groups were significantly depleted among substrates that exhibited increased phosphorylation upon EGF stimulation and reduced phosphorylation upon TKI inhibition. This is the first study to date to examine global phosphorylation changes upon erlotinib treatment of lung adenocarcinoma cells and results from this study provide new insights into signaling downstream of mutant EGFRs in lung adenocarcinoma. All MS data have been deposited in the ProteomeXchange with identifier PXD001101 (http://proteomecentral.proteomexchange.org/dataset/PXD001101).

Loss of MIG6 Accelerates Initiation and Progression of Mutant Epidermal Growth Factor Receptor-Driven Lung Adenocarcinoma

Somatic mutations in the EGFR kinase domain drive lung adenocarcinoma. We have previously identified MIG6, an inhibitor of ERBB signaling and a potential tumor suppressor, as a target for phosphorylation by mutant EGFRs. Here, we demonstrate that MIG6 is a tumor suppressor for the initiation and progression of mutant EGFR-driven lung adenocarcinoma in mouse models. Mutant EGFR-induced lung tumor formation was accelerated in Mig6-deficient mice, even with Mig6 haploinsufficiency. We demonstrate that constitutive phosphorylation of MIG6 at Y394/Y395 in EGFR-mutant human lung adenocarcinoma cell lines is associated with an increased interaction of MIG6 with mutant EGFR, which may stabilize EGFR protein. MIG6 also fails to promote mutant EGFR degradation. We propose a model whereby increased tyrosine phosphorylation of MIG6 decreases its capacity to inhibit mutant EGFR. Nonetheless, the residual inhibition is sufficient for MIG6 to delay mutant EGFR-driven tumor initiation and progression in mouse models.

SIGNIFICANCE

This study demonstrates that MIG6 is a potent tumor suppressor for mutant EGFR-driven lung tumor initiation and progression in mice and provides a possible mechanism by which mutant EGFR can partially circumvent this tumor suppressor in human lung adenocarcinoma.

Abstract 5260: Identification of substrates of lung cancer-specific mutant EGFR kinases

Among various cancers, lung cancer is the leading cause of cancer-related mortality in both men and women in the US. The major driver mutations in lung cancer are in KRAS and EGFR. Mutations in EGFR account for 10-30% of lung adenocarcinoma. Somatic activating mutations in the kinase domain of EGFR occur in a subset of patients with lung adenocarcinoma and are associated with sensitivity to EGFR-directed tyrosine kinase inhibitors (TKIs). Unfortunately, all patients who respond dramatically to TKIs (gefitinib and erlotinib) eventually develop secondary resistance. A mutation in the gatekeeper residue in the ATP binding pocket of EGFR (T790M) occurs in around 50% of such patients.

We hypothesized that mutant EGFR kinases have altered substrate specificities in vivo; these substrates play intermediary roles in transducing mutant EGFR signaling to downstream components to promote tumorigenesis. We have employed a screening method using an in vitro kinase assay on protein arrays containing around 17,000 proteins to compare the substrate specificity of the kinase domains of wild type EGFR, L858R EGFR (the most common activating mutant), and the EGFR harboring both the L858R and T790M mutations (TKI resistant mutant). We have identified several potential substrates such as Crk, Crk-like protein, Grb2, Stat3, Nck1, PIK3R3, etc., which have altered phosphorylation status in response to mutant EGFR kinase activity. We also performed a SILAC (Stable isotope labeling by amino acids in cell culture)-based global phosphoproteomic analysis in human lung adenocarcinoma cells using mass spectrometry and observed that phosphorylation of some of the potential substrates is modulated by EGF stimulation and TKI inhibition.

We are currently validating promising substrates from the above assay by performing in vitro kinase assays in presence or absence of TKIs. Furthermore, to identify specific phosphorylation sites of the validated targets in vivo, we have adapted a SILAC-based mass spectrometry approach to immunoprecipitate specific substrates from isogenic human bronchial epithelial cells expressing various EGFR mutants followed by identification and quantification of phosphorylation. We have used siRNA-mediated gene silencing to interrogate the role of several of these substrates in survival of human lung adenocarcinoma cells. Finally, we are examining the phosphorylation status of identified substrates in tumor samples from patients of lung adenocarcinoma to correlate phosphorylation with EGFR mutation status.

Citation Format: Tapan K. Maity, Hee-Sool Rho, Natalya Belinka, Zhi Xie, Xu Zhang, Abhilash Venugopalan, Romi Biswas, Constance Cultraro, Heng Zhu, Udayan Guha. Identification of substrates of lung cancer-specific mutant EGFR kinases. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5260. doi:10.1158/1538-7445.AM2013-5260

Abstract 725: In vivo imaging and quantitative proteomics to study responsiveness to EGFR targeted therapy

Lung cancer is the leading cause of cancer related mortality in the United States and is the most common cancer worldwide. Somatic mutations in the kinase domain of EGFR such as in-frame deletion of LREA amino acids in exon 19 and L858R point mutation in exon 21 largely account for 15-30% of lung adenocarcinoma. Although lung cancer patients carrying either of these mutations respond dramatically to EGFR-directed tyrosine kinase inhibitors (TKIs) such as erlotinib and gefitinib, acquired resistance to these drugs has been the main obstacle in treating these patients for the long term. Secondary mutation at the gatekeeper residue of the kinase domain (T790M) of EGFR accounts for drug resistance in about 50% of patients.

We have used doxycycline inducible mutant EGFR transgenic mice to model human lung adenocarcinoma that is sensitive and resistant to TKIs. Our overall goal is to examine the treatment response to EGFR-directed TKIs in lung adenocarcinoma harboring various EGFR mutants. Our approach is aimed to identify imaging surrogates and proteomics profile of treatment response in mouse models of mutant EGFR-driven lung tumorigenesis.

In this study, we have used transgenic mice that express exon 19 deletion mutant, L858R mutant, and L858R/T790M double mutant in type II pneumocytes upon doxycycline induction. Tumor burden in these mice was monitored by serial MRI imaging. Each group of mice with significant tumor burden was treated with erlotinib, a reversible EGFR inhibitor, BIBW-2992, an irreversible EGFR/ERBB2 dual inhibitor, or a combination of BIBW-2992 and cetuximab, an antibody directed against EGFR followed by 2[18F]Fluoro-2-deoxy-d-glucose (FDG)-PET imaging to assess any tumor regression. We observed a significant reduction of 18FDG uptake by tumors after the treatment with erlotinib in L858R mutant mice. However, in L858R/T790M mutant mice, no significant reduction of 18FDG uptake was observed upon treatment with erlotinib and BIBW-2992 had only mild effect. We are currently designing rational combination treatments based on the response in 18FDG-PET imaging. Finally, we are performing global phosphoproteomic analysis using quantitative mass spectrometry and immunohistochemistry with phospho-specific antibodies on tumor tissue before and after various treatments and correlating with the response in PET imaging. Results from these experiments will help us identify potential biomarkers (imaging and proteomic) of treatment response in lung adenocarcinoma driven by both TKI-sensitizing and resistant mutants of EGFR.

Citation Format: Abhilash Venugopalan, Niu Gang, Jinxia Guo, Tapan Maity, Xu Zhang, Constance Cultraro, Xiaoyuan Chen, Udayan Guha. In vivo imaging and quantitative proteomics to study responsiveness to EGFR targeted therapy. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 725. doi:10.1158/1538-7445.AM2013-725