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Numerous studies have implicated changes in the Y chromosome in male cancers, yet few have investigated the biological importance of Y chromosome noncoding RNA. Here we identify a group of Y chromosome–expressed long noncoding RNA (lncRNA) that are involved in male non–small cell lung cancer (NSCLC) radiation sensitivity. Radiosensitive male NSCLC cell lines demonstrated a dose-dependent induction of linc-SPRY3-2/3/4 following irradiation, which was not observed in radioresistant male NSCLC cell lines. Cytogenetics revealed the loss of chromosome Y (LOY) in the radioresistant male NSCLC cell lines. Gain- and loss-of-function experiments indicated that linc-SPRY3-2/3/4 transcripts affect cell viability and apoptosis. Computational prediction of RNA binding proteins (RBP) motifs and UV-cross-linking and immunoprecipitation (CLIP) assays identified IGF2BP3, an RBP involved in mRNA stability, as a binding partner for linc-SPRY3-2/3/4 RNA. The presence of linc-SPRY3-2/3/4 reduced the half-life of known IGF2BP3 binding mRNA, such as the antiapoptotic HMGA2 mRNA, as well as the oncogenic c-MYC mRNA. Assessment of Y chromosome in NSCLC tissue microarrays and expression of linc-SPRY3-2/3/4 in NSCLC RNA-seq and microarray data revealed a negative correlation between the loss of the Y chromosome or linc-SPRY3-2/3/4 and overall survival. Thus, linc-SPRY3-2/3/4 expression and LOY could represent an important marker of radiotherapy in NSCLC.Significance:This study describes previously unknown Y chromosome–expressed lncRNA regulators of radiation response in male NSCLC and show a correlation between loss of chromosome Y and radioresistance.

Background: While most EGFR-mutant NSCLC tumors are resistant to checkpoint inhibitors, a small subset has durable responses. Certain molecular subtypes of EGFR may be more responsive. There is a lack of clarity on the genomic and immune profiles of EGFR subtypes, and further elucidation of this may assist in optimally identifying those likely to respond to immune-based therapies. Methods: Profiles of 5,510 lung adenocarcinoma specimens were obtained utilizing next-generation sequencing of 592 genes (Caris Life Sciences) and categorized by EGFR subtype. PD-L1 expression (Ab: 22c3), tumor mutational burden (TMB), immune cell type fractions, and co-mutations in TP53 were assessed by EGFR subtype and compared to wild-type (WT) tumors. Results: Of the total cohort, 791 (14.4%) were EGFR-mutant (Table). Among EGFR-mutant tumors, exon 19 deletions were most common (49.7%), followed by L858R, (32.9%), exon 20 insertions (13.0%), L861Q (2.9%), and G719X (1.5%). PD-L1 positivity of each EGFR subtype as compared to WT did not vary, except for L858R tumors which had a significantly lower percentage of PD-L1 positive cases. Exon 19 deletion, L858R, and exon 20 insertion tumors were significantly less likely to have high PD-L1 or high TMB compared to WT. Among the EGFR subtypes, L861Q and G719X tumors had the greatest percentage with high TMB. TP53 co-mutations were frequent in EGFR tumors, especially among L861Q and G719X tumors. Exon 19 deletion and L858R tumors had significantly less CD8+ and greater CD4+ T cell fractions compared to WT. Neutrophil and M2 macrophage cell fractions were significantly higher in exon 19 deletion, L858R, and exon 20 insertion tumors compared to WT. Conclusions: Most subtypes of EGFR have profiles consistent with decreased immunogenicity; however L861Q and C719X tumors have a greater percentage with high TMB or TP53 co-mutations. Such features in uncommon EGFR subtypes may correlate with responsiveness to immune-based therapies and warrant further study. Tumor Characteristic EGFR WT(n=4719) Exon 19 del(n=393) L858R(n=260) Exon 20 ins(n=103) L861Q(n=23) G719X(n=12) PD-L1 positive (≥1%) 57.7% 51.0% 49.0% a 49.5% 47.8% 50.0% PD-L1 high (≥50%) 30.6% 19.7% a 18.8% a 14.4% a 21.7% 16.7% TMB high (≥10 mut/Mb) 35.3% 1.0% a 3.7% a 1.0% a 9.5% 18.2% TP53 co-mutation 53.9% 61.7% 63.6% a 59.2% a 69.6% a 83.3% a Median % cell fraction CD8+ 0.7 0.3 a 0.4 a 0.3 0.6 0.2 CD4+ 0.0 0.6 a 0.8 a 1.3 a 1.7 1.1 Neutrophils 5.5 8.0 a 7.3 a 7.8 a 7.4 6.4 M2 macrophages 5.5 6.4a 6.9a 6.7a 5.8 4.3 aq-value < 0.05 when compared to EGFR WT (corrected for multiple comparisons) Citation Format: J. Nicholas Bodor, Joanne Xiu, Vinicius Ernani, Supreet Kaur, Hirva Mamdani, Pavel Brodskiy, Sai-Hong I. Ou, Patrick C. Ma, Margie L. Clapper, W. Michael Korn, Joseph Treat. Genomic and immune characteristics of EGFR subtypes in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4119.

Targeted therapies for cancer are inherently limited by the inevitable recurrence of resistant disease after initial responses. To define early molecular changes within residual tumor cells that persist after treatment, we analyzed drug-sensitive lung adenocarcinoma cell lines exposed to reversible or irreversible epidermal growth factor receptor (EGFR) inhibitors, alone or in combination with MET-kinase inhibitors, to characterize the adaptive response that engenders drug resistance. Tumor cells displaying early resistance exhibited dependence on MET-independent activation of BCL-2/BCL-XL survival signaling. Further, such cells displayed a quiescence-like state associated with greatly retarded cell proliferation and cytoskeletal functions that were readily reversed after withdrawal of targeted inhibitors. Findings were validated in a xenograft model, showing BCL-2 induction and p-STAT3[Y705] activation within the residual tumor cells surviving the initial antitumor response to targeted therapies. Disrupting the mitochondrial BCL-2/BCL-XL antiapoptotic machinery in early survivor cells using BCL-2 Homology Domain 3 (BH3) mimetic agents such as ABT-737, or by dual RNAi-mediated knockdown of BCL-2/BCL-XL, was sufficient to eradicate the early-resistant lung-tumor-cells evading targeted inhibitors. Similarly, in a xenograft model the preemptive cotreatment of lung tumor cells with an EGFR inhibitor and a BH3 mimetic eradicated early TKI-resistant evaders and ultimately achieved a more durable response with prolonged remission. Our findings prompt prospective clinical investigations using BH3-mimetics combined with targeted receptor kinase inhibitors to optimize and improve clinical outcomes in lung-cancer treatment. Cancer Res; 71(13); 4494–505. ©2011 AACR.

Background: The anti-PD-L1 antibody durvalumab (D) has shown manageable safety and encouraging clinical activity in patients with advanced NSCLC. Combination of D with anti-CTLA-4 antibody tremelimumab (T) may amplify T-cell responses against tumors through non-redundant immune checkpoint blockade and provide synergistic antitumor activity. We previously reported that D+T showed antitumor activity and manageable tolerability in the dose-escalation part of a phase 1b study (NCT02000947) of patients with advanced NSCLC. Here we present safety, clinical activity, and long-term follow-up for one of 3 expansion cohorts. Methods: Immunotherapy-naive patients with non-squamous NSCLC who progressed after 1 prior platinum-based therapy, ECOG PS 0-1, received D IV 20 mg/kg every 4 weeks (Q4W) for up to 12 months and T IV 1 mg/kg Q4W with the first 4 cycles of D. Tumor PD-L1 expression (fresh biopsy or archival sample within 3 mo) was assessed with the Ventana PD-L1 (SP263) assay, PD-L1 cutoff: ≥25% of tumor cells with membrane staining. Results: As of 20 Oct 2017, 213 patients (71% ECOG PS 1) received therapy and were followed for a median of 13.3 (0.5-21.0) mo. Treatment-related adverse events (AEs) were reported in 76% of patients; the most common were fatigue (19%), pruritus (17%), diarrhea (15%), decreased appetite (14%), and rash (14%). 14 patients (7%) had a treatment-related AE leading to discontinuation, with colitis (1%), diarrhea (1%), and pneumonitis (1%) reported in more than 1 patient. Grade 3/4 treatment-related AEs occurred in 23% of patients; the most common were increased lipase (5%), colitis (3%), and increased amylase (3%). There was 1 treatment-related death (multifactorial hypoxia). The 12-month OS rate was 53.8% (95% CI, 46.4-60.6). The Table shows antitumor activity and survival by PD-L1 status. Conclusions: Second-line D+T had a manageable safety profile in patients with non-squamous NSCLC. Clinical activity was seen in both PD-L1 ≥25% and Response and survivalPD-L1 ≥25% n=57PD-L1 Citation Format: Jamie Chaft, Byoung Chul Cho, Myung-Ju Ahn, Sylvestre Le Moulec, Eun Kyung Cho, Vassiliki Papadimitrakopoulou, Edward Garon, Sylvia Lee, Santiago Ponce Aix, Patrick C. Ma, Gregory Otterson, Rajesh Narwal, Guozhi Gao, Jennifer McDevitt, Judson Englert, Scott Antonia. Safety and activity of second-line durvalumab + tremelimumab in non-squamous advanced NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr CT113.

Drug resistance emergence is a common problem that limits long term outcome benefits in the era of precision cancer therapy. Recently, we identified an early precision drug escape mechanism with adaptive tumor cellular reprogramming emerging within days after drug initiation. Here we present a mass spectrometry imaging (MSI) approach to interrogate the biomolecular changes occurring within residual tumor cells under precision treatment with an ALK-specific kinase inhibitor TAE684 in EML4-ALK fusion (ALK+) lung adenocarcinoma xenograft. ALK+ H3122 lung adenocarcinoma murine xenograft model was established for in vivo treatment with TAE684, at a daily dose of 25mg/kg by orogastric gavage (n = 6). Diluent control was included as comparison (n = 6). Tumor measurement revealed expected remarkable tumor response with TAE684. Control tumors and drug-treated residual tumor tissues were harvested for MSI studies, at day 7 and day 14 during tumor response. MSI was carried out on formalin fixed, paraffin embedded tissues to compare peptide profiles between control tumors and 7- and 14-day ALK-TKI treated tumors using a histology guided mass spectrometry approach. Briefly, two sections were collected from each sample, one for mass spectrometry and one for histology. Mass spectrometry sections were deparaffinized, antigen retrieved, and subjected to on-tissue tryptic digestion. Tumoral areas of interest (100 μm diameter, ∼20 per sample) were annotated on digital microscopy images of the stained sections. The annotated images were merged with digital images of the unstained sections using Photoshop and this combined image was used to guide data acquisition from the areas of interest. Additionally, frozen control and day 14 TAE684 treated tumors were subjected to full section MSI to determine the ALK inhibitor drug distribution as well as the changing landscape of lipids and metabolites. Statistical analysis of the peptide data resulted in determination of 580 significant peaks using Wilcoxon rank sum test with a Bonferroni correction. A genetic algorithm classification model consisting of 24 peptide peaks was generated using a leave-20%-out cross validation over 10 iterations that resulted in an overall classification accuracy across the 3 groups of over 98%. Direct MS/MS fragmentation revealed that TAE684 was detected within the frozen dosed tumors, but was absent from the control tumors. Several lipids (notably, m/z 732.78, 744.67, and 770.72 increased, m/z 769.65 and 820.71 decreased) were found to undergo alterations in expression as a result of TAE684 treatment. MSI allowed for the direct in situ determination of biomolecules that are changing in expression landscape in ALK+ lung cancer as a result of TAE684 treatment. These results provide a rationale to advance our MSI studies to deepen our insights in mechanisms of adaptive precision drug resistance to improve treatment outcomes. Citation Format: Erin H. Seeley, Pamela S. Cantrell, Callee M. Walsh, Sijin Wen, Satoshi Komo, Xiaoliang Wu, Wei Zhang, Patrick C. Ma. Mass spectrometry imaging determines biomarkers of early adaptive precision drug resistance in lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3874.

Intrinsic or acquired resistance limits the clinical effectiveness of EGFR tyrosine kinase inhibitors (TKIs) for non-small cell lung cancer (NSCLC) patients (p) with EGFR mutations. One of the signaling mediators downstream of activated EGFR is signal transducer and activator of transcription 3 (STAT3). Not only does gefitinib not inhibit STAT3, but it also augments STAT3 tyrosine phosphorylation. EGFR blockade enriches lung cancer stem cells (CSCs) through NOTCH3-dependent signaling. A co-receptor of IL-6 (gp130) associates with Src and triggers activation of YAP and NOTCH. Our study is designed with three parallel objectives: firstly, to demonstrate that single EGFR TKI treatment cannot abrogate STAT3 and Src in EGFR mutant NSCLC cell lines; secondly, to examine whether the combination of gefitinib with compounds that target STAT3, (TPCA-1) and Src (saracatinib), suppresses the mechanisms of resistance; thirdly, to identify biomarkers in clinical tumor samples that may help us predict the outcome of EGFR TKIs and design effective combination therapies. Cell viability assay (MTT), western blotting, quantitative-real time PCR (qRT-PCR) and aldefluor assay-flow cytometry were used. We found that gefitinib increases pSTAT3 Y705 in PC-9 cells (that harbor the exon 19 deletion) in a time- and dose-dependent manner. Nine days after gefitinib treatment STAT3 mRNA level was significantly elevated. PC-9 cells showed dramatic increase in the fraction of ALDH+ cells upon treatment with gefitinib. TPCA-1 increased sensitivity to gefitinib in the PC-9 cells. Combination of gefitinib with TPCA-1 abrogated pSTAT3 Y705 but neither inhibited pPaxillin Y118 (Src induced) and pYAP S127 nor prevented the increment in the ALDH+ CSCs subpopulation. The triple combination of gefitinib, TPCA-1 and saracatinib was highly synergistic and abrogated pSTAT3 Y705, pPaxillin Y118 and pYAP S127. We performed qRT-PCR at baseline tumor samples of 64 EGFR mutant NSCLC p treated with first line EGFR TKIs and found that high expression of STAT3 and YAP were significantly correlated with shorter median progression-free survival (mPFS). mPFS was 9.6 months (m) (95% CI, 5.9 to 14.1) for p with low STAT3 and 18.4m (95% CI, 8.8 to 30.2) for p with high STAT3 mRNA expression (P Citation Format: Niki Karachaliou, Imane Chaib, Sara Pilotto, Jordi Codony, Xueting Cai, Xuefei Li, Ana Drozdowskyj, Carles Codony, Andrés Felipe Cardona, Guillermo López-Vivanco, Alain Vergnenègre, José Miguel Sánchez, Mariano Provencio, Filippo de Marinis, Enric Carcereny, Noemí Reguart, Rosario García-Campelo, Silvia Marin, Cristina Teixido, Isabella Sperduti, Sonia Rodríguez, Roger Estrada, Raimon Puig de la Bellacasa, José Luis Ramírez, Miguel Angel Molina-Vila, Caicun Zhou, Peng Cao, Patrick Ma, Trever Bivona, Rafael Rosell. Cotargeting EGFR, STAT3 and Src-Notch pathways: a promising approach to improve the efficacy of EGFR-TKIs in the treatment of NSCLC patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 265.

Patients with epidermal growth factor receptor (EGFR)–mutant non–small cell lung cancer derive significant clinical benefit from treatment with the EGFR tyrosine kinase inhibitors gefitinib and erlotinib. Secondary EGFR mutations such as EGFR T790M commonly lead to resistance to these agents, limiting their long-term efficacy. Irreversible EGFR inhibitors such as CL-387,785 can overcome resistance and are in clinical development, yet acquired resistance against these agents is anticipated. We carried out a cell-based, in vitro random mutagenesis screen to identify EGFR mutations that confer resistance to CL-387,785 using T790M-mutant H1975 lung adenocarcinoma cells. Mutations at several residues occurred repeatedly leading to functional resistance to CL-387,785. These variants showed uninhibited cell growth, reduced apoptosis, and persistent EGFR activation in the presence of CL-387,785 as compared with parental H1975 cells, thus confirming their role in resistance. A screen of alternative agents showed that both an alternative EGFR inhibitor and a cyclin-dependent kinase 4 inhibitor led to significant inhibition of cell growth of the resistant mutants, suggestive of potential alternative treatment strategies. These results identify novel mutations mediating resistance to irreversible EGFR inhibitors and reveal alternative strategies to overcome or prevent the development of resistance in EGFR-mutant non–small cell lung cancers. [Cancer Res 2007;67(21):10417–27]

c-Met receptor tyrosine kinase (RTK) has not been extensively studied in malignant pleural mesothelioma (MPM). In this study, c-Met was overexpressed and activated in most of the mesothelioma cell lines tested. Expression in MPM tissues by immunohistochemistry was increased (82%) in MPM in general compared with normal. c-Met was internalized with its ligand hepatocyte growth factor (HGF) in H28 MPM cells, with robust expression of c-Met. Serum circulating HGF was twice as high in mesothelioma patients as in healthy controls. There was a differential growth response and activation of AKT and extracellular signal–regulated kinase 1/2 in response to HGF for the various cell lines. Dose-dependent inhibition (IC50 < 2.5 μmol/L) of cell growth in mesothelioma cell lines, but not in H2052, H2452, and nonmalignant MeT-5A (IC50 >10 μmol/L), was observed with the small-molecule c-Met inhibitor SU11274. Furthermore, migration of H28 cells was blocked with both SU11274 and c-Met small interfering RNA. Abrogation of HGF-induced c-Met and downstream signaling was seen in mesothelioma cells. Of the 43 MPM tissues and 7 cell lines, we have identified mutations within the semaphorin domain (N375S, M431V, and N454I), the juxtamembrane domain (T1010I and G1085X), and an alternative spliced product with deletion of the exon 10 of c-Met in some of the samples. Interestingly, we observed that the cell lines H513 and H2596 harboring the T1010I mutation exhibited the most dramatic reduction of cell growth with SU11274 when compared with wild-type H28 and nonmalignant MeT-5A cells. Ultimately, c-Met would be an important target for therapy against MPM. (Cancer Res 2006; 66(1): 352-61

Non–small cell lung cancer (NSCLC) is a difficult disease to treat. The c-Met receptor is an attractive potential target for novel therapeutic inhibition in human cancers. We provide strong evidence that c-Met is overexpressed, activated, and sometimes mutated in NSCLC cell lines and tumor tissues. Expression of c-Met was found in all (100%) of the NSCLC tumor tissues examined (n = 23) and most (89%) of the cell lines (n = 9). Sixty-one percent of tumor tissues strongly expressed total c-Met, especially adenocarcinoma (67%). Specific expression of phospho-Met (p-Met) [Y1003] and [Y1230/1234/1235] was seen by immunohistochemistry. p-Met expression was preferentially observed at the NSCLC tumor invasive fronts. c-Met alterations were identified within the semaphorin domain (E168D, L299F, S323G, and N375S) and the juxtamembrane domain (R988C, R988C + T1010I, S1058P, and alternative splice product skipping entire juxtamembrane domain) of a NSCLC cell line and adenocarcinoma tissues. We validated c-Met as potential therapeutic target using small interfering RNA down-regulation of the receptor expression by 50% to 60% in NSCLC cells. This led to inhibition of p-Met and phospho-AKT and up to 57.1 ± 7.2% cell viability inhibition at 72 hours. The selective small molecule inhibitor of c-Met SU11274 inhibited cell viability in c-Met-expressing NSCLC cells. SU11274 also abrogated hepatocyte growth factor–induced phosphorylation of c-Met and its downstream signaling. Here, we provide first direct evidence by small interfering RNA targeting and small molecule inhibitor that c-Met is important in NSCLC biology and biochemistry. These results indicate that c-Met inhibition will be an important therapeutic strategy against NSCLC to improve its clinical outcome.

Small cell lung cancer (SCLC) is an aggressive cancer, and most patients present with cancer already spread beyond the lung. The receptor tyrosine kinase (RTK) c-MET has been implicated in various solid tumors, including SCLC, and is involved in mediating tumorigenesis, cell motility, scattering, invasion and metastasis. Mutations of c-Met have been described in renal papillary carcinoma and gastrointestinal cancers including hepatocellular carcinoma. The sequence of c-MET was examined for possible mutations in the 10 SCLC cell lines and 32 paired-SCLC/normal tissues. Novel c-MET alterations were identified among 3 of 10 separate SCLC cell lines and in 4 of 32 SCLC tumor tissue samples. These include two different c-MET missense mutations in the juxtamembrane (JM) domain (R988C found in NCI-H69 and H249 cell lines; and T1010I in SCLC tumor sample T31). Also, there are one Sema domain missense mutation (E168D in SCLC tumor sample T5), two-base-pair insertional mutations (IVS13- (52-53)insCT in both SCLC tumor samples T26 and T27) within the pre-JM intron 13, as well as an alternative transcript involving exon 10 (H128 cell line). c-MET receptors are expressed at various levels among the 10 SCLC cell lines studied (high expression: H69, H345, H510, and H526; medium-expression: H128 and H146; and low/no-expression: H82, H209, H249, and H446). The level of c-MET expression does not have any apparent correlation with presence or absence of mutations of c-MET in the cell lines. We show that the two identified JM mutations (R988C and T1010I), when introduced into the interleukin-3 (IL-3)-dependent BaF3 cell line, regulated cell proliferation resulting in a small but significant growth factor independence. When introduced into a SCLC cell line (H446, with minimal endogenous wild-type c-MET expression), the JM mutations also regulated cell morphology and adhesion, as well as causing enhanced tumorigenicity by both increases in focus-formation and soft-agar colony-formation assays. Both of the JM mutations also increased cell motility and migration evident in wound healing assay and time-lapse video-microscopy speed analysis. The JM mutations also altered the c-MET RTK signaling, resulting in preferentially increased constitutive tyrosine phosphorylation of various cellular proteins, including the key focal adhesion protein paxillin on tyrosine residue Y31 (first CRKL-binding site), correlating with increased motility. These results suggest a novel and unique role of the JM domain in c-MET signaling in SCLC with significant implications in cytoskeletal functions and metastatic potential. The novel JM gain-of-function somatic mutations described are the first to be reported in SCLC, and may be associated with a more aggressive phenotype. It would now be useful to study the inhibition of c-MET as a therapeutic target against SCLC.

The regulation of biological functions including cell growth, viability, migration, and adhesion of small cell lung cancer (SCLC) cells depends largely on the autocrine or paracrine stimulation of growth factor receptors and chemokine receptors. Stem cell factor (SCF) and its receptor c-Kit have been identified as important regulators of SCLC viability and are coexpressed in approximately 40-70% of SCLC specimens. In vitro, the inhibition of c-Kit tyrosine kinase activity by the small molecule tyrosine kinase inhibitor STI571 (Gleevec) abrogates cell growth. We have investigated the role of c-Kit and chemokine receptors in the regulation of cell migration and adhesion of SCLC cells. CXCR4, the chemokine receptor for stromal cell-derived factor-1alpha (SDF-1alpha), was found to be the major chemokine receptor commonly expressed in all of the 10 SCLC cell lines tested. SCF and SDF-1alpha increased cellular proliferation over a course of 72 h in both the c-Kit- and the CXCR4-positive NCI-H69 SCLC cell line. Recently, SDF-1alpha and CXCR4 have been shown to be important regulators of migration and metastasis in breast and ovarian cancer. We found that SDF-1alpha dramatically increased cell motility and adhesion in CXCR4-expressing NCI-H446 SCLC cells. In addition, SDF-1alpha altered cell morphology with increased formation of filopodia and neurite-like projections. In NCI-H69 SCLC cells, SCF and SDF-1alpha cooperatively induced morphological changes and activated downstream signaling pathways. Treatment of NCI-H69 cells with STI571 specifically inhibited the c-Kit signaling events of Akt and p70 S6 kinase, whereas SDF-1alpha-mediated activation of Akt or p70 S6 kinase was normal. In contrast, the phosphatidylinositol 3-kinase inhibitor, LY294002, prevented these cells from adhering and completely blocked SCF- and/or SDF-1alpha-induced Akt or p70 S6 kinase phosphorylation. These results demonstrate that the CXCR4 receptor is functionally expressed in SCLC cells and may, therefore, be involved in the pathogenesis of SCLC in vivo. Inhibition of both the CXCR4 and the c-Kit downstream events could be a promising therapeutic approach in SCLC.

Despite recent advances in the understanding of the biology and genetics of lung cancer, and despite the introduction of multiplex somatic mutation testing in the clinic, the long-term survival for all lung cancer patients, particularly for those with advanced disease, remains low. Lung cancer is the leading cause of cancer death globally, resulting in 1.4 million deaths annually, including 165,000 patients in the United States per year. In order to address the critical need for comprehensive profiling of these patients, we developed a novel, CLIA-certified, whole exome and low-coverage whole genome sequencing assay that applies a disease-focused, integrated approach to identify therapeutically actionable drivers of disease. A panel (12) of surgically resected NSCLC specimens along with corresponding adjacent normal tissue underwent DNA extraction in a clinical (CLIA) environment. Tumor and normal genomic DNA was prepared for whole exome sequencing using the using the Agilent SureSelectXT Human All Exon V5 kit according to the manufacturer's instructions, and libraries were sequenced on the Illumina HiSeq2500 at an average depth of 500X. Genomic DNA was then prepared for whole genome sequencing using Illumina's Nextera system and run on the Illumina HiSeq2500 platform at an average depth of 1-2X. Somatic variants were detected using Strelka and somatic copy number alterations (SCNAs) were identified using a novel algorithm comparing normalized read counts within genomic segments as well as genes in the tumor to a panel of normal tissues. In parallel, the same tumor/normal specimens were analyzed by two separate CLIA laboratories via 1) a clinically validated Ion Torrent AmpliSeq Cancer Panel assay, and 2) a clinically validated cancer-focused, high-resolution comparative genome hybridization (CGH) array. In addition, a well-characterized panel of 10 germline samples obtained from the 1000 Genomes Project were pooled to simulate a broad spectrum of somatic single nucleotide variant and indel allele frequencies. Sequencing, data analysis and clinical reporting were completed for all 12 cases with an average turnaround time of less than 3 weeks. Single nucleotide variants and indels were identified with an accuracy of greater than 99%, with a limit of detection of 5-10% mutant allele frequency. Somatic copy number alterations were observed with an overall accuracy of greater than 95%. Actionable variants were identified by cross-referencing individual results with our internally developed, lung-cancer focused therapeutic association database. Citation Format: Catherine K. Foo, John St. John, Nicholas Hahner, Oscar Westesson, Mitchell E. Skinner, Urvish Parikh, Kimberly Lung, Aleah F. Cauhlin, Jeffrey P. Catalano, Anne S. Wellde, Jonathan K. Barry, George W. Wellde, Patrick Ma, Rafael Rosell, Andres Felipe Cardona Zorilla, William R. Polkinghorn, Trever G. Bivona, Jonathan S. Weissman, Petros Giannikopoulos. Comprehensive integrated genomic analysis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4707. doi:10.1158/1538-7445.AM2014-4707

Lung cancer is the second most common malignancy with the highest cancer-mortality rate. EML4-ALK chromosomal translocation is now known to represent a highly actionable unique molecular target in approximately 5% of non-small cell lung cancer (NSCLC) patients. The ALK tyrosine kinase inhibitor (TKI) crizotinib induces remarkably high response rates in molecularly-selected NSCLC patients harboring EML4-ALK driven tumors, and is being used in first-line therapy. Nonetheless, responsive tumors ultimately develop acquired drug resistance. We have recently investigated non-mutational mechanisms of tumor resistant escape emerging under early TKI treatment time-window. Our recent studies in EGFR-mutant NSCLC in early adaptive drug escape against EGFR TKI identified an autocrine upregulation of TGFβ2 within these survivor cells. Here, we found that TGFβ2 was elevated significantly in the EML4-ALK-driven H3122 cells undergoing early adaptive drug escape against ALK TKI (TAE684) at treatment day 14. Interestingly, we found that the augmented TGFβ signaling was specific to TGFβ2, but not TGFβ1 or TGFβ3. We also found correlative enhanced mitochondrial BCL-2/BCL-xL prosurvival signaling in the day 14 TKI surviving H3122 cells. The upregulated TGFβ2-BCL-2/BCL-xL prosurvival mitochondrial priming was further validated in H3122 xenografts by IHC. Exogenous TGFβ2 stimulation in vitro for 7 days induced a dose-dependent upregulated BCL-2 and BCL-xL expression. Inhibiting mitochondrial BCL-2/BCL-xL priming using dual BCL-2/BCL-xL inhibitor ABT-263 as BH3-mimetic led to significant reduction in early adaptive drug escape induced by ALK TKIs. Our study showed that EML4-ALK NSCLC could escape ALK TKI early in treatment through cell plasticity that involved TGFβ2-mitochondrial priming in an upregulated prosurvival state. We also found that the early adaptive drug-escaping cancer cells possessed inherently increased EMT-ness (upregulated vimentin, AXL, GAS6) and cancer stemness (upregulated OCT4, NANOG). These findings provide deeper insights into the process of drug resistance emergence and highlighted potential window-of-opportunities to therapeutically target early adaptive escape to eradicate targeted drug resistance and impact long term survival. Citation Format: Lihong Yin, Wei Zhang, Ivy Shi, Yan Feng, Rakesh Bagai, Daniel Lindner, Patrick C. Ma. Adaptive drug escape of EML4-ALK lung cancer against targeted ALK inhibitor involving TGFβ2-mitochondrial priming. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3718. doi:10.1158/1538-7445.AM2014-3718

Background. Advanced NSCLC with sensitizing EGFR mutation is being treated with EGFR inhibitor first-line. Despite initial tumor response, targeted therapy invariably fails due to acquired resistance. Classical studies of acquired drug resistance focusing on late clinical events in rebiopsy studies have identified some resistance mechanisms including T790M-EGFR, MET amplification and AXL upregulation. Methods. HCC827 and PC-9 NSCLC cells (sensitizing EGFR exon 19-del) were used in vitro and in vivo drug-sensitive models. MTS viability assay, TLVM cell mobility assay, immunoblot and immunofluorescence and in vivo xenograft IHC analysis were performed. Transcriptome analysis of HCC827 cells under erlotinib inhibition time-course was performed using Affymetrix microarray gene expression profiling (Human GeneChip 1.0 ST arrays) in triplicate at 0 hr, 8 hr, 9 days of erlotinib-treatment, and 9 days pretreatment with erlotinib followed by 7 days drug-washout. Data analysis was performed using PCA, heatmap, BAMarray and PathwayStudio 6.0 analysis. We also performed mass-spectrometry-based global profiling analysis of cellular metabolome in 5 replicate. Results. We analyzed drug-sensitive HCC827 and PC-9 cells under erlotinib inhibition to characterize the adaptive response that engenders drug resistance. We identified an early adaptive drug-escape that emerged after 9 days of erlotinib, characterized with MET-independent mitochondrial BCL-2/BCL-xL prosurvival priming to result in 100-fold IC50 increase towards resistance. These cells displayed a quiescence state associated with retarded cell proliferation/cytoskeletal functions. Transcriptome profiling analysis of the early adaptive resistant HCC827 cells revealed a remarkable genome-wide adaptive reprogramming of gene expression signature, involving pathways of cell adhesion, cell cycle regulation, cell division/mitosis, glycolysis and gluconeogenesis, response to DNA damage stimulus, and DNA repair. Metabolomic profiling revealed a global adaptive metabolic reprogramming also, with resultant suppression of glucose and TCA cycle metabolism, and lipid bioenergetics. Our studies also identified autocrine TGFβ2 signaling pathway in mediating the early adaptive resistance in the mutated-EGFR lung cancer cells that escaped erlotinib inhibition through a combination of quiescence-state and EMT, cellular metabolic reprogramming and STAT3/BCL-2/BCL-xL mitochondrial prosurvival priming. Conclusion. Early adaptive drug-escape emerges within a subpopulation of EGFR-mutant NSCLC under erlotinib inhibition. This constitutes an early-stage minimal residual disease leading to eventual resistant tumor relapse. These early drug-escaping tumor cells undergo global cellular reprogramming with upregulated mitochondrial prosurvival priming, representing attractive therapeutic targets to eradicate drug resistance. Citation Format: Patrick C. Ma, Praveena S. Thiagarajan, Patrick Leahy, Rakesh Bagai, Ivy Shi, Wei Zhang, Yan Feng, Martina L. Veigl, Daniel Lindner, David Danielpour, Lihong Yin. Transcriptome and metabolome reprogramming in EGFR-mutant NSCLC early adaptive drug-escape against erlotinib. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1835. doi:10.1158/1538-7445.AM2014-1835

Lung cancer is the second most common malignancy in the United States with the highest cancer-mortality rate. Molecular targeted therapy in oncogene addicted non-small cell lung cancer (NSCLC) has gain landmark proof-of-principle success in clinical utility in recent years. Prime examples are EGFR targeted therapy against mutated EGFR tumors using tyrosine kinase inhibitors (TKIs) such as erlotinib/gefitinib, and also ALK targeted therapy against EML4-ALK tumors using ALK inhibitor crizotinib. Superior response rates and progression free survival outcomes were observed with the use of targeted therapeutics even in first line setting. Nonetheless, targeted therapeutics against mutant-EGFR and EML4-ALK tumors invariably develop an acquired tumor resistance to the TKIs. Mutational resistant mechanism has been well-established. Alternative signal pathway activation such as MET/HGF in both EGFR and ALK TKI resistance, or HER family signaling activation in EML4-ALK resistance have also been reported. We have recently begun studies focusing on the non-mutational mechanisms of tumor resistance under early time window of TKI treatment. Using HCC827 and PC9 cells as mutant EGFR addiction model, as well as H3122 and H2228 NSCLC cells as EML4-ALK addicted model, we have uncovered a novel early adaptive TKI resistance that can be evident as early as 7-14 days under initial TKI treatment. The early adaptive tumor cells displayed remarkable tumor resistance against the TKIs with 100-fold higher IC50. In mutant-EGFR against erlotinib, there was an upregulated mitochondrial antiapoptotic/prosurvival BCL-2/BCL-xL signaling dependence that is MET-independent. The early resistant cells were adaptive, highly reversible and adopted a quiescent state during TKI-induced resistance. On the other hand, our studies of early TKI resistance in EML4-ALK fusion cells revealed that while the adaptive resistance to TAE684 was also reversible, it appears to be not dependent on BCL-2/BCL-xL upregulation. We found that in both targeted TKI early resistance, the tumor survivor cells exhibited epithelial-mesenchymal transition (EMT) markers changes with decreased E-cadherin expression and increased vimentin expression. Our studies also provided in vitro and in vivo evidence that these early adaptive TKI resistant tumor cells can be targetable for prevention or eradication of tumor resistance emergence, such as utilizing BCL-2/BCL-xL pathway inhibitors, such as ABT-737, in combination with EGFR TKI in mutant-EGFR addicted NSCLC. Further preclinical model studies will focus on investigating the molecular and genomic changes and gene network regulation in the early adaptive resistant tumor cells, to enable a new paradigm of novel therapeutic targets discovery to overcome early tumor resistance emergence and improve long term outcome of targeted therapy in lung cancer. Citation Format: Lihong Yin, Ivy Shi, Wei Zhang, Rakesh Bagai, Yan Feng, Patrick C. Ma. Studies of early adaptive resistance in mutant-EGFR and EML4-ALK addicted non-small cell lung cancer in escape against small molecule inhibitors. [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 4455. doi:10.1158/1538-7445.AM2013-4455

Background. MET is the tyrosine kinase receptor for the ligand hepatocyte growth factor (HGF). MET kinase has been identified as a novel promising target in non-small cell lung lung cancer (NSCLC). Crizotinib, a recently FDA-approved ALK inhibitor for NSCLC harboring ALK 2p23 fusion (ALK+), was initially developed as a MET inhibitor. MET expression level is a potential biomarker for response to MET inhibitors. The role of MET/HGF pathway in ALK+ NSCLC is unknown. Methods. A cohort of 51 NSCLC patients tested for ALK fusion at Cleveland Clinic (2000 to 2012), including 15 ALK(+) and 36 ALK(-) subjects, were included in the study. Immunohistochemistry (IHC) stain against MET was performed using a monoclonal CONFIRM anti-Total c-MET antibody (SP44, Ventana). Staining was performed on a Ventana Benchmark XT automated immunostainer (Ventana Medical Systems). A four-tier (0, 1+, 2+, 3+) scoring system and H-score (the sum of each intensity score x %) were used. Thirteen ALK(+) patients treated on crizotinib therapy were prospectively followed and a total of 32 blood plasma samples were collected (1) prior to crizotinib initiation, (2) during responding period and (3) at disease progression, for HGF level measurement using HGF ELISA kit (R&D). Statistical analysis was performed using Fisher exact test and Wilcoxon rank sum test in JMP. Results. Of the 51 tumor tested for MET IHC, 39 were adenocarcinoma (15 ALK+ and 24 ALK-), 6 squamous cell, 4 large cell carcinoma and 2 other NSCLC. None received any MET inhibitor when tissue was collected. The percentage of negative MET IHC (score 0 or 1+ in 50% tumor cells) was not statistically significant between ALK(+) and ALK(-) groups (40% vs 30%, p=0.5). The plasma HGF levels in ALK(+) patients varies from undetectable to 14000pg/ml. The median (25th-75th quantiles) level in patients prior to crizotinib therapy (n=5), during responding period (CR/PR/SD, n=12) and at disease progression (n=5) were 2137(767-12100)pg/ml, 1629(785-3430)pg/ml and 4064(1108-7308)pg/ml. The plasma HGF level showed a trend of decreasing during clinical response to crizotinib and elevation upon disease progression, albeit not reaching statistical significance in this small study cohort (p>0.05). Conclusions. MET expression is commonly seen in NSCLC, and no significant difference were observed between fusion ALK(+) and ALK(-) NSCLC. The baseline plasma HGF concentration varied significantly among ALK(+) NSCLC patients, but showed a trend correlating with therapeutic response and resistant progression, to crizotinib therapy. Prospective study with larger cohorts is warranted to further evaluate the role of MET/HGF as biomarker in ALK targeted therapy. Citation Format: Yan Feng, Eugen Minca, Wei Zhang, Lihong Yin, Nathan Pennell, Carol Farver, Raymond Tubbs, Angen Liu, Patrick Ma. Tumoral MET expression and plasma HGF level in patients with ALK 2p23 fusion driven lung cancer. [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 2374. doi:10.1158/1538-7445.AM2013-2374

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC Background: Recent studies revealed that ALK (anaplastic lymphoma kinase) 2p23 translocation, most commonly fused with echinoderm microtubule-associated protein-like 4 (EML4), is a novel driver oncogene in about 5% of non-small cell lung cancer (NSCLC). ALK 2p23 fusion (ALK+) can be diagnosed by dual color break-part ALK FISH assay to inform personalized targeted therapy using the ALK inhibitor crizotinib. However, the underlying mechanisms of ALK oncogenic signaling and more importantly ALK inhibitor crizotinib resistance are not well understood. Materials and Methods: To understand the mechanism of oncogenic ALK signaling, an ALK+ NSCLC microarray dataset was retrieved from NCBI-GEO data repository ([GSE31210][1]) and analyzed using data-mining bioinformatics approaches. This dataset includes the gene expression profiles of 11 ALK+ NSCLC and 20 normal lung tissue samples. Statistical analysis was carried out to identify altered genes in ALK+ NSCLC and Ingenuity Pathway Analysis (IPA) software was deployed to uncover their network interactions. To study the resistance mechanism of the ALK+ H3122 human NSCLC cell line against the specific ALK inhibitor TAE684, real-time polymerase chain reaction (qRT-PCR), cell viability assay and immunoblotting were performed using standard techniques. Results: We identified a set of 1,656 genes that were significantly altered in ALK+ NSCLC, consisting of 662 upregulated and 994 downregulated. The principal component analysis (PCA) based on the top 51 of these dysregulated genes evidently separated ALK+ and normal lung tissue samples, implicating that these genes could represent potential genomic signature of ALK+ NSCLC. The IPA analysis revealed 35 canonical pathways linked to ALK signaling, including beta-adrenergic and angiopoietin signaling pathways. The results of qRT-PCR, cell viability assay and immunoblotting showed that in translocated ALK+ H3122 human NSCLC cell line, HGF (hepatocyte growth factor) overexpression could activate ALK downstream signaling via activation of MET receptor kinase pathway, thus potentially bypassing the oncogenic ALK signaling under ALK inhibitor TAE684 treatment. Hence, alternative direct activation of ALK downstream signaling molecules via MET/HGF axis activation may potentially contribute to ALK inhibitor drug resistance. Conclusion: Using bioinformatics data-mining, we have identified dysregulated genes and pathways in ALK+ NSCLC, many of which are novel biomarkers not previously reported. We also verified the relevance and potential key role of MET/HGF signaling axis in ALK inhibitor resistance. Taken together, our results highlighted the cross-talk between ALK and MET signaling in NSCLC and shed new insights into possible pitfalls of potential specific ALK targeting inhibitor drugs. Citation Format: Ivy Shi, Lihong Yin, Patrick C. Ma. Integrative study of dysregulated genes in translocated ALK-positive non-small cell lung cancer and personalized targeted therapy resistance. [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 4466. doi:10.1158/1538-7445.AM2013-4466 [1]: /lookup/external-ref?link_type=NCBIGEO&access_num=GSE31210&atom=%2Fcanres%2F73%2F8_Supplement%2F4466.atom

Activating mutations of EGFR have been characterized as important mechanisms for carcinogenesis in a subset of EGFR-dependent non-small cell lung cancers (NSCLC). EGFR tyrosine kinase inhibitors (TKI), such as erlotinib and gefitinib, have dramatic clinical effects on EGFR-addicted lung cancers and are used as first-line therapy for EGFR-mutant tumors. However, this therapeutic sensitivity is invariably temporary and eventually all tumors acquire secondary resistance to the drugs and progress. Erlotinib-resistant EGFR mutations such as EGFR T790M and MET activation have been reported in drug-resistant tumors, but the mechanism of resistance remains unclear in a significant fraction of cases. Here we report a novel molecular mechanism leading to secondary resistance to erlotinib. HCC827, an EGFR-mutant and highly erlotinib-sensitive NSCLC cell line was exposed to increasing doses of erlotinib for 5 months and 2 subclonal cell lines were established, both of which grow well in the presence of high-dose erlotinib (15µM). In contrast to parental cells, the two erlotinib-resistant cell lines demonstrated sustained activation of Ras/Mek/Erk and Akt signaling pathways in the presence of erlotinib despite complete inhibition of EGFR phosphorylation. Sequencing of the entire EGFR gene sequence revealed no secondary changes, and expression of EGFR and MET, as well as MET activation did not differ from parental cells suggesting the presence of an alternative, novel mechanism of resistance. Gene expression profiling revealed a limited number of genes with altered expression levels which were verified by quantitative rt-PCR. We focused on the cell surface receptor tyrosine kinase, AXL (10-fold overexpressed in one resistant clone) given its known role in cell proliferation, angiogenesis and recent findings indicating its involvement in lapatinib-resistance in ErbB2-positive breast cancer. Prominent AXL overexpression was further confirmed in this clonal isolate on the protein level. siRNA-mediated downregulation of AXL reconstituted erlotinib-sensitivity, leading to cell death and was accompanied by inhibition of AKT activation. However, AXL knockdown in the absence of erlotinib did not have growth inhibitory effects on the cells. These results suggest that AXL signaling can serve as a backup control of proliferative pathways in our resistant cell models in the presence of EGFR inhibition serving as a novel paradigm of oncogenic switch. Mechanisms underlying overexpression of AXL and its restoration of TKI sensitivity are under investigation. Our results suggest that an oncogenic switch from EGFR-dependent to EGFR/AXL-codependent signaling can lead to secondary EGFR-TKI resistance in NSCLC, indicating that dual blockade of EGFR and AXL may serve as a novel therapeutic strategy for the treatment of EGFR-mutant lung cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-307.

The mesenchymal-epithelial transition (MET) receptor plays prominent role in human tumorigenesis, tumor progression and metastasis. Overexpression or mutation of MET results in activation of oncogenic signaling pathways and leads to upregulation of diverse tumor cell functions. Mounting evidence has validated MET receptor as novel target for anticancer therapy. For efficacy evaluation of various MET-targeted anticancer therapies currently under development, it is critical to develop an imaging tool that permits detection and quantification of MET expression in vivo. To date, a number of small molecule MET inhibitors have been developed, including SU11274, which is a specific, reversible MET inhibitor that induces apoptosis in cells transformed by activated MET kinase. Here, we report the radiosynthesis and evaluation of a molecular imaging probe, [11C]SU11274, for quantification of MET receptors in human cancers in vivo. The radiolabeling with C-11 was accomplished through radiomethylation using 3-[3,5-Dimethyl-4-(piperazine-1-carbonyl)-1H-pyrrol-2-ylmethylene]-2-oxo-2,3-dihyro-1H-indole-5-sulfonic acid (3-chlorophenyl)-methyl amide hydrochloride as a key precursor. Following the synthesis of the precursor that was achieved in 10 steps with a total yield of 9.7%, [11C]SU11274 was obtained through radiomethylation in a range of 5-10 % radiochemical yield and over 95% radiochemical purity. For in vivo PET studies, two human lung adenocarcinoma cancer xenograft models were established using MET-positive H1975 and MET-negative H520 cell lines. The time-radioactivity curves showed that the uptake of [11C]SU11274 in the H1975 xenograft was significantly higher than in the H520 xenograft (p = 0.00019). Compared to H520, the H1975 xenograft mice exhibited an increased tumor uptake of [11C]SU11274 throughout the entire measurement period of 90 min. At 65 min post-injection, the radioactivity concentration ratio of H1975/H520 reached a statistically significant and enhanced ratio of 2.1, and peaked at 2.6 at 80 min. The PET imaging results were consistent with their corresponding immunohistochemical tissue staining patterns of MET receptors from the same animals. Hence, our results suggest that [11C]SU11274-PET is a specific imaging marker that can differentiate and quantify MET receptor expression in vivo. These studies demonstrated that [11C]SU11274-PET can facilitate the clinical development of MET-targeted cancer therapeutics. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 836.