Matthew Meyerson, M.D. Ph.D. - US grants

DESCRIPTION (provided by applicant): We have developed a new method to discover microbial causes of human disease, sequence-based computational subtraction. In this method, sequences from diseased tissue are compared to the human genome computationally, and the filtered sequences are highly enriched for non-human nucleic acids. I propose to apply computational subtraction to search for viruses that cause lymphomas associated with immunodeficiency, most notably post-transplant lymphoproliferative disorder and HIV-associated lymphoma. First, I propose to use specimens of post-transplant lymphoproliferative disorder, known to be positive for Epstein-Barr virus, to refine our methods for library generation and sequencing. In particular, we would like to test the use of normalization, subtraction, and concatenation techniques. Once we have improved these techniques, I plan to focus on searching for novel viruses in immunodeficiency-associated lymphomas of unknown etiology. We plan to generate cDNA libraries from immunodeficiency-associated lymphoma biopsy specimens, to sequence a sampling of these libraries, and then to subtract the sequences computationally and experimentally against the human genome. Filtered sequences will be tested further for specific association with lymphoma using the polymerase chain reaction. Should we successfully identify novel lymphoma-associated sequences, we will then attempt to generate molecular clones of the entire putative viruses and begin to characterize the protein products of their genomes. Computational subtraction is a broadly applicable method. While we will begin our pathogen discovery projects in cancer, our methods will be broadly applicable to many human diseases. These include auto-immune diseases and inflammatory diseases, as well as uncharacterized epidemics, whether natural or bio-terrorist in origin.

DESCRIPTION (provided by applicant): The genetics underlying the genesis and progression of prostate cancer remain poorly understood. This lack of understanding hampers both our current ability to rationally stratify patients with respect to existing therapies and to identify novel therapeutic targets. One mechanism by which we can accelerate the targeted therapy paradigm is to systematically define somatic mutations in prostate cancer. We have recently demonstrated the utility of high-density single nucleotide polymorphism (SNP) arrays for detecting large-scale genetic alterations of the cancer genome. Specifically, we have shown that SNP arrays are an effective high throughput approach to identify loss-of-heterozygosity (LOH) events, as well as copy number alterations including amplifications and deletions in human prostate cancer; and have developed a novel informatics platform (dChipSNP) to handle and analyze SNP array data. We have now shown that the 3rd generation of SNP arrays with probes for over 100,000 SNPs can robustly detect copy number changes including hemizygous deletions, homozygous deletions, and amplifications. The preliminary data suggest that it is now feasible to use SNP arrays to detect genomic alterations in human prostate cancer samples at unprecedented resolution. We propose to apply these methods to the systematic detection of large-scale genetic alterations in human prostate cancer. To this end the specific aims of this proposal are: 1. To generate genome-wide maps for loss-of-heterozygosity, homozygous deletions and amplifications in localized, androgen-dependent metastatic and androgen-independent metastatic prostate cancer using single-nucleotide polymorphism arrays containing probes for 120,000 SNPs. 2. To identify regions of LOH, gene amplification and homozygous deletion that are statistically enriched in metastatic or androgen-independent prostate cancer samples. 3. To use integrated analysis of matched expression data and genetic maps to stratify candidate genes targeted by the relevant genetic alterations. 4. To begin the functional validation of selected candidate tumor suppressor and oncogenes identified in aims 1 through 3.

Project Summary The epidermal growth factor receptor (EGFR) tyrosine kinase is one of the most commonly activated oncoproteins in lung adenocarcinoma, glioblastoma and other cancers. The identification of cancer-associated EGFR mutants and their predictive power to select patients for treatment with EGFR inhibitors constitutes a major advance in treatment of these cancers. The collaborative efforts of the Eck and Meyerson laboratories over the past 12 years have provided a detailed structural and mechanistic understanding of selected activating and resistance mutations in EGFR, and have led to new classes of inhibitors that can overcome treatment-acquired resistance. In this renewal, we propose to perform studies that will inform the discovery of inhibitors of EGFR variants for which current treatments are ineffective, including exon20 insertion mutants in non-small cell lung cancer and EGFRvIII mutants in glioblastoma. In addition, we propose to probe the structure and regulation of the intact receptor to better understand its oncogenic activation. We will undertake the following Specific Aims: Aim 1) Analyze the biochemical and structural impact of small-molecule kinase inhibitors on EGFR exon20 insertion mutants, Aim 2) Develop allosteric inhibitors that selectively inhibit the EGFRvIII variant in glioblastoma, and Aim 3) Structure elucidation of the complete EGF receptor. Execution of these aims will lead to small molecules that will serve as templates for next-generation therapeutics for EGFR- driven cancers that do not respond to current EGFR targeted agents. Additionally, our structural and biochemical studies will illuminate mechanisms of receptor activation and signaling in both normal and oncogenic contexts that may suggest new avenues for therapeutic intervention in the future.

Arts; Bio-Informatics; Bioinformatics; Cancer of Lung; Communities; DF/HCC; Dana-Farber Cancer Institute; Data; Data Set; Data Storage and Retrieval; Dataset; Development; EGFR; ERBB Protein; ERBB1; Emergent Technologies; Emerging Technologies; Epidermal Growth Factor Receptor; Epidermal Growth Factor Receptor Kinase; Epidermal Growth Factor Receptor Protein-Tyrosine Kinase; Expertise, Technical; Future; Genetic; Genetic Alteration; Genetic Change; Genetic defect; Genomics; HER1; Investigators; Laboratories; Lung; Malignant Tumor of the Lung; Malignant neoplasm of lung; Mutation; Nature; Pathogenesis; Pulmonary Cancer; Pulmonary malignant Neoplasm; R01 Mechanism; R01 Program; RPG; Receptor, EGF; Receptor, TGF-alpha; Receptor, Urogastrone; Receptors, Epidermal Growth Factor-Urogastrone; Reproduction spores; Research; Research Grants; Research Personnel; Research Project Grants; Research Projects; Research Projects, R-Series; Research Resources; Researchers; Resources; Respiratory System, Lung; Seasons; Spores; Technical Expertise; Technology; Time; Transforming Growth Factor alpha Receptor; anticancer research; c-erbB-1; c-erbB-1 Protein; cancer research; concept; data retrieval; data storage; design; designing; erbB-1; erbB-1 Proto-Oncogene Protein; erbBl; experience; genome mutation; lung cancer; new technology; proto-oncogene protein c-erbB-1; pulmonary; tool

DESCRIPTION (provided by applicant): Our goal is to build an infrastructure to discover novel viruses associated with human cancer from next-generation sequencing data, using a sequence-based computational subtraction approach that we developed. This proposed project responds to the ARRA Research and Research Infrastructure Grand Opportunities RFA on "Identifying Potential Viral Signatures in Large Scale Studies of Germline and Somatic Changes in Cancer Genomes Pilot Program". Large-scale genome projects, including The Cancer Genome Atlas (TCGA) as well as studies of germ-line genetic correlations with cancer, are now moving towards the application of ultra-high- throughput next-generation sequencing approaches, both on the cDNA level ("RNA-seq") and the DNA level, especially whole genome sequencing ("WGS"). The study is focused on the computational analysis of large next-generation sequencing data sets for virus discovery. Specifically, we plan to build an infrastructure to apply sequence-based computational subtraction, a method developed by the PI and co-investigator jointly, to evaluate the presence of novel non-human nucleic acid sequences in databases generated by these large-scale cancer genome projects. This approach starts with the assumption that virally-induced cancers contain both human and viral nucleic acids, and that subtraction of the human genome from cancer-derived sequences will leave residual candidate non-human and potentially viral sequences. First, we will build a software pipeline for computational subtraction-based data analysis and candidate pathogen sequence discovery. Second, we will apply this pipeline to the incoming flood of next-generation sequencing data from TCGA and other large-scale data sets. Third, we will experimentally test non-human sequences that we have identified for their presence in validation cohorts for the cancers in which they were discovered. Fourth, we will use the validation data to circle back and improve the quality of our computational pipeline. In the long run, we anticipate that we can build a sustainable pipeline that could be supported either as an academic or industrial effort. Identification of a novel infectious agent associated with human cancer would have immediate preventive, diagnostic and therapeutic significance. The infrastructure that we develop in this two-year project pilot will lay the groundwork for discovering additional cancer-associated pathogens in the future, by analyzing the ever-increasing quantities of next-generation cancer sequencing data. PUBLIC HEALTH RELEVANCE: Viruses are among the major causes of human cancer. Discovering these viruses can lead to major improvements in public health, because virally induced cancers can be prevented by vaccination. In recent years, hepatitis B vaccination has led to a dramatic decrease in the occurrence of liver cancer, and human papillomavirus vaccination has been shown to decrease the rates of cervical carcinoma. Genome analysis and sequencing technologies are being used to discover the causes of human cancer, in projects such as The Cancer Genome Atlas, or TCGA. These technologies can also lead to the discovery of new viruses. Therefore the National Cancer Institute is investing funds from the American Recovery and Reinvestment Act of 2009 to support the discovery of new viruses in data from cancer genome projects such as TCGA. Our proposal is responsive to the National Cancer Institute request, entitled "Identifying Potential Viral Signatures in Large Scale Studies of Germline and Somatic Changes in Cancer Genomes Pilot Program". We have developed a powerful computational approach to compare DNA and RNA sequences from cancer, or from cancer patients, to the normal human genome. Sequences that are unique to cancers, or to cancer patients, may represent novel cancer- causing viruses. In this plan, we will build a stable software infrastructure to perform this sequence comparison, apply this infrastructure to data from large-scale cancer genome projects, test candidate sequences for whether they are likely to represent viruses, and then continue to improve the software infrastructure. This effort will enable discovery of viruses by the entire cancer research community.

DESCRIPTION (provided by applicant): We propose to operate a Genome Characterization Center for The Cancer Genome Atlas (TCGA) of the National Cancer Institute. Our goal is to characterize the genomes and transcriptomes of 10,000 human cancers over 5 years, together with the collaborators of TCGA Research Network. Given the ongoing revolution in genome analysis, our Center will transition from current-generation microarray technologies to next-generation sequencing technologies for cancer genome characterization. We will accomplish this by benchmarking the next-generation technologies against state-of-the-art array technologies used in the pilot project of TCGA. Our Center is uniquely qualified for this effort, because of our expertise in next-generation sequencing as well as current-generation microarray production and technology development, our knowledge and demonstrated accomplishments in cancer genomics, and our commitment to and experience with multi-institutional collaborations including the pilot project of TCGA. Specifically, we intend to accomplish the following aims for TCGA: Aim 1. Using microarray technologies: Characterize DNA and RNA from 2000 cancer samples and appropriate controls during year 1. Aim 2. Using next-generation sequencing: (i) Perform direct comparison and validation of the three alternative platforms during year 1, by characterizing DNA from 300 cancer/normal sample pairs and RNA from 100 cancer samples. (ii) Select the most cost-effective sequencing platform at the end of year 1, based on the results and in conjunction with NCI staff. (iii) Implement this sequencing platform to characterize DNA and RNA from 2000 cancer samples and appropriate controls in Years 2-5. (iv) Continue to decrease cost and increase resolution of genomic analysis.

Project Summary This proposal aims to understand the role of NKX2-1 amplification, the most common focal copy number alteration of lung adenocarcinoma, in the pathogenesis of this disease. Lung cancer is the leading cause of cancer death in the United States and lung adenocarcinoma is the most common type of lung cancer. NKX2-1 amplification occurs in approximately 12% of lung adenocarcinomas. NKX2-1 is required for the development of type II pneumocytes within the terminal respiratory unit, and is required for survival of lung adenocarcinoma cells in culture. Thus NKX2-1 exhibits many of the hallmarks of a lineage survival oncogene. The proposed research aims to understand the mechanisms by which NKX2-1 amplification contributes to lung adenocarcinoma pathogenesis, by accomplishing four specific aims. Specific Aim 1. Identify the transcriptional targets of NKX2-1 in lung adenocarcinoma. Specific Aim 2. Determine whether NKX2-1 is the only gene in the 14q13.3 amplicon that is required for lung adenocarcinoma cell survival. Specific Aim 3. Assess whether the LMO3 transcription factor gene is required for the survival of lung adenocarcinoma cells with and without NKX2-1 amplification. Specific Aim 4. Perform shRNA screens to identify cellular genes that are specifically required for the survival of lung adenocarcinoma cells with amplified NKX2-1 but not of cells that lack NKX2-1 expression. Through these aims, the proposed research will attempt to identify new therapeutic targets for the treatment of lung adenocarcinomas harboring NKX2-1 amplification. In this way, it should contribute to the broad goal of improving lung cancer treatment, which motivates this research program.

PROJECT SUMMARY (See instructions): The purpose of the Administrative Core is to provide support for the integrated Program on Lung Cancer Targeted Therapies, whose ultimate goal is to translate genomic events into the therapy of patients with nonsmall cell lung cancer (NSCLC) by discovery, testing, and validating kinase inhibitors as targeted therapies for genomically selected NSCLC . Specifically, the Core Director and Co-Director will provide guidance and oversight to the Projects and shared research Cores and will lead the evaluation of research progress including consultation with an Internal Advisory Committee and an External Advisory Board. The Administrative Core of this Program Project application is to coordinate these interrelated complementary research projects to maximize their scientific synergy and to share the findings with the scientific community. The Core Directors will co-ordinate staff assistance to projects including administrative support to facilitate scientific progress including meeting arrangements, editorial services for manuscript preparation, and web development services for internal and external communications. The specific aims of the Administrative Core are summarized below. Specific Aim 1: Monitor projects and shared resource cores and to evaluate overall research progress. Specific Aim 2: Foster collaboration and communication among the projects and shared resource cores. Specific Aim 3; Provide fiscal oversight and support for the program. Specific Aim 4: Promote the clinical translation of diagnostic and therapeutic discoveries from the program.

PROJECT SUMMARY (See instructions): In our Preliminary Studies, we found that DDR2, the discoidin domain receptor 2 tyrosine kinase gene, is somatically mutated in 3 to 4% of lung squamous cell carcinomas (lung SCC). Knock-down of DDR2 kills lung SCC cells bearing DDR2 mutations. Furthermore, treatment of DDR2-mutant lung SCC cells with the tyrosine kinase inhibitor dasatinib significantiy decreases cell proliferation; the effects of dasatinib are rescued by over-expression of DDR2 bearing the dasatinib-resistant T654M gatekeeper mutation. We now aim to develop DDR2 further as a therapeutic target for lung SCC. Our specific aims are to work with the other Projects and the shared resource Cores as follows: -Specific Aim 1. We will characterize the oncogenic potential of tumor-derived DDR2 mutants in the basal epithelium of the lung using cellular and animal model systems. We will work with Core C (Animal) to generate transgenic mouse models for lung basal epithelium-specific expression of DDR2 mutants and assay for tumor formation. We will also express DDR2 mutant mRNA in basal lung epithelium and test for oncogenic effects. These animal and cellular models will be used to assess the impact of disruption of DDR2 function both by genetic modification and by small molecule inhibitors. -Specific Aim 2. We will evaluate mechanisms of resistance to the DDR2 inhibitor, dasatinib, in squamous lung cancer models. To study c/s resistance to dasatinib, we will engineer and/or select for dasatinib resistance alleles in DDR2 and test their sensitivities to dasatinib and other kinase inhibitors. In addition, we will screen for trans resistance by ectopic expression of open reading frame libraries. -Specific Aim 3. Develop potent and selective inhibitors of DDR2 using biochemical and cellular assays, their effects. We will collaborate with Core A (Chemistry) and Core B (Structure) to optimize lead compounds identified by Core A as mutant-specific inhibitors of DDR2 with greater DDR2 kinase specificity relative to dasatinib. These optimized inhibitors will be tested in both lung SCC-derived cell lines and in the cellular and animal model systems developed in Aim 1, including models engineered to be resistant to dasatinib. Through these efforts, this project will advance the development of DDR2 inhibitors as potential treatments for squamous cell carcinomas of the lung.

Lung cancer is the leading cause of cancer death in the United States and world-wide, with over 85% of cases due to non-small cell lung cancer (NSCLC). The goal of our Program is to advance the pre-clinical science of NSCLC therapeutics. During the current funding period, our Program has advanced inhibitors of EGFR, promoting the pre-clinical development of osimertinib and related molecules, of TBK1, and of DDR2. In its next 5 years, our Program aims to develop compounds that will lead to more effective treatments for NSCLC and prevent or overcome resistance to existing and future targeted therapies. To accomplish these goals, the Program seeks to achieve the following overall aims via 3 inter-related and collaborative Projects and 4 intellectually driven Shared Resource Cores. --Overall Aim 1. Develop inhibitors and/or degraders focused on mutant EGFR, KRAS signaling effectors, and mechanisms of transcriptional adaptation in non-small cell lung cancer. --Overall Aim 2. Characterize these compounds and their targets pharmacologically using genetically defined cellular and animal models of lung cancer. --Overall Aim 3. Develop and assess combinations of these potent and selective novel agents with existing therapies to prevent and overcome therapeutic resistance. These aims leverage innovations in chemistry and structural biology?the development of allosteric kinase inhibitors and selective degraders?coupled with expertise in lung cancer biology, lung cancer cellular and animal modeling, and functional genomic approaches to understanding pathways, through the Projects and Cores. The broad aims will be implemented with three focused projects aimed at developing inhibitors of key pathways in NSCLC as well as over-arching mechanisms of resistance: --Project 1: Development of pharmacologic strategies to degrade mutant EGFR. --Project 2: Identification of combination therapy for KRAS-driven lung cancers. --Project 3: Targeting transcriptional mechanisms of therapeutic resistance in non-small cell lung cancer. Each Project and the overall Program is based on the innovative, technology-driven Cores, each led by faculty with expertise in the specific areas. Core A: Medicinal Chemistry. Core B: Structure and Biochemistry. Core C: Animal Modeling and Preclinical Therapeutics. Core D: Program Administration. The integration of the three Projects and the four Cores will enable an effective co-ordination to meet Program aims by cross-fertilization of lung cancer focus and technological expertise.

? DESCRIPTION (provided by applicant): Lung cancer accounts for more cancer-related deaths worldwide, per year, than the next three most prevalent cancers combined; sadly, more than 50% of patients die within a year of diagnosis. Our lab has made significant contributions to understanding the genomic underpinnings of non-small cell lung cancer, which accounts for ~85% of lung cancers. As one of the groups at the forefront of cancer genomics research, we and others have uncovered many major genome alterations in lung adenocarcinomas and squamous cell carcinomas, with profound clinical implications. These studies have resulted in the development of-and understanding of patient response to-molecularly targeted therapies, notably our demonstration that mutations within the EGFR gene dictate tumor response to the anti-EGFR drug, gefitinib. Although we can now offer patients many more therapeutic options than imaginable even a few years ago, disease progression inevitably ensues, underscoring the need for development of different and newer approaches to treating this scourge. The answer may lie in the numerous major, but still poorly understood, genomic aberrations that drive pathogenesis of these cancers. Some of the most perplexing genomic events in this regard relate to (i) the role of focal amplification of lineage-specific oncogenes, such as we discovered for NKX2-1 in lung adenocarcinomas and SOX2 in lung squamous cell carcinomas, (ii) the finding of somatic mutations in splicing factor genes, specifically U2AF1 and RBM10, in lung adenocarcinoma; and (iii) the observation of frequent large-scale chromosomal alterations such as gains or losses of chromosomal arms or even entire chromosomes, in these-and indeed most other-cancers. Having made these discoveries in lung adenocarcinomas and squamous cell carcinomas, we now intend to focus on delineating the mechanisms through which these complex and mysterious genomic aberrations promote oncogenesis. Here, we will take advantage of new, tractable genome engineering approaches to model each of these genomic events in both cell-based and mouse model systems. We will also employ a full spectrum of functional and systematic methodologies such as transcriptomic, proteomic, genetic screening and dependency analyses to uncover the biological relevance of such alterations. By addressing these challenging questions in lung cancer biology from all possible angles, we anticipate that we will gain a comprehensive understanding of how these mysterious genome alterations fuel pathogenesis of lung cancers, thereby informing novel therapeutic approaches.

The Program Administration Core will facilitate the overall goals of the Program by providing administrative and fiscal support as well as scientific oversight, to ensure that the activities of the Program are consistent with its ultimate goal i.e. the development of new targeted therapies for non-small cell lung cancer. This involves coordination of all Programmatic activities, in particular promoting collaboration, cross-talk and sharing of information and ideas between the various Projects and Cores. This includes the assessment and implementation of changes in research trajectory, as required, to ensure research progress and alignment of activities with the overall goals of the program. This will be accomplished via the following Specific Aims: Specific Aim 1: Monitor projects and shared resource cores and evaluate overall research progress. a) Coordinate regular meetings of a Program Executive Committee, including each of the Project Leaders and Core Directors, to monitor the progress of each Project and Shared Resource Core. b) Provide regular guidance to the Project Leaders and Core Directors, including critical evaluation of research progress and direction. c) Obtain advice from an Internal Advisory Committee of scientists within Dana-Farber Cancer Institute, and monitor the integration of the committee?s suggestions into the performance of the Projects and Cores. d) Hold meetings of an External Advisory Board of scientists with expertise in lung cancer targeted therapies. Specific Aim 2: Foster collaboration and communication among the projects and shared resource cores. a) Arrange bi-weekly group meetings of the Program to share research ideas, results, and methods. b) Monitor and encourage the interactions between projects and cores. Specific Aim 3: Provide fiscal oversight and support for the program. a) Assist with grants management and disbursement of funds. b) Analyze and adjust budgets to incorporate ongoing innovations and as the program evolves. Specific Aim 4: Promote the clinical translation of diagnostic and therapeutic discoveries from the program. a) Ensure that translatable discoveries are effectively communicated to the Dana-Farber/Harvard Cancer Center Lung Cancer Program. b) Organize a retreat to disseminate the research findings and prompt synergistic interactions. c) Assist in manuscript submission and subsequent publication.

The use of genomically targeted therapies has improved treatment response and clinical outcomes for molecularly defined subsets of patients with non-small cell lung cancers. While responses to these therapies can often be dramatic, they are rarely durable, and there is a significant need to improve the duration of response and delay or prevent treatment resistance. Studies from our group and others have characterized the properties of cancer cells which escape initial treatment with a targeted agent. Analyses of these data have revealed transcriptional and epigenetic adaptation as a requirement for the survival of cells that persist in the face of targeted therapy. Working with Core A (Chemistry) and Core B (Structure), we have obtained Preliminary Data suggesting that inhibitors of higher-order cyclin dependent kinases (CDKs), enzymes which perform key roles in transcriptional initiation and elongation, display potent synergy with targeted kinase inhibitors in a diverse array of NSCLC models both in vitro and in vivo. Specifically, we have identified THZ1, a covalent CDK7/12 inhibitor designed by Core A leader Dr. Gray, as a tool compound which synergizes with inhibitors of EGFR (Project 1), MEK (Project 2) as well as ALK, HER2, BRAF, FGFR and PI3K in genetically selected NSCLC models. In this project, we will advance our efforts in targeting transcriptional adaptation to targeted therapies by using genetic tools to define the key CDK/cyclin genes responsible for therapeutic synergy and using this information to design more selective CDK inhibitors and selective degraders with improved specificity and in vivo pharmacology as compared to THZ1. Further, we will use transcriptional and epigenetic analysis to define the mechanisms governing therapeutic synergy among targeted therapies and CDK inhibitors. This project will be amenable to clinical translation given the broad applicability of this approach and ongoing efforts to develop transcriptional CDK inhibitors for clinical use.

Project Summary The introduction of new targeted therapies and immunotherapies has led to significant decreases in lung cancer mortality in the United States in recent years. However, lung cancer continues to kill over 135,000 Americans each year, and over a million people annually world-wide. Thus, there remains an urgent need to continue to improve the prevention, diagnosis and treatment of this deadly disease. Our research focuses on lung adenocarcinoma, the most common form of lung cancer. Lung adenocarcinoma is, at its root, a disease of the genome. The focus of my laboratory is to understand somatic genome alterations in human lung cancer, to use this understanding to elucidate lung cancer pathogenesis, and in turn to improve diagnosis and treatment. We have been honored to participate in many clinically impactful genomic discoveries, including the discoveries of BRAF and EGFR mutations that guide targeted therapy use. In recent work, we continue to advance knowledge of lung cancer genomes and their function. We described novel oncogenic mutations in lung cancer, the duplication of super-enhancer elements near known oncogenes. We analyzed the cancer-causing activity of lung adenocarcinoma mutated genes such as SOS1 and MGA; we initiated genomic approaches to immunological targets such as the ADAR RNA deaminase gene; and we generated a genomically engineered model of aneuploidy for lung cancer. Our proposed research falls into three broad categories: 1. Single gene alterations: we will analyze the mechanisms by which both mutations and copy number alterations underlie the pathogenesis of lung adenocarcinoma. Examples described in this proposal include the tumor suppressor gene CMTR2 and the lineage oncogene NKX2-1, which is the most significantly amplified gene in lung adenocarcinoma. 2. Immunological target identification: we will use genomic approaches to characterize immunological features of lung cancer and potential vulnerabilities. Examples shown here include continued studies of genes involved in RNA sensing & modification in the interferon pathway that are also cancer dependencies, as well as large-scale functional genomic screens to identify epitopes that are antigenic targets of T cells in lung cancer. 3. Genome-wide features. We continue to study aneuploidy and the function of gene dosage effects on cell growth and proliferation. In addition, we are developing a new approach for genome-based therapy: nucleic acid cleavage therapies that target the ?neo-genome? in lung cancer DNA. This approach would exploit the novel genomic sequences that result from chromosomal rearrangements in cancer by using genome engineering tools to specifically target cancer cells. My goal is that the knowledge gained from the proposed research will deepen our understanding of human lung adenocarcinoma and will drive novel and effective treatments for lung cancer patients.