Victor Velculescu - US grants

[unreadable] DESCRIPTION (provided by applicant): It is now generally accepted that cancer is a genetic disease, mediated in large part by somatic mutations in specific genes. However, many of the key tumor suppressor genes and oncogenes responsible for cancer initiation and progression remain to be identified. Although technical hurdles have limited our ability to identify such genes in a comprehensive fashion, the delineation of the sequence of the human genome, coupled with recent advances DMA analysis technologies, have created an unprecedented opportunity for progress in this area. Over the past several years we have developed high throughput technologies for sequencing and mutational analyses to rapidly analyze gene families in human cancer. We have specifically focused on gene families involved in signal transduction, as these have been implicated in tumorigenesis and may be amenable to therapeutic intervention. These approaches have recently permitted the mutational analysis of all members of the PI-3 kinase, tyrosine kinase, tyrosine phosphatase, and serine/threonine kinase gene families. These genetic analyses have identified a high frequency of somatic mutations in PIK3CA as well as mutations in several kinases and phosphatases not previously implicated in human cancers. The purpose of this proposal is to use our cancer sequencing technologies to perform large-scale genetic analyses of gene families involved in signal transduction in human cancer. These families will include the serine/threonine protein phosphatase family, the lipid phosphatase gene family, the G protein-coupled receptor gene family, the heterotrimeric G protein gene family, the GTPase gene superfamily, and the G protein modulator gene family. Initially, the genes comprising these families will be analyzed for somatic alterations in colorectal cancers. Subsequently, selected genes will be further analyzed in lung, breast, gastric, brain, pancreatic and ovarian cancers to determine whether mutations in these genes provide common mechanisms of tumorigenesis shared by different cancer types. Finally, we will examine the mutation spectrum observed in the different tumors in order to determine if the mutated genes may have equivalent tumorigenic effects and are involved in specific signaling pathways. We envision that analyses of these gene families will allow us to identify genes not previously implicated in human cancer and provide insights into signaling pathways involved in tumor progression. The studies described in this application should lead to a greater understanding of cancer etiology, improved tools for cancer detection and diagnosis, new targets for therapeutic and preventative intervention, and opportunities for individualized treatment. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): For this ARRA RFA-OD-09-004 GO application, we propose to perform an integrated genome-wide mutational analysis of oral cancers using high throughput sequence analysis of coding genes combined with analyses of copy number, gene expression, and methylation. Genetic alterations represent the underlying cause of human cancer, including tumors of the oral cavity. In the United States, oral cancers represent ~50% of the 46,000 cases of head and neck cancers. Oral cancer affects physical appearance and vital functions, including taste, swallowing, and speech/phonation. In addition to significant morbidity, head and neck cancer result in ~12,000 deaths, of which oral cancer will be responsible for ~5,400 deaths. Given the significant morbidity and mortality of these tumors, there is a profound need for novel clinical approaches for oral cancer. This project will identify potential new avenues for therapeutic, diagnostic and prognostic intervention in oral cancer, and will serve as a model for genomic analyses of other head and neck cancers. For mutational screening, we will employ the two stage, high throughput DNA sequencing approach that we have recently refined and used to identify novel tumor-relevant mutations in breast, colon, pancreatic, and glioblastoma tumors. This strategy significantly increases the power and reduces the cost of large scale tumor sequencing, providing highly sensitive mutational analysis of >95% of bases of ~200,000 exons from over 20,000 coding genes. In the first stage of this approach, exon sequencing analysis will be performed on a set of 24 clinically annotated oral cancer samples. All mutations will be examined in a normal DNA sample from the same patient to identify and confirm tumor-specific mutations. In the second stage, the mutated genes will be analyzed by sequencing a larger set of at least 48 tumors. Previously developed biostatistical criteria will be applied to discriminate between tumor-relevant driver and irrelevant passenger mutations. In the same set of oral cancer samples examined for mutations, we will also perform copy number analysis using high density SNP microarrays, gene expression analysis by combination of next generation sequencing and serial analysis of gene expression (SAGE), and gene methylation analysis by Infinium methylation microarrays. Bioinformatics analyses will integrate these findings with mutational data, following a signaling pathways perspective that has proved to be powerful in our recent studies. Our hypothesis, based on experience in other tumor types, is that copy number changes and expression loss by promoter methylation, acting in concert with mutations, will be enriched in pathways that are important for development of oral cancer. As has been the case in other cancer types, identification of these altered signaling pathways is likely to provide potential therapeutic strategies for oral cancer. This grant is expected to have a significant economic effect, resulting in the employment of individuals performing genomic research on oral cancer and in subsequent studies of head and neck cancers in general. PUBLIC HEALTH RELEVANCE: We propose to perform an integrated genome-wide mutational analysis of oral cancers using high throughput sequence analysis of coding genes combined with analyses of copy number, gene expression, and methylation.

DESCRIPTION (provided by applicant): Human cancers are caused by the accumulation of mutations in specific genes. Technological developments have recently made it possible to analyze genetic alterations in human cancer at unprecedented scale. However, many of the key tumor suppressor genes and oncogenes responsible for cancer initiation and progression remain to be identified. During the previous project period, our group was the first to determine the sequence of the protein coding genes in any human cancer and we have completed this analysis in several tumor types. Through this work, we were able to identify candidate genes which had not been previously linked to tumorigenesis, define the basic genetic landscape of common human tumors, and point to pathways that underlie the complex genetic alterations in individual tumor types. These have included IDH genes in gliomas, PI3K pathway genes in colorectal and breast cancers, ARID1A in ovarian clear cell carcinoma, chromatin remodeling genes in medulloblastoma, and NOTCH1 in head and neck cancers. We have also used whole-genome sequencing approaches to analyze chromosomal rearrangements, copy number changes, and sequence alterations in the pediatric tumor neuroblastoma and identified rearrangements and sequence changes in the chromatin remodeling genes ARID1A and ARID1B in this tumor type. The purpose of this competitive renewal application is to use whole-genome cancer sequencing approaches to perform large-scale analyses of structural and sequence alterations in a variety of human cancers. These will include colorectal, breast, pancreatic, ovarian, brain, and head and neck tumors. Twenty four tumors of each type will be analyzed for rearrangements including those resulting from translocations, inversions, deletions, duplications and amplifications. In parallel, we will perform high resolution analyses of copy number alterations using a modification of an approach we have previously termed Digital Karyotyping. These analyses will be integrated with the sequence alterations of the protein coding genes we have already obtained in these tumor samples, thereby leveraging valuable information from the previous project period. These data will be analyzed to identify the compendium of genes and pathways enriched for genetic alterations in these tumors. Finally, we will use our recently developed personalized analysis of rearranged ends (PARE) approach to evaluate the use of tumor-specific rearrangements as personalized biomarkers for detection and monitoring of human cancers. We envision that whole-genome analyses of structural alterations in human tumors will allow us to identify genes not known to be involved in human cancer, provide insights into pathways involved in tumor initiation and progression, and allow direct translation of patient-specific genomic alterations for diagnostic analyses. The studies described in this application should lead to a greater understanding of cancer etiology, improved tools for cancer detection and diagnosis, new targets for therapeutic and preventative intervention, and opportunities for individualized detection, monitoring and treatment. PUBLIC HEALTH RELEVANCE: The research project in this application is focused on identifying changes in the genomes of human cancers, namely rearrangements, copy number changes and sequence alterations. The proposed studies are likely to lead to a greater understanding of cancer etiology, improved tools for cancer detection and monitoring, new targets for therapeutic and preventative intervention, and opportunities for individualized diagnosis and treatment.