Search

PDF file - 84K

PDF file - 1MB

PDF file - 1MB

Purpose: Problems in management of oral cancers or precancers include identification of patients at risk for metastasis, tumor recurrence, and second primary tumors or risk for progression of precancers (dysplasia) to cancer. Thus, the objective of this study was to clarify the role of genomic aberrations in oral cancer progression and metastasis.Experimental Design: The spectrum of copy number alterations in oral dysplasia and squamous cell carcinomas (SCC) was determined by array comparative genomic hybridization. Associations with clinical characteristics were studied and results confirmed in an independent cohort.Results: The presence of one or more of the chromosomal aberrations +3q24-qter, -8pter-p23.1, +8q12-q24.2, and +20 distinguishes a major subgroup (70%–80% of lesions, termed 3q8pq20 subtype) from the remainder (20%–30% of lesions, non-3q8pq20). The 3q8pq20 subtype is associated with chromosomal instability and differential methylation in the most chromosomally unstable tumors. The two subtypes differ significantly in clinical outcome with risk for cervical (neck) lymph node metastasis almost exclusively associated with the 3q8pq20 subtype in two independent oral SCC cohorts.Conclusions: Two subtypes of oral lesions indicative of at least two pathways for oral cancer development were distinguished that differ in chromosomal instability and risk for metastasis, suggesting that +3q,–8p, +8q, and +20 constitute a biomarker with clinical utility for identifying patients at risk for metastasis. Moreover, although increased numbers of genomic alterations can be harbingers of progression to cancer, dysplastic lesions lacking copy number changes cannot be considered benign as they are potential precursors to non-3q8pq20 locally invasive, yet not metastatic oral SCC. Clin Cancer Res; 17(22); 7024–34. ©2011 AACR.

PDF file - 3.7MB

Summary Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery‐driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.

Purpose: To identify mechanisms and mediators of resistance to antiangiogenic therapy in human glioblastoma. Experimental Design: We carried out microarray gene expression analysis and immunohistochemistry comparing 21 recurrent glioblastomas progressing during antiangiogenic treatment with VEGF neutralizing antibody bevacizumab to paired pretreatment tumors from the same patients. Results: Microarray analysis revealed that bevacizumab-resistant glioblastomas (BRG) had two clustering patterns defining subtypes that reflect radiographic growth patterns. Enhancing BRGs (EBRG) exhibited MRI enhancement, a long-established criterion for glioblastoma progression, and expressed mitogen-activated protein kinases, neural cell adhesion molecule-1 (NCAM-1), and aquaporin 4. Compared with their paired pretreatment tumors, EBRGs had unchanged vascularity and hypoxia, with increased proliferation. Nonenhancing BRGs (NBRG) exhibited minimal MRI enhancement but had FLAIR-bright expansion, a newer criterion for glioblastoma recurrence since the advent of antiangiogenic therapy, and expressed integrin α5, laminin, fibronectin1, and PDGFRβ. NBRGs had less vascularity, more hypoxia, and unchanged proliferation than their paired pretreatment tumors. Primary NBRG cells exhibited more stellate morphology with a 3-fold increased shape factor and were nearly 4-fold more invasive in Matrigel chambers than primary cells from EBRGs or bevacizumab-naive glioblastomas (P < 0.05). Conclusion: Using microarray analysis, we found two resistance patterns during antiangiogenic therapy with distinct molecular profiles and radiographic growth patterns. These studies provide valuable biologic insight into the resistance that has limited antiangiogenic therapy to date. Clin Cancer Res; 18(10); 2930–42. ©2012 AACR.

The clinical, pathologic, and molecular features of pleomorphic lobular carcinoma in situ (PLCIS) and the relationship of PLCIS to classic LCIS (CLCIS) are poorly defined. In this study, we analyzed 31 cases of PLCIS (13 apocrine and 18 nonapocrine subtypes) and compared the clinical, pathologic, immunophenotypic, and genetic characteristics of these cases with those of 24 cases of CLCIS. Biomarker expression was examined using immunostaining for E-cadherin, gross cystic disease fluid protein-15, estrogen, progesterone, androgen receptor, human epidermal growth factor receptor2, CK5/6, and Ki67. Array-based comparative genomic hybridization to assess the genomic alterations was performed using microdissected formalin-fixed paraffin-embedded samples. Patients with PLCIS presented with mammographic abnormalities. Histologically, the tumor cells were dyshesive and showed pleomorphic nuclei, and there was often associated necrosis and microcalcifications. All lesions were E-cadherin negative. Compared with CLCIS, PLCIS showed significantly higher Ki67 index, lower estrogen receptor and progesterone receptor expression, and higher incidence of HER2 gene amplification. The majority of PLCIS and CLCIS demonstrated loss of 16q and gain of 1q. Apocrine PLCIS had significantly more genomic alterations than CLCIS and nonapocrine PLCIS. Although lack of E-cadherin expression and the 16q loss and 1q gain-array-based comparative genomic hybridization pattern support a relationship to CLCIS, PLCIS has clinical, mammographic, histologic, immunophenotypic, and genetic features that distinguish it from CLCIS. The histologic features, biomarker profile, and genomic instability observed in PLCIS suggest a more aggressive phenotype than CLCIS. However, clinical follow-up studies will be required to define the natural history and most appropriate management of these lesions.

Tumors vary widely in chromosomal level genome instability. To gain a better understanding of the underlying defects which foster specific types of aberrations, we investigated the response of cells of related genetic backgrounds to challenge with methotrexate. We studied mismatch repair deficient HCT116 cells, two derivatives also deficient in XRCC5 (HCT116 Ku86+/−) or BLM (HCT116 BLM−/−), and mismatch repair competent HCT116+chr3 cells. We show that colony formation occurred at a significantly higher frequency in HCT116 cells and HCT116 Ku86+/− cells compared to HCT116 BLM−/− and HCT116+chr3 cells. Visible colonies arose most rapidly in HCT116 Ku86+/− cells, whereas they formed most slowly in HCT116+chr3 cells. Copy number changes acquired by the methotrexate resistant HCT116 and HCT116 BLM−/− cells most often included whole chromosome gains or losses or no acquired copy number changes, whereas resistance in HCT116+chr3 and HCT116 Ku86+/− cells was associated with amplification of DHFR and copy number transitions leading to increased copy number of DHFR, respectively. The additional copies of DHFR were present on unstable chromosomes and organized as inverted repeats in HCT116+chr3 cells, while they were most often present as direct repeats in HCT116 Ku86+/− cells. These observations suggest that different mutational mechanisms promote drug resistance in these genetic backgrounds; mismatch repair deficiency in HCT116, high rates of chromosomal instability in HCT116 Ku86+/−, and low rates of chromosomal instability in HCT116+chr3. On the other hand, it appears that loss of BLM function suppresses the mismatch repair mutator mechanism in mismatch repair and BLM deficient HCT116 BLM−/− cells. © 2007 Wiley-Liss, Inc.

SummaryeIF4E, the major cap-binding protein, has long been considered limiting for translating the mammalian genome. However, the eIF4E dose requirement at an organismal level remains unexplored. By generating an Eif4e haploinsufficient mouse, we found that a 50% reduction in eIF4E expression, while compatible with normal development and global protein synthesis, significantly impeded cellular transformation. Genome-wide translational profiling uncovered a translational program induced by oncogenic transformation and revealed a critical role for the dose of eIF4E, specifically in translating a network of mRNAs enriched for a unique 5′ UTR signature. In particular, we demonstrate that the dose of eIF4E is essential for translating mRNAs that regulate reactive oxygen species, fueling transformation and cancer cell survival in vivo. Our findings indicate eIF4E is maintained at levels in excess for normal development that are hijacked by cancer cells to drive a translational program supporting tumorigenesis.

Natural evolutionary forces and selective inbreeding have given rise to many different mouse strains that exhibit specific characteristics and traits (Beck et al. 2000). The publication of the mouse genome sequence has accelerated investigation of genomic variation among different types of mice. Indeed, genome-wide single-nucleotide polymorphism (SNP) comparison studies across different inbred strains of mice have not only elucidated haplotype structure (Wade et al. 2002; Wiltshire et al. 2003), but have also provided markers for mapping phenotypic differences between strains. Sequence analysis has also identified segmental duplications in genomes, which are defined as stretches of DNA sequence ≥1-5 kb in length with ≥90% sequence conservation that are present in more than one location in the genome. They make up ∼5% of the human genome (Bailey et al. 2002) and lesser proportions of rodent genomes, 2.92% in the rat (Tuzun et al. 2004) and 1%-1.2% in the mouse (Cheung et al. 2003). These studies have found that both intrachromosomal and interchromosomal or transchromosomal segmental duplications are mosaics of sequences duplicated from within one chromosome or nonhomologous chromosomes, respectively. Transchromosomal duplications are predominantly located in regions close to the centromere and/or telomere and contain few functional genes, whereas intrachromosomal segmental duplications harbor functional genes and gene families and are predominantly found in euchromatic regions (Eichler et al. 1996; Jackson et al. 1999; Horvath et al. 2001; Cheung et al. 2003; Tuzun et al. 2004). Since both types appear to be recent evolutionary events (Cheung et al. 2001), they are likely to contribute to the generation of phenotypic diversity among laboratory mice. In the course of application of BAC array comparative genomic hybridization (array CGH) to characterize tumors in mouse models, we noticed large strain-specific ratio variations for many BACs, indicating probable germ-line copy number variations. Since these relative increases and decreases in copy number at particular loci could underlie certain strain specific phenotypes, we undertook a systematic study to detect and map variant loci among laboratory mouse genomes. This approach provides complementary information to genome sequencing, because large-scale copy number differences are not easily identified by sequence analysis (Locke et al. 2003), and it allows investigation of mouse genomes that have not been scheduled for whole-genome sequencing. Here, we report on the substantial copy number variation we found among mouse strains. Careful analysis of the results of our interstrain comparisons indicated that the BAC arrays also provided the ability to detect small ratio variations that presumably reflect nucleotide level variation among the strains. We show that this capability can be used to distinguish chromosomal regions of heterozygosity and homozygosity in interspecific backcross mice. These regions differ by log2ratio ∼ 0.1. Given the high density of genome coverage possible on BAC arrays and the rate at which hybridizations can be performed, this novel application of array CGH provides a highly efficient means to genotype progeny of interspecific backcross mice.

DNA microarrays are now widely used to measure expression levels and DNA copy number in biological samples. Ratios of relative abundance of nucleic acids are derived from images of regular arrays of spots containing target genetic material to which fluorescently labeled samples are hybridized. Whereas there are a number of methods in use for the quantification of images, many of the software systems in wide use either encourage or require extensive human interaction at the level of individual spots on arrays. We present a fully automatic system for microarray image quantification. The system automatically locates both subarray grids and individual spots, requiring no user identification of any image coordinates. Ratios are computed based on explicit segmentation of each spot. On a typical image of 6000 spots, the entire process takes less than 20 sec. We present a quantitative assessment of performance on multiple replicates of genome-wide array-based comparative genomic hybridization experiments. By explicitly identifying the pixels in each spot, the system yields more accurate estimates of ratios than systems assuming spot circularity. The software, called UCSF Spot, runs on Windows platforms and is available free of charge for academic use.

Purpose: To identify mediators of glioblastoma antiangiogenic therapy resistance and target these mediators in xenografts. Experimental Design: We conducted microarray analysis comparing bevacizumab-resistant glioblastomas (BRG) with pretreatment tumors from the same patients. We established novel xenograft models of antiangiogenic therapy resistance to target candidate resistance mediator(s). Results: BRG microarray analysis revealed upregulation versus pretreatment of receptor tyrosine kinase c-Met, which underwent further investigation because of its prior biologic plausibility as a bevacizumab resistance mediator. BRGs exhibited increased hypoxia versus pretreatment in a manner correlating with their c-Met upregulation, increased c-Met phosphorylation, and increased phosphorylation of c-Met–activated focal adhesion kinase and STAT3. We developed 2 novel xenograft models of antiangiogenic therapy resistance. In the first model, serial bevacizumab treatment of an initially responsive xenograft generated a xenograft with acquired bevacizumab resistance, which exhibited upregulated c-Met expression versus pretreatment. In the second model, a BRG-derived xenograft maintained refractoriness to the MRI tumor vasculature alterations and survival-promoting effects of bevacizumab. Growth of this BRG-derived xenograft was inhibited by a c-Met inhibitor. Transducing these xenograft cells with c-Met short hairpin RNA inhibited their invasion and survival in hypoxia, disrupted their mesenchymal morphology, and converted them from bevacizumab-resistant to bevacizumab-responsive. Engineering bevacizumab-responsive cells to express constitutively active c-Met caused these cells to form bevacizumab-resistant xenografts. Conclusion: These findings support the role of c-Met in survival in hypoxia and invasion, features associated with antiangiogenic therapy resistance, and growth and therapeutic resistance of xenografts resistant to antiangiogenic therapy. Therapeutically targeting c-Met could prevent or overcome antiangiogenic therapy resistance. Clin Cancer Res; 19(7); 1773–83. ©2012 AACR.

Purpose: Problems in management of oral cancers or precancers include identification of patients at risk for metastasis, tumor recurrence, and second primary tumors or risk for progression of precancers (dysplasia) to cancer. Thus, the objective of this study was to clarify the role of genomic aberrations in oral cancer progression and metastasis. Experimental Design: The spectrum of copy number alterations in oral dysplasia and squamous cell carcinomas (SCC) was determined by array comparative genomic hybridization. Associations with clinical characteristics were studied and results confirmed in an independent cohort. Results: The presence of one or more of the chromosomal aberrations +3q24-qter, -8pter-p23.1, +8q12-q24.2, and +20 distinguishes a major subgroup (70%–80% of lesions, termed 3q8pq20 subtype) from the remainder (20%–30% of lesions, non-3q8pq20). The 3q8pq20 subtype is associated with chromosomal instability and differential methylation in the most chromosomally unstable tumors. The two subtypes differ significantly in clinical outcome with risk for cervical (neck) lymph node metastasis almost exclusively associated with the 3q8pq20 subtype in two independent oral SCC cohorts. Conclusions: Two subtypes of oral lesions indicative of at least two pathways for oral cancer development were distinguished that differ in chromosomal instability and risk for metastasis, suggesting that +3q,–8p, +8q, and +20 constitute a biomarker with clinical utility for identifying patients at risk for metastasis. Moreover, although increased numbers of genomic alterations can be harbingers of progression to cancer, dysplastic lesions lacking copy number changes cannot be considered benign as they are potential precursors to non-3q8pq20 locally invasive, yet not metastatic oral SCC. Clin Cancer Res; 17(22); 7024–34. ©2011 AACR.

The EGAN software is a functional implementation of a simple yet powerful paradigm for exploration of large empirical data sets downstream from computational analysis. By focusing on systems-level analysis via enrichment statistics, EGAN enables a human domain expert to transform high-throughput analysis results into hypergraph visualizations: concept maps that leverage the expert's semantic understanding of metadata and relationships to produce insight.

Constitutional submicroscopic DNA copy number alterations have been shown to cause numerous medical genetic syndromes, and are suspected to occur in a portion of cases for which the causal events remain undiscovered. Array comparative genomic hybridization (array CGH) allows high-throughput, high-resolution genome scanning for DNA dosage aberrations and thus offers an attractive approach for both clinical diagnosis and discovery efforts. Here we assess this capability by applying array CGH to the analysis of copy number alterations in 44 patients with a phenotype of the 22q11.2 deletion syndrome. Twenty-five patients had the deletion on chromosome 22 characteristic of this syndrome as determined by fluorescence in situ hybridization (FISH). The array measurements were in complete concordance with the FISH analysis, supporting their diagnostic utility. These data show that a genome-scanning microarray has the level of sensitivity and specificity required to prospectively interrogate and identify single copy number aberrations in a clinical setting. We demonstrate that such technology is ideally suited for microdeletion syndromes such as 22q11.2. © 2007 Wiley-Liss, Inc.

Background Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability phenotypes when mutated (e.g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes. Methods We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability. Results We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability. Conclusion Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome.

Purpose: Although liver resection is the primary curative therapy for patients with colorectal hepatic metastases, most patients have a recurrence. Identification of molecular markers that predict patients at highest risk for recurrence may help to target further therapy. Experimental Design: Array-based comparative genomic hybridization was used to investigate the association of DNA copy number alterations with outcome in patients with colorectal liver metastasis resected with curative intent. DNA from 50 liver metastases was labeled and hybridized onto an array consisting of 2,463 bacterial artificial chromosome clones covering the entire genome. The total fraction of genome altered (FGA) in the metastases and the patient's clinical risk score (CRS) were calculated to identify independent prognostic factors for survival. Results: An average of 30 ± 14% of the genome was altered in the liver metastases (14% gained and 16% lost). As expected, a lower CRS was an independent predictor of overall survival (P = 0.03). In addition, a high FGA also was an independent predictor of survival (P = 0.01). The median survival time in patients with a low CRS (score 0-2) and a high (≥20%) FGA was 38 months compared with 18 months in patients with a low CRS and a low FGA. Supervised analyses, using Prediction Analysis of Microarrays and Significance Analysis of Microarrays, identified a set of clones, predominantly located on chromosomes 7 and 20, which best predicted survival. Conclusions: Both FGA and CRS are independent predictors of survival in patients with resected hepatic colorectal cancer metastases. The greater the FGA, the more likely the patient is to survive.

Array comparative genomic hybridization (cgh) is a microarray technology for measuring the relative copy number of thousands of genomic regions. Visual examination of cgh profiles shows that genomic changes occur on a variety of length scales. Such changes may be characteristic of phenotypic variables such as tumor type and gene mutational status. To aid in identifying such features and exploring their relationship with phenotypic outcomes, we are applying wavelet transforms to the analysis of such profiles. This allows us to decompose a cgh signal into components on different length scales, even when the genome is severely aberrated, providing a convenient basis for exploring their behavior. Wavelet transforms may also be useful in the realm of gene expression. The expression signal given by genes in clustered order can be wavelet transformed, which compresses the signal from many genes into a few components, possibly aiding in the development of new tumor classifiers.

Summary: Exploratory Gene Association Networks (EGAN) is a Java desktop application that provides a point-and-click environment for contextual graph visualization of high-throughput assay results. By loading the entire network of genes, pathways, interactions, annotation terms and literature references directly into memory, EGAN allows a biologist to repeatedly query and interpret multiple experimental results without incurring additional delays for data download/integration. Other compelling features of EGAN include: support for diverse -omics technologies, a simple and interactive graph display, sortable/searchable data tables, links to external web resources including ≥240 000 articles at PubMed, hypergeometric and GSEA-like enrichment statistics, pipeline-compatible automation via scripting and the ability to completely customize and/or supplement the network with new/proprietary data. Availability: Runs on most operating systems via Java; downloadable from http://akt.ucsf.edu/EGAN/ Contact: jesse.paquette@cc.ucsf.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract 3526 Background: Acute Promyelocytic Leukemia (APL) is characterized by the accumulation in the blood and bone marrow of abnormal promyelocytes, which have the ability to transfer the disease to secondary recipients in animal models. The PML-RARα fusion protein is thought to be the primary abnormality implicated in the pathology, and is believed to prevent transcription of genes necessary for normal myeloid development and differentiation. Identifying PML-RARα targets is critical for understanding the road to leukemic transformation. However, such targets have so far been identified using cell line assays in vitro, murine cells differentiated into promyelocytes in vitro, or fully transformed murine or human leukemic cells. Focusing on the cell population in which the transforming potential is acquired, we describe here a novel strategy to identify the transcriptomic dysregulation induced by PML-RARα expression in maturing myeloid populations in vivo. Methods: We utilize a murine model of human APL in which the human PML-RARα fusion gene is expressed under the control of the MRP8 promoter, driving its expression in maturing myeloid populations. Those animals can be described as pre-leukemic since they eventually develop leukemia when additional mutations occur. Fresh bone marrows from normal (Fvb/n) or pre-leukemic (PML-RARα) animals were harvested. Using an improved cell surface antigen staining strategy and fluorescence-activated cell sorting, three populations of increasingly differentiated myeloid populations have been sorted (Granulocyte Macrophage Progenitor, Early promyelocyte and Late promyelocyte). RNA was extracted and submitted for whole-genome microarray analysis. In addition, we are using a variety of bioinformatics approaches to decipher the network of novel interactions driven by PML-RARα expression. Results: Markers used in our sorting strategy were validated in the dataset, including CD34 and Gr1. In the normal samples, markers of neutrophil maturation increased, largely as expected, and a number of early transcription factors decreased in an expected manner including Hoxa9 and Meis1. One remarkable finding was that despite the previously described ability of PML-RARα to regulate transcription from multiple sites in the genome, only a small number of genes were differentially impacted by the expression of this protein. Surprisingly, well-known regulators of myeloid differentiation that have been implicated in the retinoic acid responsiveness of APL including Sfpi1 (PU.1) and Cebpa were not differentially expressed. However, in pre-leukemic samples PML-RARα did cause decreased expression of multiple neutrophilic granule genes including Ltf, Mmp9 and Ngp. The gene most upregulated in the pre-leukemic samples was Spp1 which encodes the osteopontin phosphoprotein. Of interest, we identified the myeloid tumor suppressor Irf8 to be downregulated 5 fold in the presence of PML-RARα. To investigate the importance of IRF8 levels in APL initiation, we transplanted Irf8+/+ PML-RARα or Irf8+/− PML-RARα bone marrow into irradiated recipients. Despite the potential for decreased expression of IRF8 to contribute to APL, we observed no difference. This result does not confirm a role for IRF8 in APL pathogenesis, but further investigations are needed to exclude such a role. Bioinformatics studies highlighted enrichment in cell cycle-related genes upon PML-RARα expression, suggesting a possible difference in the proliferation capacity of the pre-leukemic cells, which is currently under investigation. Conclusions: We found that in vivo the transcriptome was only modestly dysregulated by the presence of PML-RARα. These observations open up new questions on the role of the fusion protein in pathogenesis: How does PML-RARα prime pre-leukemic cells for full transformation? How do secondary events allow an initiated cell to advance to a fully transformed state? Such questions are currently being investigated, with a special interest on looking at the cooperation between PML-RARα and activated cytokine signaling in leukemia initiation. Disclosures: No relevant conflicts of interest to declare.

The biologic behavior of oral dysplasia (precancers) and squamous cell carcinoma (SCC) is unpredictable, the main problems in management being identification of patients at risk for metastasis or risk of progression of dysplasias to cancer. Neck metastasis, the most significant clinical factor causing death in oral SCC, reduces survival by 50%. We utilized array comparative genomic hybridization (CGH) to clarify the role of genomic aberrations in oral cancer progression and metastasis. Two oral SCC cohorts: cohort#1, n=89 (Snijders et al, 2005)) and cohort#2, n=63 (with associated pathologic nodal status and 5 year clinical follow up) were profiled using BAC CGH arrays. Two dysplasia cohorts, one with no association to cancer (cohort D1, n=29) and one associated with previous or subsequent cancer (cohort D2, n=10) were also profiled for recurrent copy number aberrations using array CGH. Associations with clinical characteristics were studied and results confirmed in an independent SCC cohort (cohort#3, n=14, Smeets et al., 2009). All samples used in this study were restricted to oral cavity sites only and were archival formalin fixed paraffin embedded tissue. Copy number alterations distinguished two oral dysplasia and cancer subtypes. The presence of one or more of the chromosomal aberrations +3q24-qter, -8pter-p23.1, +8q12-q24.2, and +20 distinguished a major subgroup (70%-80% of lesions, termed 3q8pq20 subtype) from the remainder (20%-30% of lesions, non-3q8pq20). Most notably, 3q8pq20 and non-3q8pq20 subtypes differed significantly in clinical outcome with risk for cervical (neck) lymph node metastasis almost exclusively associated with the 3q8pq20 subtype in two independent oral SCC cohorts (cohort#2 and cohort#3). As metastasis to the cervical lymph nodes is a major determinant of survival in oral SCC patients, our findings indicate that chromosomal aberrations +3p, -8p, +8q and +20 provide a potential biomarker to identify patients at no or low risk of metastasis. The negative predictive value (NPV) i.e. the ability to predict N0 cases at biopsy was 93% for cohort#2 and 100% in cohort#3. Currently, almost all patients diagnosed with oral SCC are treated with comprehensive neck dissection at the time of tumor resection, as salvage of patients who subsequently develop neck metastasis is poor. We propose that the +3q, -8p, +8q and +20 signature is suitable for stratifying patients for risk of metastasis prior to surgery, and so can guide surgical treatment for one of the most challenging treatment decisions - how to treat patients with clinically node-negative (N0) necks. Identification of patients with low risk for metastasis would spare them additional major surgery with its risks and morbidity, as well as reduce medical costs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5079. doi:1538-7445.AM2012-5079

A numerical renormalization group technique based on Wilson's momentum shell method is presented for interacting, finite fermi systems. Results for small fullerene analogs show that the method is quite accurate to moderate values of $U$, and qualitatively better than other approximation methods. The method has potential applicability far beyond the fullerenes., Comment: 11 pages, 4 figures upon request, REVTeX

The 5-year survival rate for oral squamous cell carcinoma (SCC) patients at 40% has not improved over the past 40 years. Since genomes of 75-80% of oral SCCs are characterized by regions of gains and losses, we investigated whether copy number aberrations could be used to address two important problems in oral cancer management - identification of (a) tumors with metastatic potential and (b) dysplastic lesions at risk for progression to cancer. Neck metastasis, the most significant clinical factor responsible for death from oral cancer reduces survival by 50%. To determine if copy number aberrations would distinguish tumors with metastatic potential, we carried out array comparative genomic hybridization (CGH) on 26 N0 and 38 N+ cases with at least 5-year follow up (diagnosed between 1997 and 2005). In order to reduce the multiple testing correction, regions of recurrent aberration were identified in an independent set of 89 oral SCCs (Snijders et al. 2005). A comparison of the frequency of aberrations affecting these regions in the N0 and N+ cases revealed no significant differences between the N0 and N+ cases after correction for multiple testing. We used a similar approach to determine if there are significant copy number differences between oral dysplasia and oral SCC. Most oral SCCs are preceded by precancerous lesions, characterized by varying degrees of dysplasia (graded from mild to severe). Transformation to oral SCC is associated with 16% of mild and 55% of moderate/severe dysplasia. Copy number profiles for 44 dysplasia samples comprised of approximately equal numbers of cases graded mild, moderate or severe were obtained by array CGH. Although fewer copy number changes were observed in dysplasia compared to SCC, gains of 3q, 8q and/or chromosome 20 were present at approximately equal frequencies in dysplasia and SCC. In addition, the rare narrow amplicons, characteristic of oral SCC (Snijders et al. 2005), were present in dysplasia. To identify copy number alterations distinguishing dysplasia and SCC, regions of recurrent aberration were defined in an independent set of oral SCCs (the 64 cases from the metastasis study described above). The frequency of these copy number alterations was compared between the dysplasia and the 89 SCC cases (Snijders et al. 2005). Gain of 7p, including EGFR in SCC was found to be significant after correction for multiple testing. This observation is consistent with previous reports of increased expression of EGFR with progression of dysplasia to cancer (Garnis et al., 1998). Since 20-25% of oral SCC harbor almost no copy number changes, suggesting that dysplasia lacking copy number changes may have potential to progress to SCC with chromosomally stable genomes, we suggest that measurement of EGFR expression and/or other genes on 7p may provide a more effective biomarker for dysplasia progression than 7p copy number. 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 2137.

Advances on several fronts have led to increases in survival duration and to reduced mortality in patients with breast cancer. These include improved procedures for earlier detection, optimization of combined surgical and radiotherapy, and use of optimized selective estrogen receptor modifiers (SERMS) and new chemotherapeutic strategies including gene-targeted therapies. In addition, molecular stratification strategies have been developed that stratify patients according to outcome. Stratification based on measurement of expression 'signatures' have been particularly effective and seem likely to improve treatment strategies. Patients at increased risk of progressive disease can be offered standard of care chemotherapy. However, some of these patients do not respond well to these treatments and current stratification strategies provide little information to guide treatment of these patients. This study of tumors from patients treated according to standard of care identifies genomic and coordinated transcriptional aberrations – especially amplification at 11q, and 20q in tumors with the luminal A expression phenotype, and at 17q in tumors associated with the ERBB2 expression phenotype – that are strongly associated with poor response to such treatment. Our study identifies genes in these regions of amplification that can be assessed to identify patients that will respond poorly to the current standard of care and that are targets for therapies that will be effective against these poorly responding tumors. Interesting, this study also shows that patients with basal-like tumors do not have substantially shorter survival durations than patients with luminal-like tumors, suggesting that basal-like tumors respond well to the adjuvant adriamycin and cyclophosphamide therapies employed during their treatment.

SummaryThis study explores the roles of genome copy number abnormalities (CNAs) in breast cancer pathophysiology by identifying associations between recurrent CNAs, gene expression, and clinical outcome in a set of aggressively treated early-stage breast tumors. It shows that the recurrent CNAs differ between tumor subtypes defined by expression pattern and that stratification of patients according to outcome can be improved by measuring both expression and copy number, especially high-level amplification. Sixty-six genes deregulated by the high-level amplifications are potential therapeutic targets. Nine of these (FGFR1, IKBKB, ERBB2, PROCC, ADAM9, FNTA, ACACA, PNMT, and NR1D1) are considered druggable. Low-level CNAs appear to contribute to cancer progression by altering RNA and cellular metabolism.

Genomic analyses of human cells expressing dihydrofolate reductase provide insight into the effects of genome position on the propensity for a drug-resistance gene to amplify in human cells., Background Amplifications, regions of focal high-level copy number change, lead to overexpression of oncogenes or drug resistance genes in tumors. Their presence is often associated with poor prognosis; however, the use of amplification as a mechanism for overexpression of a particular gene in tumors varies. To investigate the influence of genome position on propensity to amplify, we integrated a mutant form of the gene encoding dihydrofolate reductase into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells. Results We observed site-specific differences in methotrexate sensitivity, amplicon organization and amplification frequency. One site was uniquely associated with a significantly enhanced propensity to amplify and recurrent amplicon boundaries, possibly implicating a rare folate-sensitive fragile site in initiating amplification. Hierarchical clustering of gene expression patterns and subsequent gene enrichment analysis revealed two clusters differing significantly in expression of MYC target genes independent of integration site. Conclusion These studies suggest that genome context together with the particular challenges to genome stability experienced during the progression to cancer contribute to the propensity to amplify a specific oncogene or drug resistance gene, whereas the overall functional response to drug (or other) challenge may be independent of the genomic location of an oncogene.