1996 — 2000 |
Futscher, Bernard W |
R29Activity Code Description: Undocumented code - click on the grant title for more information. |
Genomic Methylation--a Mechanism to Alter Phenotypes |
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2001 — 2005 |
Futscher, Bernard W |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Genomic Methylation--Mechanism to Alter Tumor Phenotypes
The long-term objective of this study is to determine the molecular mechanisms of maspin gene silencing in human breast cancer and to use this information to identify strategies to reactivate its expression. Maspin is a tumor suppressor whose expression is frequently lost via transcriptional down-regulation in human breast cancers. Forced re- expression of maspin in maspin-negative breast cancer cells inhibits the growth, motility, neovascularization, and metastatic potential of breast cancer cells in mouse xenografts. Our preliminary results show that the loss of maspin expression is associated with aberrant methylation.of the maspin 5' regulatory region in human breast cancer cell lines as well as clinical breast cancer specimens. In addition, we show that it is possible to pharmacologically reactivate maspin gene expression using the demethylating agent 5-aza-2' deoxycytidine, the histone deacetylase inhibitor Trichostatin A, as well as through increased levels of Mn2+ Superoxide Dismutase (MnSOD). Based on the data described above, 3 specific aims are designed to achieve the stated long-term objective and test the hypothesis that therapeutic strategies designed to reactivate maspin expression will inhibit tumor growth and have a beneficial impact on the treatment of breast cancer. Aim #1 Determine if deacetylation of core histones in the maspin promoter is associated with 5-methylcytosine-linked chromatin condensation and transcriptional repression of the maspin gene. This will be accomplished using chromatin immunoprecipitations assays. Aim #2 Determine if the condensed chromatin structure of the maspin promoter blocks the access of transcription factors to their recognition sequence. Chromatin immunoprecipitations will be used to determine transcription factor binding in cells that contain both an unmethylated active maspin promoter and a methylated inactive maspin promoter. Aim #3 Identify and optimize pharmacological strategies for reactivation of maspin gene expression in aberrantly-methylated maspin-negative breast cancer cells. Agents that can reactivate maspin expression by distinct mechanisms of action will analyzed for their ability to maximize maspin gene reactivation in combination regimens.
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2002 — 2005 |
Futscher, Bernard W |
R21Activity Code Description: To encourage the development of new research activities in categorical program areas. (Support generally is restricted in level of support and in time.) R33Activity Code Description: The R33 award is to provide a second phase for the support for innovative exploratory and development research activities initiated under the R21 mechanism. Although only R21 awardees are generally eligible to apply for R33 support, specific program initiatives may establish eligibility criteria under which applications could be accepted from applicants demonstrating progress equivalent to that expected under R33. |
Microarray Technology to Profile Cpg Island Methylation
DESCRIPTION (provided by applicant): The long-term objective of this research project is to adapt microarray-based technology to measure CpG island methylation in human cancer cells. CpG islands are approximately 1kb stretches of DNA that have a high CG content, are enriched in the dinucleotide 5'-CG -3', are found at the 5' end of about 50% of all human genes, and participate in the transcriptional regulation of these genes. The cytosines in the CpG dinucleotides of CpG islands are unmethylated in normal tissue; however, CpG islands become aberrantly methylated during oncogenesis and has been linked to the transcriptional repression of the associated gene. In addition, from the limited number of CpG islands and tumors that have been analyzed to date, it appears that patterns of aberrant methylation occur in a tumor-specific and stage-specific fashion, suggesting that CpG island methylation profiles may be useful as a tumor- specific fingerprint to monitor disease activity and burden. Thus, a multiplexed assay where the cytosine methylation status of thousands of CpG islands can be determined simultaneously would be useful in the molecular profiling of human tumors, and will likely provide insights into the biology of cancer. To this end we have formed a multidisciplinary team to use human CpG island microarrays (CGI arrays) as a tool for determining CpG island methylation profiles in cancer, and from these profiles identify characteristic patterns of CpG island methylation that correlate with the tumor's clinical phenotype. The 4 integrated specific aims that follow are designed to reach our objective. 1) Construct CpG island microarrays for use in CpG island methylation analysis. 2) Optimize methylation analysis using CpG island microarrays 3) Determine CpG island methylation signatures in AML cell lines and in AML samples obtained from patients with known clinical outcome. 4) Develop and implement a public database for the dissemination and mining of the CGI array data
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2005 — 2009 |
Futscher, Bernard W |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Genomic Methylation: a Mechanism to Alter Tumor Phenotype
DESCRIPTION (provided by applicant): The long term objective of this research application is to examine the epigenetic mechanisms that participate in human cancer, and to determine how distinct genetic mutations cooperate and/or influence epigenetic control. Cytosine methylation of CpG dinucleotides in gene regulatory regions is an important epigenetic mechanism involved in gene silencing, whereas, mutations in critical transcription factors, such as p53, is an example of a genetic mechanism involved in silencing target genes. We provide evidence that aberrant cytosine methylation and p53 mutation can cooperate to silence genes with tumor suppressor function. We hypothesize pharmacologic strategies that target epigenetic and genetic lesions can synergize to transcriptionally reprogram cells to a near normal state that will result in efficient tumor cell kill or reversal of malignant properties. Three Specific Aims are proposed to address the hypothesis and investigate in greater detail the cooperation between genetic and epigenetic mechanisms in the control of gene expression. Studies will focus on human breast cancer; however, the general rules identified will likely extend to other human cancers. 1) Determine if p53 plays a role in the maintenance of the unmethylated state of target gene promoters. 2) Define further the mechanism by which reversal of genetic and epigenetic lesions synergize to reactivate silenced genes. 3) Identify new genes that are controlled by 5-methylcytosine in breast cancer.
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2006 — 2009 |
Futscher, Bernard W |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Epigenetic Remodeling by Environmental Arsenicals
DESCRIPTION (provided by applicant): Environmental exposure to arsenic and its metabolites is a significant health concern to US and world populations, playing a causative role in the etiology of human pathologies, including cancer. The long-term goal of the proposed study is designed to identify mechanisms of toxicity that are a result of environmental exposures to arsenicals. It is hypothesized that arsenical toxicity, in part, is mediated through its disruption of the normal epigenetic state of cells, and this hypothesis is based on reports in the extant literature as well as these preliminary studies. This premise will be tested using advanced epigenetic technologies to analyze models of arsenical exposure. These models range from in vitro models of arsenical-mediated malignant transformation of human uroepithelial cells to well-characterized, ethnically important human populations exposed to known levels of environmental arsenicals through drinking water. Through three specific aims the effects of arsenicals on epigenetic regulation from the level of the individual gene to the level of the entire genome will be tested. The aims are to: 1) Investigate the mechanisms and phenotypic consequences of epigenetic activation of Wnt5a gene that has been observed in an in vitro model of arsenical-induced malignant transformation. 2) Identify the decisive changes in the epigenomic landscape over the time course of arsenical induced malignant conversion of the immortalized human bladder cell UROtsa, and determine the stability of these changes after removal of this stressor. 3) Identify epigenetic targets of arsenic in human populations exposed to known levels of arsenic in their drinking water. While this research application focuses on the epigenetic perturbations induced by arsenicals with respect to human cancer, it is likely that if the hypothesis is backed by the studies, that of arsenical induced epigenetic changes as a mechanism of long-term toxicity, then the knowledge generated will likely extend to other metal-induced human pathologies, such as diabetes and cardiovascular disease.
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2010 — 2014 |
Futscher, Bernard W Martinez, Maria Elena [⬀] |
U01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Epigenetic Features of Pregnancy-Associated Breast Cancer in Hispanic Women
DESCRIPTION (provided by applicant): Risk of breast cancer (BC) increases in the period immediately following pregnancy. BCs that occur in the post-partum period have more aggressive histopathological features, are more likely to metastasize, and are associated with worse patient outcomes. On average, they also affect younger women and may represent a substantial proportion of early onset breast cancer (EOBC), a phenomenon that disproportionately affects racial/ethnic minority populations, such as Hispanics and African American (AA) women. We propose that pregnancy enhances development of BC in women whose breast tissue is vulnerable to the promotional effects of pregnancy via as yet unknown genetic and/or environmental factors and that this vulnerability explains at least part of the increased risk of EOBC and poor outcomes observed in women with higher fertility. The immediate objective of this research project is to examine epigenetic profiles of BCs that occur in the transient high-risk post-partum period versus those diagnosed outside of this period. Studies will be conducted in BC case series of Hispanic women, a population characterized by high parity. Our specific aims are to: 1) Define the risk factors, tumor sub-types, and clinicopathological characteristics associated with BCs occurring in the post-partum period of increased risk relative to those outside this period in Hispanic women;2) Test the hypothesis that methylation of specific protein-coding gene promoters is more frequent in tumors that are diagnosed in the post-partum period of increased risk vs. those occurring outside the transient high risk period;and, 3) Test the hypothesis that miRNA genes are more likely to be epigenetically altered in tumors diagnosed in the post-partum period. Results of the proposed work may further elucidate possible mechanisms that play a role in pre-menopausal EOBC, particularly those mechanisms that are temporally related to a recent pregnancy. PUBLIC HEALTH RELEVANCE: The proposed studies have tremendous relevance to elucidating breast cancer health disparities pertaining to tumors that occur in pre-menopausal women, which disproportionately affect racial/ethnic minority populations, including Hispanic and African-American women.
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2010 — 2014 |
Futscher, Bernard W |
P42Activity Code Description: Undocumented code - click on the grant title for more information. |
Project 2: Epigenomic Actions of Environmental Arsenicals
Exposure to environmental arsenicals has been linked to a number of human pathologies, include bladder and lung cancer. We hypothesize that arsenical-mediated perturbation of the epigenetic landscape is an important factor that drives malignant progression. Three integrated specific aims are described in this proposal will address this hypothesis from a gene to genome wide analysis, and from in vitro to real world settings. Aim 1 is designed to develop epigenetic targets as biomarkers of arsenical exposure. Preliminary epigenome-wide scanning studies of urine sediments from individuals with known exposure levels in their drinking water have identified candidate epigenetic biomarkers are correlated with arsenical exposure level. The utility of these candidate biomarkers will be evaluated using high sensitivity, high resolution technologies in a new cohort population. Aim 2 will determine if arsenicals produce common perturbations to the epigenomic landscape in their distinct epithelial targets. Experimental strategies of arsenical exposure that caused malignant transformation of urothelial cells will be expanded to lung epithelial model systems. Results from these experiments will help determine if there are seminal epigenetic changes that are common to epithelial malignant transformation in general, as well as the epigenetic changes that display tissue-origin specificity. Aim 3 will provide a detailed investigation of the phenotypic consequences of epigenetic gene inactivation of an arsenical target gene, G0S2, which is closely linked to the malignant transformation of urothelial cells. If our hypothesis is correct, then results from these studies will provide new insights into the mechanisms of their chronic arsenical exposure, as well as serve as a platform for inquiries into other, non-cancer, arsenic-induced human pathologies, such as diabetes and cardiovascular disease.
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2016 — 2021 |
Futscher, Bernard W |
P30Activity Code Description: To support shared resources and facilities for categorical research by a number of investigators from different disciplines who provide a multidisciplinary approach to a joint research effort or from the same discipline who focus on a common research problem. The core grant is integrated with the center's component projects or program projects, though funded independently from them. This support, by providing more accessible resources, is expected to assure a greater productivity than from the separate projects and program projects. |
Genomics
Project Summary / Abstract: Genomics Shared Resource (GSR) The goal of the Genomics Shared Resource (GSR) is to provide advanced genomics technology and services required to support the full range of cancer research conducted at the University of Arizona Cancer Center (UACC). Single gene to full genome analyses is one cornerstone of cancer biology research and discovery. The GSR provides UACC Members with guided, high-quality, cost-efficient access to a full spectrum of genomic cornerstone technologies. The GSR delivers the following services: 1) next-generation sequencing; 2) epigenetic analysis; 3) gene expression profiling; 4) genome-wide DNA analysis; and 5) genomic DNA variance. Within these categories of service, techniques include whole genome expression profiling, comparative genomic hybridization, sequence-based copy number variance, whole exome sequencing, shotgun sequencing, targeted sequencing panels, RNA-seq, chromatin immunoprecipitation (ChIP)-seq, genotyping, epigenomic ChIP-chip assays, real-time quantitative PCR (qPCR), sample quality assurance/quality control (QA / QC), sample isolation, experimental consultation, data analysis, and data archiving. With the ability to analyze single gene/small gene sets as well as genome wide analyses, the GSR offers great flexibility in analytical approaches. In addition, the GSR provides the capability for developing custom applications and makes new technologies available to address the specific needs of UACC investigators. GSR equipment includes: two Ion Torrent Personal Genome Machines, an Ion Torrent Proton (for small to large next-generation sequencing needs), Affymetrix and Agilent microarray platforms (for hybridization-based services), and three Applied Biosystems qPCR machines (for full service and self-service PCR applications). The GSR provides consultation on experiment design, and sample preparation, followed by sample QA / QC in preparation for the analysis. Data analysis and storage are critical to investigator's ability to access their data for publication and dissemination. Accordingly, the GSR provides microarray, sequence, and qPCR analysis to support the preparation of publications and grants. In addition, the Service provides access to raw data through a password protected website, along with triply redundant backup of investigator's data for five years.
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