2001 — 2004 |
Eng, Charis |
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. |
Ret Receptor Polymorphisms &Hirschsprung Disease
DESCRIPTION (Adapted from investigator's abstract): The RET proto-oncogene, encoding a receptor tyrosine kinase, is the susceptibility gene for Hirschsprung disease (HSCR), a congenital absence of enteric ganglia, and for multiple endocrine neoplasia type 2 (MEN 2), an inherited cancer syndrome and neurocristopathy. MEN 2 are characterized by medullary thyroid carcinoma (MTC), pheochromocytoma and parathroid hyperplaisa. Four related ligands are needed to bind to four related coreceptors before binding to RET. High penetrance gain of function mutations cause MEN 2 and loss of function mutations cause a subset of HSCR (30-50 percent of familial and 3 percent of isolated cases). Recently, the PIs have found 2 polymorphisms, A45A and L769L within the RET gene that are associated with HSCR in small sample. In contrast S836S are over-represented in individuals with sporadic MTC, particularly those with M918T polymorphism in their tumors. Based on these preliminary genetic findings, the PIs hypothesize that common low penetrance alleles within RET can act as low level susceptibility alleles predisposing to HSCR. Further, they hypothesize that the variants associated with HSCR will be underrepresented in sporadic MTC cases and vice versa. To test these hypotheses, the PIs will accrue a large population-based series of HSCR cases (n=250) and sporadic MTC (n=200) to determine the frequency of polymorphic variants in RET and to determine their haplotypes. Race-matched, region-matched normal controls will be accrued with cases: control ratio of 1:3. These data will be analyzed using the standard case-control matched association analysis, the transmission-disequilibrium test, and the haplotype-based linkage disequilibrium analysis. These methods have been used on a pilot series of 64 HSCR and unaffected parents and found evidence for a novel low penetrance locus with 15kb upstream and including codon 45 which could predispose to the majority of isolated HSCR. The PIs plan to extend their investigations to isolate this new locus and to directly test this locus in the extended series of HSCR. Further, the genes encoding the ligands and coreceptors of RET are equally good candidates for low penetrance susceptibility genes. Genotyping and haplotyping of these genes and similar tests of association will be performed in HSCR and MTC. Finally variants found to be associated with disease status will be tested functionally at the transcript, protein and cell biological level.
|
1 |
2002 — 2003 |
Eng, Charis |
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.) |
Genetic Etiologies of Esophageal Barrett's and Cancer
[unreadable] DESCRIPTION (provided by applicant): While the incidence of adenocarcinomas of the esophagus (EAC) and of the esophagogastric junction (EGJAC) continue to rise, the prognosis remains poor. Despite the accumulation of data regarding the somatic genetics of EAC and Barrett esophagus (BE), the etiology of genetic predisposition to BE and EAC/EGJAC is still unknown. Preliminary investigations in the literature and our own multi-disciplinary, multi-center group, the Ohio Familial Barrett Esophagus Consortium (OFBEC), have revealed that approximately 20% of BE have familial aggregations which comprise BE, EAC and/or EGJAC, and that the inheritance pattern is most likely autosomal dominant. Further, the PI has a putative susceptibility locus on chromosome 20 with suggestion of linkage to BE/EAC in a single multiplex family. Two small families are consistent with linkage to this putative locus and 2 others are not linked. This proposal will, therefore, test the hypotheses: [unreadable] [unreadable] 1. There exist at least two susceptibility genes predisposing to BE/EAC; and [unreadable] 2. These susceptibility genes that play a role in germline predisposition to familial BE/EAC are tumor suppressor genes which also play some rote in the genesis of sporadic BE and EAC. [unreadable] [unreadable] First, using a 400-marker autosomal genome scan, the PI will seek to confirm the chromosome 20 linkage and will determine what fraction of all affected families are linked to this putative locus. At the same time, the PI will seek the other putative locus (loci) which is linked to FBE/EAC/EGJAC. Second, the PI will use array-based expression analysis to look for genes whose transcripts are over- or under-expressed that reside within the critical interval in chromosome 20 as well as within novel regions defined by genome scan. Together with LOH analysis in these regions, this will supplement virtual physical mapping and candidate gene analysis in searching for the susceptibility genes for familial BE/EAC/EGJAC. If successful, this project promises to yield clues to the genetic etiology (and hence genetic risk) for BE, EAC and EGJAC. This might facilitate molecular diagnostics and early prediction as well as targeted surveillance and prophylaxis. [unreadable] [unreadable] [unreadable]
|
1 |
2004 — 2006 |
Eng, Charis |
P01Activity Code Description: For the support of a broadly based, multidisciplinary, often long-term research program which has a specific major objective or a basic theme. A program project generally involves the organized efforts of relatively large groups, members of which are conducting research projects designed to elucidate the various aspects or components of this objective. Each research project is usually under the leadership of an established investigator. The grant can provide support for certain basic resources used by these groups in the program, including clinical components, the sharing of which facilitates the total research effort. A program project is directed toward a range of problems having a central research focus, in contrast to the usually narrower thrust of the traditional research project. Each project supported through this mechanism should contribute or be directly related to the common theme of the total research effort. These scientifically meritorious projects should demonstrate an essential element of unity and interdependence, i.e., a system of research activities and projects directed toward a well-defined research program goal. |
Genetic Alteration in the Epithelial and Stromal
Most breast cancers are sporadic but approximately 5-10% are hereditary. Despite knowing the importance of the role of the microenvironment in tumor development, genetic studies of solid tumors, whether sporadic or hereditary, to date, have treated them as single amorphous entities. Genetic analyses of adenocarcinomas of the breast are no exception. We have preliminary loss of heterozygosity (LOH) and somatic TP53/PTEN mutation data in sporadic human breast cancer, which demonstrates that genetic alterations can differentially occur in the neoplastic epithelial compartment as well as the surrounding stromal compartment. We hypothesize that the tumor microenvironment, especially the stromal compartments, play an essential, albeit largely undefined role, in breast carcinogenesis, whether in the sporadic setting or in the hereditary setting. This application will use a genetic approach to address the hypothesis that LOH in the stromal and epithelial compartments of breast adenocarcinomas differentially contribute to tumor growth, such that they affect clinical outcomes differently. Thus, this project will take several genetic approaches to study the role of the tumor microenvironment in breast cancer development. First, genetic alterations in the epithelial and stromal cellular compartments of 225 human breast tumor samples will be assessed by genome-wide LOH as well as PTEN and TP53 mutation analyses on template cells obtained by laser-capture microdissection (LCM). Further, these somatic genetic alterations in the epithelial and stromal components of this same large series of breast cancers will be correlated with clinical outcomes. Second, a murine model will be developed to examine the issue of epithelial-stromal interaction in mammary carcinogenesis, specifically, targeted disruption of Pten, which is known to participate in inherited and sporadic human breast carcinogenesis. Targeted disruption of Pten, using cre-loxP technology, will be performed separately in the epithelium and in the stroma and the consequences of each analyzed. In the future, examination of genetic alterations in the mammary neoplastic stroma and epithelium downstream of each of the mouse models developed in the Program Project is envisioned. Thus, the goals of the proposed project are to elucidate, at the clinical and molecular level, the relevant mesenchymal (stromal)-epithelial interactions, which impact on the control of the cell cycle, apoptosis and invasiveness of tumor cells. These might have future implications for clinical targeting for therapy or prevention.
|
1 |
2004 — 2008 |
Eng, Charis |
U54Activity Code Description: To support any part of the full range of research and development from very basic to clinical; may involve ancillary supportive activities such as protracted patient care necessary to the primary research or R&D effort. The spectrum of activities comprises a multidisciplinary attack on a specific disease entity or biomedical problem area. These differ from program project in that they are usually developed in response to an announcement of the programmatic needs of an Institute or Division and subsequently receive continuous attention from its staff. Centers may also serve as regional or national resources for special research purposes, with funding component staff helping to identify appropriate priority needs. |
Integrating Genomic and Epigenomic Alterations in Cancer and Its Microenvironment
Despite knowing the importance of the role of the microenvironment in tumor development, genetic studies of solid tumors, whether sporadic or hereditary, to date, have treated them as single amorphous entities. Genetic and epigenetic analyses of breast carcinomas are no exception. Using 381-microsatellite marker loss-of-heterozygosity (LOH) scan in 135 distinct sporadic invasive breast cancers, we have identified 19 key loci on 15 chromosomes with significant LOH in the epithelium and 38 key loci on 19 chromosomes with significant LOH in the stroma (chromosome-wise modeling). We therefore initially hypothesize that these regions which when loss would play a role in breast cancer progression; we also hypothesize that these regions act as signposts for genes which when epigenetically modified which together with structural loss play some role in breast cancer progression as germane to epithelial-stromal interactions. We believe therefore that the tumor microenvironment, especially the stroma plays an essential, but largely undefined role, in breast carcinogenesis. Bringing together experimental and computational biologists, Project 2 will use a rolling model iterative, integrative approach of directed genetic and epigenetic analysis and validation as well as informatics model building to understand breast cancer progression. This will involve hypothesis generation and testing, with the initial hypothesis that LOH and/or epigenetic inactivation of genes within the 19 epithelial loci would occur in initiation or earlier in progression and the multiple stromal targets would be involved to facilitate progression, invasion and metastases. We will take a directed SNP-based LOH and hypermethylation-based strategy to examine the 58 initial target regions in stroma and epithelium of 150 invasive breast carcinomas for key genes undergoing LOH and/or hypermethylation during progression. These experimental data will be used for model building, one taking a phylogenetics-type approach and the other utilizing a network-like approach to help integrate genetic and epigenetic alterations in tumor progression in the context of the epithelium and stroma. Model building and experimentation will continue until a model(s) are derived that can accurately predict the alterations in the 2 compartments as they relate to progression. In the near future, these somatic genetic and epigenetic progression-related alterations in epithelium and stroma will be correlated with clinical outcomes. Elucidation of novel regions of LOH and hypermethylation relevant in the stromal compartment might ultimately reveal novel targets for prevention and therapy.
|
1 |
2007 — 2008 |
Eng, Charis |
P01Activity Code Description: For the support of a broadly based, multidisciplinary, often long-term research program which has a specific major objective or a basic theme. A program project generally involves the organized efforts of relatively large groups, members of which are conducting research projects designed to elucidate the various aspects or components of this objective. Each research project is usually under the leadership of an established investigator. The grant can provide support for certain basic resources used by these groups in the program, including clinical components, the sharing of which facilitates the total research effort. A program project is directed toward a range of problems having a central research focus, in contrast to the usually narrower thrust of the traditional research project. Each project supported through this mechanism should contribute or be directly related to the common theme of the total research effort. These scientifically meritorious projects should demonstrate an essential element of unity and interdependence, i.e., a system of research activities and projects directed toward a well-defined research program goal. |
Genetic Alteration in Epithelial and Stromal Compartment of Breast Adenocarcinoma
Most breast cancers are sporadic but approximately 5-10% are hereditary. Despite knowing the importance of the role of the microenvironment in tumor development, genetic studies of solid tumors, whether sporadic or hereditary, to date, have treated them as single amorphous entities. Genetic analyses of adenocarcinomas of the breast are no exception. We have preliminary loss of heterozygosity (LOH) and somatic TP53/PTEN mutation data in sporadic human breast cancer, which demonstrates that genetic alterations can differentially occur in the neoplastic epithelial compartment as well as the surrounding stromal compartment. We hypothesize that the tumor microenvironment, especially the stromal compartments, play an essential, albeit largely undefined role, in breast carcinogenesis, whether in the sporadic setting or in the hereditary setting. This application will use a genetic approach to address the hypothesis that LOH in the stromal and epithelial compartments of breast adenocarcinomas differentially contribute to tumor growth, such that they affect clinical outcomes differently. Thus, this project will take several genetic approaches to study the role of the tumor microenvironment in breast cancer development. First, genetic alterations in the epithelial and stromal cellular compartments of 225 human breast tumor samples will be assessed by genome-wide LOH as well as PTEN and TP53 mutation analyses on template cells obtained by laser-capture microdissection (LCM). Further, these somatic genetic alterations in the epithelial and stromal components of this same large series of breast cancers will be correlated with clinical outcomes. Second, a murine model will be developed to examine the issue of epithelial-stromal interaction in mammary carcinogenesis, specifically, targeted disruption of Pten, which is known to participate in inherited and sporadic human breast carcinogenesis. Targeted disruption of Pten, using cre-loxP technology, will be performed separately in the epithelium and in the stroma and the consequences of each analyzed. In the future, examination of genetic alterations in the mammary neoplastic stroma and epithelium downstream of each of the mouse models developed in the Program Project is envisioned. Thus, the goals of the proposed project are to elucidate, at the clinical and molecular level, the relevant mesenchymal (stromal)-epithelial interactions, which impact on the control of the cell cycle, apoptosis and invasiveness of tumor cells. These might have future implications for clinical targeting for therapy or prevention.
|
1 |
2008 — 2017 |
Eng, Charis |
P01Activity Code Description: For the support of a broadly based, multidisciplinary, often long-term research program which has a specific major objective or a basic theme. A program project generally involves the organized efforts of relatively large groups, members of which are conducting research projects designed to elucidate the various aspects or components of this objective. Each research project is usually under the leadership of an established investigator. The grant can provide support for certain basic resources used by these groups in the program, including clinical components, the sharing of which facilitates the total research effort. A program project is directed toward a range of problems having a central research focus, in contrast to the usually narrower thrust of the traditional research project. Each project supported through this mechanism should contribute or be directly related to the common theme of the total research effort. These scientifically meritorious projects should demonstrate an essential element of unity and interdependence, i.e., a system of research activities and projects directed toward a well-defined research program goal. |
Genetic Alterations That Initiate Follicular Thyroid Carcinogenesis
Project 2 takes a clinical and translational genetics approach to identify and characterize genes and their pathways that play a role In the initiation of differentiated thyroid cancer (DTC) for the purposes of the eariiest diagnosis via gene-enabled cancer risk assessment. We will utilize human Cowden syndrome (CS), and a mouse model of human Carney Complex (CNC), as our models epitomizing germline (inherited) predisposition as the first event in initiation in a heritable thyroid neoplasia disorder. CS is a difficult-to- recognize, under-diagnosed heritable disorder characterized by follicular thyroid adenomas (FA), DTC and breast cancer. We found that germline PTEN mutations cause finite subsets of CS and other clinical syndromes, which we collectively term PTEN hamartoma-tumor syndrome (PHTS). Germline PRKR1A mutations associate with CNC. In the first grant period, we have prospectively accrued >3,000 probands from community and academic medical centers who meet CS or CS-like (CSL) criteria and created a web- based PTEN risk calculator based on presence/absence of pathogenic PTEN mutations and clinical characteristics; and showed 32% lifetime risk of DTC in PHTS. We found functional germline variants in SDHB and SDHD, encoding 2 subunits of succinate dehydrogenase, resulting in destabilization of p53 via NQ01 and decreasing ATP levels associated with PTEN nuclear trapping, we developed mouse models of the spectrum of FTC, including FA (thyroid-specific Pten knock-out), locally invasive FTC (Prkaria KO), and metastatic FTC (Pten/Prkaria double KO); preliminary data Indicating downregulation of Sdhb and other Sdh subunits in the FTC models, we broadly hypothesize that Interactions of PTEN, SDHx and PRKR1A play a role in thyroid neoplasia initiation by modulating ROS and other mitochondria-associated energetics. We will (1) analyze SDHx and PRKARIA germline variants In modifying the risk and sub-histology of DTC and of other component cancers in PTEN mutation positive CS/CSL patients; (2) mitochondrial energetics-relevant in vitro functional assays to analyse the interaction of PTEN and SDHx; and (3) physiological validate our human in vivo and in vitro observations in murine models.
|
1 |
2019 — 2021 |
Eng, Charis |
U54Activity Code Description: To support any part of the full range of research and development from very basic to clinical; may involve ancillary supportive activities such as protracted patient care necessary to the primary research or R&D effort. The spectrum of activities comprises a multidisciplinary attack on a specific disease entity or biomedical problem area. These differ from program project in that they are usually developed in response to an announcement of the programmatic needs of an Institute or Division and subsequently receive continuous attention from its staff. Centers may also serve as regional or national resources for special research purposes, with funding component staff helping to identify appropriate priority needs. |
Natural History of Individuals With Autism Spectrum Disorder and Germline Pten Mutations @ Boston Children's Hospital
Autism spectrum disorders (ASD) are an etiologically heterogeneous set of neurodevelopmental disorders marked by social communication/interaction deficits and restricted/repetitive behaviors. Genetic studies have identified a strong heritable component, yet >80% of ASD remains idiopathic. Marked heterogeneity has slowed attempts to identify pathophysiology and related therapeutic targets. One promising strategy to reduce complexity is to focus on subgroups with a specific genetic etiology, such as ASD associated with germline heterozygous PTEN mutations (PTEN-ASD, who are always macrocephalic). In the last 4 years, we characterized cross-sectional neurobehavioral and neurocognitive differences among PTEN-ASD, those with PTEN mutations but no ASD (PTEN-no ASD) and macrocephalic ASD without PTEN mutations (Macro-ASD) and begun longitudinal data collection in individuals aged 3-21. We propose a natural history study of the neurophenotypic and molecular characteristics of PTEN-ASD with the goals of understanding risk management and treatment planning as well as identifying sensitive biomarkers for intervention studies. We will recruit 170 (70 from current cohort) individuals with PTEN-ASD, Macro-ASD, and PTEN no-ASD, and expanding recruitment to aged 18 months to 45 years. Data collected will include: (a) cancer occurrence, (b) autism and other behavioral symptoms, (c) neurocognitive profiles, (d) adaptive function, (e) genomic modifiers, (f) protein levels from PI3K/AKT/mTOR/S6K pathway, and (g) EEG, in order to: (Aim 1) Determine cross-sectional and longitudinal neurobehavioral and medical differences between PTEN-ASD and other groups in an expanded age range. This aim seeks to describe initial levels and longitudinal changes in cancer occurrence, behavioral signs/symptoms, and cognitive function in PTEN-ASD; (Aim 2) Identify EEG and molecular biomarkers specific to PTEN-ASD and those shared with other groups. This aim seeks to identify biomarkers that may be treatment targets in intervention studies; and (Aim 3) Develop a comprehensive, multi-level, longitudinal model of PTEN-ASD to inform future clinical trials and the development of consensus care guidelines. We will use data from Aims 1 and 2 and from TSC Associated Neuropsychiatric Disorders (TAND) Checklist (after validation). This first comprehensive longitudinal evaluation of the phenotypic and molecular characteristics of PTEN ASD, to identify specific molecular pathway and correlated neural abnormalities responsible for ASD symptoms in these individuals, which can be ably compared to TSC and PMS. It is a crucial next step toward the development of personalized genetic treatment approaches for PTEN-ASD. Prior to initiating further clinical trials, it will be critical to identify treatment targets at the molecular, neurophysiological, and behavioral levels.
|
0.909 |