16 results on '"Samuel J. Shelton"'
Search Results
2. OS12.4 In vivo dynamics and targeting of vessel co-option in glioma
- Author
-
Tracy T. Batchelor, Shanmugarajan Krishnan, Rakesh K. Jain, Manish K. Aghi, David H. Rowitch, Emmanuelle Huillard, Samuel J. Shelton, Amelie Griveau, Jonas Kloepper, Anat Stemmer-Rachamimov, Giorgio Seano, and Nancy Wang
- Subjects
Cancer Research ,Oncology ,In vivo ,Chemistry ,Glioma ,Dynamics (mechanics) ,Cancer research ,medicine ,Oral Presentations ,Neurology (clinical) ,medicine.disease - Abstract
BACKGROUND Gliomas comprise heterogeneous malignant glial and stromal cells. While blood vessel co-option is a potential mechanism to escape anti-angiogenic therapy, the relevance of glial phenotype in this process is unclear. MATERIAL AND METHODS Here, we intravitally study preclinical syngenetic models of glioma as well as patient-derived cells transplanted orthotopically. Moreover, we profoundly confirm our preclinical results with histological studies on patient specimens. RESULTS We show that Olig2+ oligodendrocyte precursor-like glioma cells invade by single-cell vessel co-option and preserve the blood-brain barrier (BBB). Conversely, Olig2-negative glioma cells form dense perivascular collections and promote angiogenesis and BBB breakdown, leading to innate immune cell activation. Experimentally, Olig2 promotes Wnt7b expression, a finding that correlates in human glioma profiling. Targeted Wnt7a/7b deletion or pharmacologic Wnt inhibition blocks Olig2+ glioma single-cell vessel co-option and enhances responses to temozolomide. Finally, Olig2 and Wnt7 become upregulated after anti-VEGF treatment in preclinical models and patients. CONCLUSION Here, we show that glioma is able to employ vessel co-option, i.e. the movement of tumor cells towards and along the pre-existing vasculature. Glioma oligodendrocyte-like (OPCL) cells express Wnt7 that is necessary for vessel co-option and Wnt inhibitors significantly improve survival with temozolomide. Moreover, we demonstrated that anti-VEGF-treatment of glioma selects for Olig2/Wnt7+ cells
- Published
- 2019
3. MicroRNA Ratios Distinguish Melanomas from Nevi
- Author
-
Rodrigo Torres, Samuel J. Shelton, Michael C. Oldham, Ursula E. Lang, Maria L. Wei, A. Hunter Shain, Miroslav Hejna, Nancy M. Joseph, Robert L. Judson-Torres, Boris C. Bastian, and Iwei Yeh
- Subjects
0301 basic medicine ,Oncology ,medicine.medical_specialty ,Skin Neoplasms ,Datasets as Topic ,Dermatology ,Biochemistry ,Sensitivity and Specificity ,Article ,Diagnosis, Differential ,Machine Learning ,03 medical and health sciences ,0302 clinical medicine ,Text mining ,Patient age ,Internal medicine ,microRNA ,medicine ,Biomarkers, Tumor ,Humans ,Molecular Biology ,Melanoma ,Nevus ,Receiver operating characteristic ,MicroRNA sequencing ,business.industry ,Sequence Analysis, RNA ,External validation ,High-Throughput Nucleotide Sequencing ,Cell Biology ,medicine.disease ,Prognosis ,Paraffin embedded ,MicroRNAs ,030104 developmental biology ,ROC Curve ,030220 oncology & carcinogenesis ,Melanocytes ,business ,Biomarkers - Abstract
The use of microRNAs as biomarkers has been proposed for many diseases, including the diagnosis of melanoma. Although hundreds of microRNAs have been identified as differentially expressed in melanomas as compared to benign melanocytic lesions, a limited consensus has been achieved across studies, constraining the effective use of these potentially useful markers. In this study, we applied a machine learning-based pipeline to a dataset consisting of genetic features, clinical features, and next-generation microRNA sequencing from micro-dissected formalin-fixed paraffin embedded melanomas and their adjacent benign precursor nevi. We identified patient age and tumor cellularity as variables that frequently confound the measured expression of potentially diagnostic microRNAs. By employing the ratios of microRNAs that were either enriched or depleted in melanoma compared to the nevi as a normalization strategy, we developed a model that classified all the available published cohorts with an area under the receiver operating characteristic curve of 0.98. External validation on an independent cohort classified lesions with 81% sensitivity and 88% specificity and was uninfluenced by the tumor content of the sample or patient age.
- Published
- 2019
4. A machine-learning classifier trained with microRNA ratios to distinguish melanomas from nevi
- Author
-
Iwei Yeh, Miroslav Hejna, Rodrigo Torres, Samuel J. Shelton, Nancy M. Joseph, Maria L. Wei, Ursula E. Lang, Michael C. Oldham, Boris C. Bastian, Robert L. Judson-Torres, and Alan Hunter Shain
- Subjects
Oncology ,0303 health sciences ,medicine.medical_specialty ,Small RNA ,Learning classifier system ,Microarray ,business.industry ,Melanoma ,Confounding ,Biology ,medicine.disease ,03 medical and health sciences ,0302 clinical medicine ,Text mining ,Patient age ,030220 oncology & carcinogenesis ,Internal medicine ,microRNA ,medicine ,business ,neoplasms ,030304 developmental biology - Abstract
The use of microRNAs as biomarkers has been proposed for many diseases including the diagnosis of melanoma. Although hundreds of microRNAs have been identified as differentially expressed in melanomas as compared to benign melanocytic lesions, limited consensus has been achieved across studies, constraining the effective use of these potentially useful markers. In this study we quantified microRNAs by next-generation sequencing from melanomas and their adjacent benign precursor nevi. We applied a machine learning-based pipeline to identify a microRNA signature that separated melanomas from nevi and was unaffected by confounding variables, such as patient age and tumor cell content. By employing the ratios of microRNAs that were either enriched or depleted in melanoma compared to nevi as a normalization strategy, the classifier performed similarly across multiple published microRNA datasets, obtained by microarray, small RNA sequencing, or RT-qPCR. Validation on separate cohorts of melanomas and nevi correctly classified lesions with 83% sensitivity and 71-83% specificity, independent of variation in tumor cell content of the sample or patient age.
- Published
- 2018
- Full Text
- View/download PDF
5. GENE-47. A 3D ATLAS TO EVALUATE THE SPATIAL PATTERNING OF GENETIC ALTERATIONS AND TUMOR CELL STATES IN GLIOMA
- Author
-
Josie Hayes, Edward F. Chang, Stephanie Hilz, Marram P. Olson, Joseph F. Costello, Marisa Lafontaine, Joanna J. Phillips, Janine M. Lupo, Henrik Bengtsson, Chibo Hong, Aaron Diaz, Michael Martin, Sarah J. Nelson, Anny Shai, Anupam Kumar, Karen Wong, Annette M. Molinaro, Michael C. Oldham, Yao Yu, Michael W. McDermott, Michael Zhang, Adam B. Olshen, Llewellyn E. Jalbert, Daniel A. Lim, Shawn L. Hervey-Jumper, Tali Mazor, Susan M. Chang, Samuel J. Shelton, Mitchel S. Berger, and Tracy Luks
- Subjects
Genetics and Epigenetics ,Cancer Research ,Tumor microenvironment ,Tumor cells ,medicine.disease ,Gene expression profiling ,Oncology ,Glioma ,Gene expression ,medicine ,Cancer research ,Neurology (clinical) ,Gene ,Exome sequencing ,Glioblastoma - Abstract
BACKGROUND Previous studies of solid tumors have been restricted in their ability to map how heterogeneous cell populations evolved within the tumor in three-dimensional (3D) space due to insufficient sampling, typically one sample per tumor, and a lack of knowledge of where within the tumor the sample was obtained. Knowledge of the extensivity of heterogeneity and how it is spatially distributed is crucial for assessing whether a therapeutic target is truly tumor-wide, and for exploring how mutations relate to heterogeneity in the local microenvironment. METHODS We developed a novel platform to integrate and visualize in 3D multi-omics data generated from each of 8–10 spatially mapped samples per tumor. Together, the 171 samples collected using this approach from 16 adult diffuse glioma at diagnosis and recurrence form a novel resource – the 3D Glioma Atlas. RESULTS By maximally sampling the tumor geography without excluding samples based on low cancer cell fraction (CCF), we identify a subpopulation of glioblastoma with pervasively lower CCF likely excluded by other atlases, such as the TCGA, that used stringent CCF cutoffs. Exome sequencing of 3D-mapped samples from lower-grade tumors revealed that clonal expansions are typically spatially segregated, implying minimal tumor-wide intermixing of genetically heterogenous cells. Heterogeneity is less spatially segregated for faster-growing high-grade tumors, suggesting that cell populations expand in these tumors differently. Recurrent low-grade tumors have greater intratumoral mutational heterogeneity than newly diagnosed tumors, though this did not translate into greater dissimilarity in gene expression profiles for recurrent tumors, suggesting minimal functional impact of this additional mutational diversity on gene expression. CONCLUSIONS The delineation of spatial patterns of heterogeneity that our work provides enables more informed interpretation of biopsies and greater insight into the factors shaping intratumoral variation of gene expression patterns. Ongoing work is exploring the spatial patterning of amplification events and the tumor microenvironment.
- Published
- 2019
- Full Text
- View/download PDF
6. GENE-33. THE 3D EVOLUTION AND IN VIVO GROWTH PATTERNS OF GLIOMA CELL POPULATIONS
- Author
-
Llewellyn E. Jalbert, Daniel A. Lim, Michael C. Oldham, Tali Mazor, Michael W. McDermott, Samuel J. Shelton, Mitchel S. Berger, Hang K Wong, Josie Hayes, Annette M. Molinaro, Tracy Luks, Joseph F. Costello, Aaron Diaz, Henrik Bengtsson, Chibo Hong, Joanna J. Phillips, Sarah J. Nelson, Stephanie Hilz, and Susan M. Chang
- Subjects
Cancer Research ,Interferon type II ,Astrocytoma ,Cancer ,Glioma cell ,Biology ,medicine.disease ,Cell biology ,Gene expression profiling ,Abstracts ,Oncology ,In vivo ,Gene expression ,medicine ,Neurology (clinical) ,Gene ,medicine.drug - Abstract
Most cancers result from multiple clonal expansion events, resulting in tumors comprised of many subclones. The coexistence of these genetically distinct populations within a single tumor is thought to underlie the failure of most current treatments. Ascertaining how diverse populations of cells evolve within tumors, and the functional implications of this diversity, are the next steps to developing more informed treatments that overcome the barrier currently posed by intratumoral heterogeneity (ITH). Previous studies of adult diffuse glioma have been restricted in their ability to provide a detailed understanding of the spatial evolution of solid tumors due to insufficient sampling, typically just one biopsy per patient, and a lack of knowledge of where within the heterogeneous tumor the sample was obtained. We have developed a unique sample collection protocol, in which we record the precise, three-dimensional (3D) coordinate for each of 10 spatially-distinct samples obtained from each patient’s tumor. Whole exome data from IDH1 mutant grade II astrocytomas analyzed in this manner have revealed that expansion events are typically spatially segregated, suggesting minimal tumor-wide intermixing of subclonal cell populations in these low grade gliomas. Expression profiling of one particular case has furthermore revealed ITH of the immune microenvironment, uncovering a region of increased PD-L1 expression and IFN-gamma signaling. Ongoing analysis is focused on integrating genetic and expression profiles from these and additional spatially-mapped cases. This integrative analysis aims to dissect the relative contributions of subclonal variation and location within the tumor on gene expression patterns and ITH of the immune microenvironment. The delineation of the spatial patterns of ITH our work provides will enable more informed selection of biopsy targets in the future. It also lends greater insight into the factors shaping intratumoral variation of gene expression patterns and the immune microenvironment in adult diffuse glioma.
- Published
- 2017
7. 1220 MicroRNA signature distinguishing nevi from primary melanoma
- Author
-
Robert L. Judson, Ursula E. Lang, Samuel J. Shelton, Boris C. Bastian, Nancy M. Joseph, Maria L. Wei, Iwei Yeh, Yıldıray Yeniay, Michael C. Oldham, Rodrigo Torres, and Alan Hunter Shain
- Subjects
Primary (chemistry) ,Melanoma ,microRNA ,medicine ,Cancer research ,Cell Biology ,Dermatology ,Biology ,medicine.disease ,Signature (topology) ,Molecular Biology ,Biochemistry - Published
- 2018
- Full Text
- View/download PDF
8. A Glial Signature and Wnt7 Signaling Regulate Glioma-Vascular Interactions and Tumor Microenvironment
- Author
-
Arman Jahangiri, Tracy T. Batchelor, Itay Tirosh, William A. Weiss, Emmanuelle Huillard, Ivy X. Chen, Nancy Wang, Anders Persson, Shanmugarajan Krishnan, Rakesh K. Jain, Joanna J. Phillips, Louis Larrouquere, David H. Rowitch, Tracy J. Yuen, Michael C. Oldham, Robert Kupp, Jennifer K. Sabo, Mitrajit Ghosh, Samuel J. Shelton, Amelie Griveau, Mario L. Suvà, Olle R. Lindberg, Anat Stemmer-Rachamimov, Kirsten Obernier, Manish K. Aghi, Arturo Alvarez-Buylla, Giorgio Seano, Shwetal Mehta, Jonas Kloepper, An-Chi Tien, Rowitch, David [0000-0002-0079-0060], and Apollo - University of Cambridge Repository
- Subjects
p53 ,0301 basic medicine ,Cancer Research ,Angiogenesis ,Mice ,angiogenesis ,glioma ,Tumor Cells, Cultured ,Tumor Microenvironment ,2.1 Biological and endogenous factors ,Aetiology ,Wnt Signaling Pathway ,Cancer ,Tumor ,Cultured ,Brain Neoplasms ,Chemistry ,Tumor Cells ,Gene Expression Regulation, Neoplastic ,Bevacizumab ,Oligodendroglia ,medicine.anatomical_structure ,Oncology ,Olig2 ,Cell activation ,oligodendrocyte precursor ,Astrocyte ,Stromal cell ,invasiveness ,Oncology and Carcinogenesis ,Article ,Cell Line ,OLIG2 ,Wnt ,03 medical and health sciences ,astrocyte ,Rare Diseases ,Cell Line, Tumor ,Glioma ,Temozolomide ,medicine ,Animals ,Humans ,Oncology & Carcinogenesis ,Neoplastic ,Tumor microenvironment ,Neurosciences ,vessel co-option ,Cell Biology ,Oligodendrocyte Transcription Factor 2 ,blood-brain barrier ,medicine.disease ,Oligodendrocyte ,Brain Disorders ,Wnt Proteins ,Brain Cancer ,030104 developmental biology ,Gene Expression Regulation ,Cancer research ,Neoplasm Transplantation - Abstract
Gliomas comprise heterogeneous malignant glial and stromal cells. While blood vessel co-option is a potential mechanism to escape anti-angiogenic therapy, the relevance of glial phenotype in this process is unclear. We show that Olig2+ oligodendrocyte precursor-like glioma cells invade by single-cell vessel co-option and preserve the blood-brain barrier (BBB). Conversely, Olig2-negative glioma cells form dense perivascular collections and promote angiogenesis and BBB breakdown, leading to innate immune cell activation. Experimentally, Olig2 promotes Wnt7b expression, a finding that correlates in human glioma profiling. Targeted Wnt7a/7b deletion or pharmacologic Wnt inhibition blocks Olig2+ glioma single-cell vessel co-option and enhances responses to temozolomide. Finally, Olig2 and Wnt7 become upregulated after anti-VEGF treatment in preclinical models and patients. Thus, glial-encoded pathways regulate distinct glioma-vascular microenvironmental interactions.
- Published
- 2018
- Full Text
- View/download PDF
9. GENT-15. INTEGRATED MOLECULAR PROFILING OF HUMAN BRAIN TUMORS THROUGH MULTIOMIC ANALYSIS OF SERIAL SECTIONS (MASS)
- Author
-
Brett Johnson, Daniel Lim, Joseph F. Costello, Michael F. McDermott, Joanna J. Phillips, Michael C. Oldham, Eric J. Huang, Tali Mazor, Samuel J. Shelton, Mitchel S. Berger, Russel O. Pieper, and Matthew B. Potts
- Subjects
Cancer Research ,medicine.anatomical_structure ,Oncology ,medicine ,Profiling (information science) ,Neurology (clinical) ,Computational biology ,Human brain ,Biology - Published
- 2016
- Full Text
- View/download PDF
10. IMMU-52. SELECTION OF GLIOMA T-CELL THERAPY TARGETS BASED ON THE ANALYSIS OF TUMOR IMMUNOPEPTIDOME AND EXPRESSION PROFILES
- Author
-
Oliver Schoor, Jens Fritsche, Joseph F. Costello, Toni Weinschenk, Norbert Hilf, Gary Kohanbash, Josie Hayes, Payal Watchmaker, Sabrina Kuttruff-Coqui, Hideho Okada, Samuel J. Shelton, Colette Song, Diego Carrera, Michael C. Oldham, Soeren Mueller, and Harpreet Singh
- Subjects
Primary Glioblastoma ,Cancer Research ,medicine.medical_treatment ,T cell ,Immunotherapy ,Biology ,medicine.disease ,Epitope ,Abstracts ,medicine.anatomical_structure ,Oncology ,Glioma ,medicine ,Cancer research ,Low-Grade Glioma ,Neurology (clinical) ,Gene ,Selection (genetic algorithm) - Abstract
Diffuse infiltrating low-grade gliomas (WHO grade II or III) are slow-growing primary brain tumors, but are considered malignant due to their invasive growth with a high risk of recurrence and progression to higher-grade tumors. While novel immunotherapeutic approaches are being developed, the paucity of well-characterized antigens that can be safely targeted remains a challenge; this led us to conduct an extensive evaluation searching for targetable T-cell epitopes in gliomas. In the current study, we report our analysis on a set of 64 glioma-associated antigens. Initial screening was based on the presentation of at least one of their epitopes by human leukocyte antigen (HLA)-A*0201 or A*2401 in primary glioblastoma tissue, their oncogenic role as proteins in glioma-genesis and their capability of inducing an antigen-specific T-cell response in human peripheral blood samples. Furthermore, we assessed differential expression of these epitopes in 39 primary gliomas paired with their corresponding recurrent tumors, and then evaluated datasets containing RNA expression levels for normal brain and other organs. As a result, we found 5 antigen epitopes being exclusively expressed in all WHO grade II gliomas, with even higher expression in their corresponding recurrent tumors, without significant levels measured in normal brain or peripheral organs. Our results strongly suggest that immunotherapy targeting these epitopes can be highly glioma-specific and safe, reducing the likelihood of adverse events such as on-target, off-tumor toxicity. These results are especially significant given the marked heterogeneity of gene and protein expression in gliomas. Moreover, our methods can be applied to increase the rate of discovery for neoantigens and naturally-occurring epitopes in this and other types of tumors.
- Published
- 2017
- Full Text
- View/download PDF
11. ERK phosphorylation of MED14 in promoter complexes during mitogen-induced gene activation by Elk-1
- Author
-
Hong-Mei Zhang, Samuel J. Shelton, Janice Saxton, Li Li, Peter E. Shaw, Joaquín M. Espinosa, and Matthew D. Galbraith
- Subjects
Transcriptional Activation ,MAPK/ERK pathway ,RNA polymerase II ,Gene Regulation, Chromatin and Epigenetics ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Genetics ,Animals ,Humans ,Phosphorylation ,Extracellular Signal-Regulated MAP Kinases ,Promoter Regions, Genetic ,Genes, Immediate-Early ,Transcription factor ,ets-Domain Protein Elk-1 ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,Mediator Complex ,biology ,Kinase ,Promoter ,Molecular biology ,Genes, ras ,HEK293 Cells ,Mutation ,NIH 3T3 Cells ,biology.protein ,Mitogens ,030217 neurology & neurosurgery ,HeLa Cells - Abstract
The ETS domain transcription factor Elk-1 stimulates expression of immediate early genes (IEGs) in response to mitogens. These events require phosphorylation of Elk-1 by extracellular signal-regulated kinase (ERK) and phosphorylation-dependent interaction of Elk-1 with co-activators, including histone acetyltransferases and the Mediator complex. Elk-1 also recruits ERK to the promoters of its target genes, suggesting that ERK phosphorylates additional substrates in transcription complexes at mitogen-responsive promoters. Here we report that MED14, a core subunit of the Mediator, is a bona fide ERK substrate and identify serine 986 (S986) within a serine-proline rich region of MED14 as the major ERK phosphorylation site. Mitogens induced phosphorylation of MED14 on S986 at IEG promoters; RNAi knockdown of MED14 reduced CDK8 and RNA polymerase II (RNAPII) recruitment, RNAPII C-terminal domain phosphorylation and impaired activation of IEG transcription. A single alanine substitution at S986 reduced activation of an E26 (ETS)-responsive reporter by oncogenic Ras and mitogen-induced, Elk-1-dependent transcription, whereas activities of other transcriptional activators were unaffected. We also demonstrate that Elk-1 can associate with MED14 independently of MED23, which may facilitate phosphorylation of MED14 by ERK to impart a positive and selective impact on mitogen-responsive gene expression.
- Published
- 2013
12. Dimer formation and conformational flexibility ensure cytoplasmic stability and nuclear accumulation of Elk-1
- Author
-
Peter E. Shaw, Samuel J. Shelton, Emma L. Evans, Nicholas D. Holliday, Janice Saxton, Andreas Begitt, Robert A. Hipskind, Institut de Génétique Moléculaire de Montpellier (IGMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
- Subjects
Cytoplasm ,Proteasome Endopeptidase Complex ,Protein Conformation ,animal diseases ,Gene Regulation, Chromatin and Epigenetics ,Biology ,Cell Line ,03 medical and health sciences ,0302 clinical medicine ,Protein structure ,fluids and secretions ,Serum response factor ,Genetics ,medicine ,Humans ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Amino Acid Sequence ,Transcription factor ,Sequence Deletion ,ets-Domain Protein Elk-1 ,030304 developmental biology ,Cell Nucleus ,0303 health sciences ,Protein Stability ,Promoter ,DNA ,Protein Structure, Tertiary ,Cell biology ,Cell nucleus ,medicine.anatomical_structure ,Biochemistry ,030220 oncology & carcinogenesis ,Phosphorylation ,Degron ,Dimerization - Abstract
The ETS (E26) protein Elk-1 serves as a paradigm for mitogen-responsive transcription factors. It is multiply phosphorylated by mitogen-activated protein kinases (MAPKs), which it recruits into pre-initiation complexes on target gene promoters. However, events preparatory to Elk-1 phosphorylation are less well understood. Here, we identify two novel, functional elements in Elk-1 that determine its stability and nuclear accumulation. One element corresponds to a dimerization interface in the ETS domain and the second is a cryptic degron adjacent to the serum response factor (SRF)-interaction domain that marks dimerization-defective Elk-1 for rapid degradation by the ubiquitin-proteasome system. Dimerization appears to be crucial for Elk-1 stability only in the cytoplasm, as latent Elk-1 accumulates in the nucleus and interacts dynamically with DNA as a monomer. These findings define a novel role for the ETS domain of Elk-1 and demonstrate that nuclear accumulation of Elk-1 involves conformational flexibility prior to its phosphorylation by MAPKs.
- Published
- 2011
- Full Text
- View/download PDF
13. MPTH-29CONNECTING MUTANT GENOTYPES TO ABERRANT TRANSCRIPTIONAL SIGNATURES ACROSS SERIAL SECTIONS OF A HUMAN TUMOR
- Author
-
Russell O. Pieper, Tali Mazor, Matthew B. Potts, Joseph F. Costello, Michael W. McDermott, Michael C. Oldham, Daniel A. Lim, Samuel J. Shelton, Mitchel S. Berger, Brett Johnson, Eric J. Huang, and Joanna J. Phillips
- Subjects
Genetics ,Cancer Research ,Tumor microenvironment ,Cell type ,IDH1 ,Mutant ,Clone (cell biology) ,RNA ,Biology ,Oncology ,Genotype ,Neurology (clinical) ,Abstracts from the 20th Annual Scientific Meeting of the Society for Neuro-Oncology ,Gene - Abstract
Identifying the transcriptional consequences of mutations that cause tumors may reveal new targets for the development of cancer therapies. However, this task is complicated by the variability that characterizes tumors from different individuals, which arise from unique genetic backgrounds, consist of various cell types in different proportions, and often exhibit clonal heterogeneity. Here we present a novel strategy to connect mutant genotypes to aberrant transcriptional signatures within individual human tumors. This strategy deconstructs a tumor by extracting RNA from serial sections and comparing genome-wide gene coexpression relationships to control samples analyzed in a similar fashion. In parallel, quantitative genomic analysis of the same serial sections enables identification and mapping of clonal populations within the tumor. We apply this strategy to a single grade II human astrocytoma and identify tumor-specific transcriptional signatures. Genomic analysis reveals clonal heterogeneity, including a dominant clone marked by mutations in IDH1 and TP53. Expression patterns of the two largest tumor-specific transcriptional signatures are almost perfectly associated with the spatial distribution of the dominant clone and consist of genes that are activated or repressed within malignant cells and their microenvironment. Our experimental strategy offers an unbiased and personalized method for identifying aberrant transcriptional signatures that are associated with specific mutant genotypes in any solid tumor while preserving the complex cellular milieu of the tumor microenvironment. More generally, this strategy can reveal shared and distinct patterns of transcriptional organization between any pair of tissue samples, thereby facilitating novel comparisons of diverse biological systems in health and disease.
- Published
- 2015
- Full Text
- View/download PDF
14. ANGI-04Olig2 REGULATES Wnt7b EXPRESSION AND VASCULATURE CHARACTERISTICS IN GLIOMA
- Author
-
An-Chi Tien, Giorgio Seano, Tracy J. Yuen, Michael C. Oldham, Manish K. Aghi, Jasmine Lau, Charles D. Stiles, Emmanuelle Huillard, David H. Rowitch, Shwetal Mehta, Jennifer K. Sabo, Tracy T. Batchelor, Anders Persson, Amelie Griveau, William A. Weiss, Samuel J. Shelton, Arman Jahangiri, Rakesh K. Jain, and Joanna J. Phillips
- Subjects
Cancer Research ,Pathology ,medicine.medical_specialty ,Angiogenesis ,Wnt signaling pathway ,Biology ,medicine.disease ,Oligodendrocyte ,OLIG2 ,medicine.anatomical_structure ,WNT7A ,Oncology ,Downregulation and upregulation ,Glioma ,medicine ,Cancer research ,Neurology (clinical) ,Oligodendroglioma ,Abstracts from the 20th Annual Scientific Meeting of the Society for Neuro-Oncology - Abstract
Treatment of malignant gliomas has been a challenge due to their transient response to surgical resection and inhibitors of VEGF signaling. Recurrent tumors become resistant to anti-angiogenesis inhibitors and were proposed to convert to a mode of vessel “co-option” whereby they invade into brain parenchyma along the pre-existing vasculature. The genetic and signaling mechanisms that govern vascular co-option just recently started to be investigated and remain poorly understood. We have recently shown that immature oligodendrocyte precursors (OPCs) regulate angiogenesis in developing white matter through canonical Wnt7 signaling. In this study, we show that mRNA levels of OLIG2 and other OPC signature genes strongly correlate with WNT7B in human gliomas, especially oligodendroglioma. OLIG2+ oligodendroglial cells express high levels of WNT7A/B in close vicinity to vascular endothelial cells that express the Wnt target, LEF1. Furthermore, we demonstrate that Olig2 function regulates OPC-like features, Wnt7a/7b expression/activity and enhanced migration along a pre-existing vasculature in a p53-null murine glioma model. Conversely, Olig2-null tumors showed increased vascular density, VEGF expression and limited migration. We report that p53 acts as a direct repressor of the Wnt7b locus and that Olig2 promotes Wnt7b expression in a p53-mutant context. Intracranial administration of the Wnt inhibitor XAV939 with mouse oligodendroglioma cells significantly affected vessel density and migration of tumor cells. Finally, we observed selective upregulation of Wnt7b expression in a model of VEGF-resistant glioma. These findings indicate that OPC-like cells in glioma promote Wnt7b signaling providing an alternative pathway to VEGF signaling.
- Published
- 2015
- Full Text
- View/download PDF
15. GE-31 * DECONSTRUCTING TUMOR HETEROGENEITY THROUGH DIFFERENTIAL GENE COEXPRESSION ANALYSIS OF SERIAL SECTIONS (DGCASS)
- Author
-
Samuel J. Shelton and Michael C. Oldham
- Subjects
Genetics ,Cancer Research ,Oligoastrocytoma ,Brain tumor ,Computational biology ,Biology ,Amplicon ,medicine.disease ,Transcriptome ,Abstracts ,Oncology ,Glioma ,medicine ,Neurology (clinical) ,Gene ,Exome sequencing ,Epigenomics - Abstract
Gliomas are a common type of brain tumor accounting for ∼80% of malignant brain tumors. Low-grade gliomas have better prognosis than high-grade gliomas but inevitably recur at higher grades, highlighting the need for improved understanding of molecular mechanisms of disease progression. Recent advances in molecular profiling of tumors have raised hopes for the development of targeted therapeutics based on specific genomic, epigenomic, and transcriptomic patterns. However, these efforts are complicated by the highly heterogeneous nature of glioma and the fact that tumor classification can depend on sampling strategy. Therefore, it is important to develop new tools to assess the full extent of tumor heterogeneity in a systematic and unbiased manner. Here we present an approach for deconstructing tumor heterogeneity using common laboratory equipment called Differential Gene Coexpression Analysis of Serial Sections (DGCASS). DGCASS combines a novel sampling strategy of serial cryo-sections with unbiased gene coexpression analysis to reveal patterns of gene activity that are shared or unique within tissue samples. We apply DGCASS to a single grade II oligoastrocytoma and identify groups of genes whose expression patterns are highly correlated within the tumor but not within normal human brain samples. In parallel, we employ a combination of exome sequencing, amplicon deep-sequencing, and droplet-digital PCR to identify and quantify the frequencies of somatic mutations over serial sections of the same tumor sample, revealing the existence of distinct clonal populations within the tumor. We show that specific clonal populations are associated with specific aberrant patterns of gene activity within the tumor. Our results indicate that DGCASS is an effective strategy for identifying the transcriptional consequences of specific mutations (or combinations thereof) within a single tissue sample, and suggest a simple and generalizable approach for deconstructing heterogeneity in other solid tumors.
- Published
- 2014
- Full Text
- View/download PDF
16. PU.1 is a major transcriptional activator of the tumour suppressor gene LIMD1
- Author
-
Samuel J. Shelton, Peter E. Shaw, Tyson V. Sharp, Daniel E. Foxler, Victoria James, and Thomas Q. de Aguiar Vallim
- Subjects
Transcriptional Activation ,Molecular Sequence Data ,Biophysics ,Biology ,LIMD1 ,Biochemistry ,Article ,03 medical and health sciences ,0302 clinical medicine ,Structural Biology ,Transcription (biology) ,Cell Line, Tumor ,Proto-Oncogene Proteins ,microRNA ,Consensus Sequence ,Genetics ,Gene Knockdown Techniques ,Consensus sequence ,Gene silencing ,Animals ,Humans ,Leukaemia ,Genes, Tumor Suppressor ,RNA, Small Interfering ,Promoter Regions, Genetic ,Molecular Biology ,Transcription factor ,030304 developmental biology ,0303 health sciences ,Proto-Oncogene Proteins c-ets ,Activator (genetics) ,PU.1 ,Intracellular Signaling Peptides and Proteins ,MicroRNA ,Cell Biology ,LIM Domain Proteins ,3. Good health ,Hematopoiesis ,Protein Structure, Tertiary ,CpG site ,Mutagenesis ,030220 oncology & carcinogenesis ,Mutation ,Cancer research ,Trans-Activators ,CpG Islands - Abstract
LIMD1 is a tumour suppressor gene (TSG) down regulated in ∼80% of lung cancers with loss also demonstrated in breast and head and neck squamous cell carcinomas. LIMD1 is also a candidate TSG in childhood acute lymphoblastic leukaemia. Mechanistically, LIMD1 interacts with pRB, repressing E2F-driven transcription as well as being a critical component of microRNA-mediated gene silencing. In this study we show a CpG island within the LIMD1 promoter contains a conserved binding motif for the transcription factor PU.1. Mutation of the PU.1 consensus reduced promoter driven transcription by 90%. ChIP and EMSA analysis demonstrated that PU.1 specifically binds to the LIMD1 promoter. siRNA depletion of PU.1 significantly reduced endogenous LIMD1 expression, demonstrating that PU.1 is a major transcriptional activator of LIMD1.
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.