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Integrated molecular analysis reveals complex interactions between genomic and epigenomic alterations in esophageal adenocarcinomas.
Peng D, Guo Y, Chen H, Zhao S, Washington K, Hu T, Shyr Y, El-Rifai W
(2017) Sci Rep 7: 40729
MeSH Terms: Adenocarcinoma, Cell Line, Tumor, Comparative Genomic Hybridization, Computational Biology, DNA Copy Number Variations, DNA Methylation, Epigenesis, Genetic, Epigenomics, Esophageal Neoplasms, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Gene Ontology, Gene Regulatory Networks, Genomics, Humans
Show Abstract · Added April 18, 2017
The incidence of esophageal adenocarcinoma (EAC) is rapidly rising in the United States and Western countries. In this study, we carried out an integrative molecular analysis to identify interactions between genomic and epigenomic alterations in regulating gene expression networks in EAC. We detected significant alterations in DNA copy numbers (CN), gene expression levels, and DNA methylation profiles. The integrative analysis demonstrated that altered expression of 1,755 genes was associated with changes in CN or methylation. We found that expression alterations in 84 genes were associated with changes in both CN and methylation. These data suggest a strong interaction between genetic and epigenetic events to modulate gene expression in EAC. Of note, bioinformatics analysis detected a prominent K-RAS signature and predicted activation of several important transcription factor networks, including β-catenin, MYB, TWIST1, SOX7, GATA3 and GATA6. Notably, we detected hypomethylation and overexpression of several pro-inflammatory genes such as COX2, IL8 and IL23R, suggesting an important role of epigenetic regulation of these genes in the inflammatory cascade associated with EAC. In summary, this integrative analysis demonstrates a complex interaction between genetic and epigenetic mechanisms providing several novel insights for our understanding of molecular events in EAC.
0 Communities
1 Members
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15 MeSH Terms
Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control.
Guo Y, Sheng Q, Samuels DC, Lehmann B, Bauer JA, Pietenpol J, Shyr Y
(2013) Biomed Res Int 2013: 915636
MeSH Terms: Algorithms, Breast Neoplasms, Cell Line, Tumor, Comparative Genomic Hybridization, DNA Copy Number Variations, Exome, Female, Genome, Human, Humans
Show Abstract · Added December 12, 2013
Exome sequencing using next-generation sequencing technologies is a cost-efficient approach to selectively sequencing coding regions of the human genome for detection of disease variants. One of the lesser known yet important applications of exome sequencing data is to identify copy number variation (CNV). There have been many exome CNV tools developed over the last few years, but the performance and accuracy of these programs have not been thoroughly evaluated. In this study, we systematically compared four popular exome CNV tools (CoNIFER, cn.MOPS, exomeCopy, and ExomeDepth) and evaluated their effectiveness against array comparative genome hybridization (array CGH) platforms. We found that exome CNV tools are capable of identifying CNVs, but they can have problems such as high false positives, low sensitivity, and duplication bias when compared to array CGH platforms. While exome CNV tools do serve their purpose for data mining, careful evaluation and additional validation is highly recommended. Based on all these results, we recommend CoNIFER and cn.MOPs for nonpaired exome CNV detection over the other two tools due to a low false-positive rate, although none of the four exome CNV tools performed at an outstanding level when compared to array CGH.
1 Communities
5 Members
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9 MeSH Terms
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment.
Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ
(2011) Mol Cell 44: 17-28
MeSH Terms: Adult, Binding Sites, Cell Differentiation, Cell Lineage, Comparative Genomic Hybridization, DNA Methylation, Epigenesis, Genetic, Female, Gene Expression Regulation, Genome, Human, Hematopoietic Stem Cells, Hematopoietic System, Humans, Models, Biological, Promoter Regions, Genetic
Show Abstract · Added February 15, 2016
DNA methylation has been implicated as an epigenetic component of mechanisms that stabilize cell-fate decisions. Here, we have characterized the methylomes of human female hematopoietic stem/progenitor cells (HSPCs) and mature cells from the myeloid and lymphoid lineages. Hypomethylated regions (HMRs) associated with lineage-specific genes were often methylated in the opposing lineage. In HSPCs, these sites tended to show intermediate, complex patterns that resolve to uniformity upon differentiation, by increased or decreased methylation. Promoter HMRs shared across diverse cell types typically display a constitutive core that expands and contracts in a lineage-specific manner to fine-tune the expression of associated genes. Many newly identified intergenic HMRs, both constitutive and lineage specific, were enriched for factor binding sites with an implied role in genome organization and regulation of gene expression, respectively. Overall, our studies represent an important reference data set and provide insights into directional changes in DNA methylation as cells adopt terminal fates.
Copyright © 2011 Elsevier Inc. All rights reserved.
0 Communities
1 Members
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15 MeSH Terms
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE.
Celestino-Soper PB, Shaw CA, Sanders SJ, Li J, Murtha MT, Ercan-Sencicek AG, Davis L, Thomson S, Gambin T, Chinault AC, Ou Z, German JR, Milosavljevic A, Sutcliffe JS, Cook EH, Stankiewicz P, State MW, Beaudet AL
(2011) Hum Mol Genet 20: 4360-70
MeSH Terms: Autistic Disorder, Comparative Genomic Hybridization, DNA Copy Number Variations, Exons, Female, Humans, Male, Mixed Function Oxygenases
Show Abstract · Added February 20, 2014
Autism is a neurodevelopmental disorder with increasing evidence of heterogeneous genetic etiology including de novo and inherited copy number variants (CNVs). We performed array comparative genomic hybridization using a custom Agilent 1 M oligonucleotide array intended to cover 197 332 unique exons in RefSeq genes; 98% were covered by at least one probe and 95% were covered by three or more probes with the focus on detecting relatively small CNVs that would implicate a single protein-coding gene. The study group included 99 trios from the Simons Simplex Collection. The analysis identified and validated 55 potentially pathogenic CNVs, categorized as de novo autosomal heterozygous, inherited homozygous autosomal, complex autosomal and hemizygous deletions on the X chromosome of probands. Twenty percent (11 of 55) of these CNV calls were rare when compared with the Database of Genomic Variants. Thirty-six percent (20 of 55) of the CNVs were also detected in the same samples in an independent analysis using the 1 M Illumina single-nucleotide polymorphism array. Findings of note included a common and sometimes homozygous 61 bp exonic deletion in SLC38A10, three CNVs found in lymphoblast-derived DNA but not present in whole-blood derived DNA and, most importantly, in a male proband, an exonic deletion of the TMLHE (trimethyllysine hydroxylase epsilon) that encodes the first enzyme in the biosynthesis of carnitine. Data for CNVs present in lymphoblasts but absent in fresh blood DNA suggest that these represent clonal outgrowth of individual B cells with pre-existing somatic mutations rather than artifacts arising in cell culture. GEO accession number GSE23765 (http://www.ncbi.nlm.nih.gov/geo/, date last accessed on 30 August 2011). Genboree accession: http://genboree.org/java-bin/gbrowser.jsp?refSeqId=1868&entryPointId=chr17&from=53496072&to=53694382&isPublic=yes, date last accessed on 30 August 2011.
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1 Members
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8 MeSH Terms
Nevus versus melanoma: to FISH, or not to FISH.
Song J, Mooi WJ, Petronic-Rosic V, Shea CR, Stricker T, Krausz T
(2011) Adv Anat Pathol 18: 229-34
MeSH Terms: Comparative Genomic Hybridization, Humans, In Situ Hybridization, Fluorescence, Melanoma, Nevus, Pigmented, Sensitivity and Specificity
Show Abstract · Added March 28, 2014
Fluorescence in-situ hybridization (FISH) has arisen as a novel ancillary test for the pathological diagnosis of melanoma. It is an outgrowth of studies using comparative genomic hybridization, a technique capable of surveying the entire genome for DNA copy number changes. An original report published in 2009 showed high sensitivity (87%) and specificity (95%) for diagnosing melanoma, using a combination of 4 FISH probes that target 6p25 (RREB1), 6q23 (MYB), 11q13 (CCND1), and chromosome 6 centromere. Since then, a number of studies have been published, supporting the high accuracy of FISH for diagnosing melanoma. In addition, various clinicopathological settings where FISH may be particularly useful are explored. FISH tests for melanoma are now commercially available. Meanwhile, questions have been raised by some about the true diagnostic value of FISH, particularly in melanocytic lesions with ambiguous histopathology. This review will briefly introduce the historical development of FISH for melanoma diagnosis and discuss its diagnostic value as well as its potential limitations at present.
0 Communities
1 Members
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6 MeSH Terms
Molecular profiling of cancer--the future of personalized cancer medicine: a primer on cancer biology and the tools necessary to bring molecular testing to the clinic.
Stricker T, Catenacci DV, Seiwert TY
(2011) Semin Oncol 38: 173-85
MeSH Terms: Chromosome Aberrations, Clinical Trials as Topic, Comparative Genomic Hybridization, DNA Methylation, DNA Repair, Gene Fusion, Humans, Mutation, Neoplasms, Oncogenes, Precision Medicine, Systems Biology
Show Abstract · Added March 28, 2014
Cancers arise as a result of an accumulation of genetic aberrations that are either acquired or inborn. Virtually every cancer has its unique set of molecular changes. Technologies have been developed to study cancers and derive molecular characteristics that increasingly have implications for clinical care. Indeed, the identification of key genetic aberrations (molecular drivers) may ultimately translate into dramatic benefit for patients through the development of highly targeted therapies. With the increasing availability of newer, more powerful, and cheaper technologies such as multiplex mutational screening, next generation sequencing, array-based approaches that can determine gene copy numbers, methylation, expression, and others, as well as more sophisticated interpretation of high-throughput molecular information using bioinformatics tools like signatures and predictive algorithms, cancers will routinely be characterized in the near future. This review examines the background information and technologies that clinicians and physician-scientists will need to interpret in order to develop better, personalized treatment strategies.
Copyright © 2011 Elsevier Inc. All rights reserved.
0 Communities
1 Members
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12 MeSH Terms
Copy number variations and clinical outcome in atypical spitz tumors.
Raskin L, Ludgate M, Iyer RK, Ackley TE, Bradford CR, Johnson TM, Fullen DR
(2011) Am J Surg Pathol 35: 243-52
MeSH Terms: Adolescent, Adult, Aged, Child, Child, Preschool, Chromosome Aberrations, Comparative Genomic Hybridization, DNA, Neoplasm, Female, Gene Dosage, Humans, In Situ Hybridization, Fluorescence, Male, Melanoma, Middle Aged, Nevus, Epithelioid and Spindle Cell, Skin Neoplasms, Young Adult
Show Abstract · Added March 5, 2014
Atypical Spitz tumors (ASTs) are rare spitzoid neoplasms of uncertain biological behavior. Our study was designed to characterize genetic abnormalities that may help to differentiate ASTs from melanoma or Spitz nevi. We examined copy number variation in formalin-fixed, paraffin-embedded samples using an Agilent 44k array comparative genomic hybridization platform. Sixteen patients with AST (8 with positive sentinel lymph node biopsy, 1 with distant metastasis), 8 patients with Spitz nevi, and 3 patients with melanoma (2 spitzoid, 1 superficial spreading) were evaluated. Chromosomal aberrations were found in 7 of 16 ASTs, 1 with fatal outcome, 2 spitzoid melanomas, and 1 conventional melanoma. We found no difference in chromosomal instability between AST patients with positive and negative sentinel lymph node biopsies. Our patient with widely metastatic AST lacked the most frequent aberrations in melanoma involving chromosomes 6 and 11q that are loci targeted by fluorescence in situ hybridization (FISH) probes developed to distinguish malignant melanoma from benign melanocytic lesions. The vast majority of chromosomal abnormalities observed in ASTs are not commonly found in melanomas, suggesting that AST may be a distinct clinical entity and raising additional questions regarding their malignant potential, prognosis, and clinical management. The current FISH probes failed to detect 1 spitzoid melanoma, 1 fatal metastatic AST case, and the other chromosomally aberrant ASTs in our series, but detected 1 spitzoid melanoma and 1 conventional melanoma. Thus, a comprehensive, genome-wide approach to chromosomal abnormalities offered greater sensitivity and specificity than current FISH probes in identifying spitzoid lesions of uncertain malignant potential in this series.
0 Communities
1 Members
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18 MeSH Terms
Developmental control of the DNA replication and transcription programs.
Nordman J, Li S, Eng T, Macalpine D, Orr-Weaver TL
(2011) Genome Res 21: 175-81
MeSH Terms: Animals, Comparative Genomic Hybridization, DNA Replication, DNA-Binding Proteins, Drosophila Proteins, Drosophila melanogaster, Gene Expression Profiling, Gene Expression Regulation, Developmental, Male, Molecular Sequence Data, Mutation, Ploidies
Show Abstract · Added March 3, 2020
Polyploid or polytene cells, which have more than 2C DNA content, are widespread throughout nature and present in most differentiated Drosophila tissues. These cells also can display differential replication, that is, genomic regions of increased or decreased DNA copy number relative to overall genomic ploidy. How frequently differential replication is used as a developmental strategy remains unclear. Here, we use genome-wide array-based comparative genomic hybridization (aCGH) to profile differential DNA replication in isolated and purified larval fat body and midgut tissues of Drosophila, and we compare them with recent aCGH profiles of the larval salivary gland. We identify sites of euchromatic underreplication that are common to all three tissues and others that are tissue specific. We demonstrate that both common and tissue-specific underreplicated sites are dependent on the Suppressor of Underreplication protein, SUUR. mRNA-seq profiling shows that whereas underreplicated regions are generally transcriptionally silent in the larval midgut and salivary gland, transcriptional silencing and underreplication have been uncoupled in the larval fat body. In addition to revealing the prevalence of differential replication, our results show that transcriptional silencing and underreplication can be mechanistically uncoupled.
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1 Members
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MeSH Terms
DNA copy number aberrations in small-cell lung cancer reveal activation of the focal adhesion pathway.
Ocak S, Yamashita H, Udyavar AR, Miller AN, Gonzalez AL, Zou Y, Jiang A, Yi Y, Shyr Y, Estrada L, Quaranta V, Massion PP
(2010) Oncogene 29: 6331-42
MeSH Terms: Carcinoma, Small Cell, Cell Adhesion, Cell Line, Tumor, Comparative Genomic Hybridization, Focal Adhesion Protein-Tyrosine Kinases, Focal Adhesions, Gene Dosage, Humans, Lung Neoplasms, Quinolones, Sulfones
Show Abstract · Added February 27, 2013
Small-cell lung cancer (SCLC) is the most aggressive subtype of lung cancer in its clinical behavior, with a 5-year overall survival as low as 5%. Despite years of research in the field, molecular determinants of SCLC behavior are still poorly understood, and this deficiency has translated into an absence of specific diagnostics and targeted therapeutics. We hypothesized that tumor DNA copy number alterations would allow the identification of molecular pathways involved in SCLC progression. Array comparative genomic hybridization was performed on DNA extracted from 46 formalin-fixed paraffin-embedded SCLC tissue specimens. Genomic profiling of tumor and sex-matched control DNA allowed the identification of 70 regions of copy number gain and 55 regions of copy number loss. Using molecular pathway analysis, we found a strong enrichment in these regions of copy number alterations for 11 genes associated with the focal adhesion pathway. We verified these findings at the genomic, gene expression and protein level. Focal Adhesion Kinase (FAK), one of the central genes represented in this pathway, was commonly expressed in SCLC tumors and constitutively phosphorylated in SCLC cell lines. Those were poorly adherent to most substrates but not to laminin-322. Inhibition of FAK phosphorylation at Tyr(397) by a small-molecule inhibitor, PF-573,228, induced a dose-dependent decrease of adhesion and an increase of spreading in SCLC cell lines on laminin-322. Cells that tended to spread also showed a decrease in focal adhesions, as demonstrated by a decreased vinculin expression. These results support the concept that pathway analysis of genes in regions of copy number alterations may uncover molecular mechanisms of disease progression and demonstrate a new role of FAK and associated adhesion pathways in SCLC. Further investigations of FAK at the functional level may lead to a better understanding of SCLC progression and may have therapeutic implications.
2 Communities
6 Members
0 Resources
11 MeSH Terms
Co-occurrence of Langerhans cell histiocytosis and Rosai-Dorfman disease: possible relationship of two histiocytic disorders in rare cases.
O'Malley DP, Duong A, Barry TS, Chen S, Hibbard MK, Ferry JA, Hasserjian RP, Thompson MA, Richardson MS, Jaffe R, Sidhu JS, Banks PM
(2010) Mod Pathol 23: 1616-23
MeSH Terms: Adult, Child, Preschool, Comparative Genomic Hybridization, Female, Histiocytosis, Langerhans-Cell, Histiocytosis, Sinus, Humans, Immunohistochemistry, Infant, Male, Middle Aged
Show Abstract · Added June 26, 2014
Rosai-Dorfman disease and Langerhans cell histiocytosis are both disorders of accessory immune cells. Two cases have been previously reported of concurrent Langerhans cell histiocytosis and Rosai-Dorfman disease. In this report, we characterize the findings and selected molecular studies in nine additional cases. Histology was reviewed. Immunohistochemical stains were performed on all cases in which slides or blocks were available. A combination of CD1a, S-100, CD3, CD20, langerin, CD68, CD163, CD21, CD35 and CD123 immunohistochemical stains were performed. High-resolution array comparative genomic hybridization was performed on six samples from five cases. In these cases, seven were female and two male, with an average age of 25 years (15 months-59 years). A majority of the cases were identified in lymph node. Areas of Langerhans cell histiocytosis had a typical appearance with the existence of bland 'coffee-bean' nuclei, clear cytoplasm and associated eosinophils. The immunophenotype was typical, including expression of CD1a, S100, CD68 and langerin. In areas of Rosai-Dorfman disease, there was emperipolesis seen in all cases. Cells were intermediate-large in size with large round nuclei and ample clear or pale cytoplasm. The lesional cells were positive for S100, CD68, CD163, without expression of langerin or CD1a. Array comparative genomic hybridization showed gains and/or losses in four of the six samples. One case showed no gains or losses and one additional case showed gains and losses in the Langerhans cell histiocytosis, while no abnormalities were discovered in the Rosai-Dorfman disease component. These findings are comparable to those seen in previous studies of Langerhans cell histiocytosis. We report the clinical and pathologic findings of the combination of Langerhans cell histiocytosis and Rosai-Dorfman disease. Furthermore, we suggest on the basis of evidence from our cases that, when simultaneous, the two entities may be pathophysiologically related.
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11 MeSH Terms