scholarly journals High-Density Gene Expression Analysis of Tumor-Associated Macrophages from Mouse Mammary Tumors

2009 ◽  
Vol 174 (3) ◽  
pp. 1048-1064 ◽  
Author(s):  
Laureen S. Ojalvo ◽  
William King ◽  
Dianne Cox ◽  
Jeffrey W. Pollard
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Mammary Tumors ◽  
High Density ◽  
Tumor Associated Macrophages ◽  
Mouse Mammary Tumors

High Resolution Epigenomic Mapping of Myelodysplastic Syndrome Reveals a High Level of Functionally Important Methylation.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2637-2637
Author(s):  
Li Zhou ◽  
Joanna Opalinska ◽  
Davendra Sohal ◽  
Simrit Parmar ◽  
Perry Pahanish ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Cpg Island ◽  
High Density ◽  
High Rate ◽  
Comparative Genomic ◽  
Differentially Methylated Genes ◽  
High Level ◽  
Very High

Abstract The myelodysplastic syndromes (MDS) are collections of heterogeneous hematologic diseases characterized by clonal hematopoietic defects. Even though gene expression studies have tried to differentiate between prognostic subgroups, there are concerns with standardization and validity of these studies. Decitabine and 5-azacytidine have shown activity in MDS, but it is unclear if hypomethylation can explain their efficacy. To address these issues we have developed a novel platform that uses a combination of gene expression analysis, high density array based comparative genomic hybridization (aCGH) and genome wide methylation analysis to perform an integrated high throughput epigenomic analysis of MDS. Using this approach, we conducted a pilot study in 5 patients with MDS. Gene expression analysis was performed using 37K oligo maskless arrays and high density aCGH was performed at 6Kb resolution using the Nimblegen platform. Whole genome methylation was analyzed by a recently described novel method ( Khulan et al, Genome Res. 2006 Aug;16(8)) that uses differential methylation specific digestion by HpaII and MspI followed by pcr amplification, two color labeling and hybridization to quantitatively determine individual promoter CpG island methylation. aCGH revealed a very high number of deletions (range 515–2722, mean 1073±937) and amplifications (range 614–1247, mean 843±254) not visualized by conventional cytogenetic analysis. These were also seen on peripheral blood mononuclear cells and correlated with those seen in the bone marrow. 22 common regions were found to amplified and 15 regions commonly deleted in 80% of the samples and contained genes involved in transcription and signaling. A custom human oligo array was used to determine methylation by calculating HpaII/MspI cut fragment intensity ratio. MDS samples demonstrated a very high level of methylation (range 70–84%). Expression was found to be significantly decreased for the genes that were methylated (p<.0001, T test) demonstrating the functional relevance of this assay. Analysis of common differentially methylated genes (when compared to normal samples) and their validation are ongoing. Micro deletions and amplifications seen on aCGH did not correlate with changes in global expression of the involved genes. Interestingly, large deletions (-7q) and large amplifications (+1p) correlated significantly with corresponding changes in gene expression when compared to the rest of the chromosome. (p<.0001, Anova) Integration of methylation data with aCGH data increased the predictive value of corresponding changes in gene expression. This result demonstrates that loss of heterozygosity coupled with the methylation of the remaining allele may result in pathogenic gene silencing in MDS. The high rate of methylation and DNA copy number alterations demonstrated in MDS in our study suggest that this integrated approach mightl be useful to define prognostic subgroups in future studies and aid in gene discovery.

scholarly journals Microscale Gene Expression Analysis of Tumor-Associated Macrophages

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Kuldeep S. Attri ◽  
Kamiya Mehla ◽  
Surendra K. Shukla ◽  
Pankaj K. Singh
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Tumor Associated Macrophages

GENE EXPRESSION ANALYSIS IN HUMAN RENAL ALLOGRAFT BIOPSY SAMPLES USING HIGH-DENSITY OLIGOARRAY TECHNOLOGY1

2001 ◽  
Vol 72 (5) ◽  
pp. 948-953 ◽  
Author(s):  
Enver Akalin ◽  
Rose C. Hendrix ◽  
Rathna Giri Polavarapu ◽  
Thomas C. Pearson ◽  
John F. Neylan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Renal Allograft ◽  
High Density ◽  
Allograft Biopsy

A High Resolution Epigenomic Map of Myelofibrosis Reveals Multiple Chromosomal Deletions and Amplifications Accompanied by a High Level of Functionally Important Methylation.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2684-2684 ◽  
Author(s):  
Joanna Opalinska ◽  
Davendra Sohal ◽  
Simrit Parmar ◽  
Li Zhou ◽  
Andrew Yeatts ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Copy Number ◽  
Gene Expression Analysis ◽  
T Test ◽  
High Density ◽  
Comparative Genomic ◽  
Differentially Methylated Genes ◽  
High Level ◽  
Very High

Abstract Chronic idiopathic myelofibrosis (MF) is a clonal hematopoietic disorder that leads to progressive marrow fibrosis and peripheral cytopenias. Very little is known about the role of chromosomal alterations and DNA methylation in the pathobiology of this disease. We used a combination of gene expression analysis, high density array based comparative genomic hybridization (aCGH) and genome wide methylation analysis to perform an integrated genomic analysis of MF. Gene expression analysis was performed using 37K oligo maskless arrays and high density aCGH was performed at 6Kb resolution using Nimblegen platform. Whole genome methylation was analyzed by a recently described novel method ( Khulan et al, Genome Res. 2006 Aug;16(8)) that uses differential methylation specific digestion by HpaII and MspI followed by pcr amplification, two color labeling and hybridization to quantitatively determine individual promoter CpG island methylation. aCGH revealed a very high number of microdeletions (range 622–1148, mean ± SD 555±144 ) and amplifications (range 463–770, mean ± SD 781±246) in a pilot study conducted in 4 patients with MF. Twenty three common regions were found to amplified in all patients which included regions of chr3p25, chr8p21, chr12q24, chr14q32, chr17p13 and chr17q12, which code for a novel set of genes including B-cell CLL/lymphoma 7A, GTPase activating Rap, BRF1 and others. Five regions were found to be commonly deleted in all samples (chr1q31, chr5q12, chr20p13, chrXq21, chrXq28). Thirty eight DNA segments were found to be deleted and 142 amplified in 75% of the samples. Several potential pathogenic genes encoding for transcription factors, cytokines and cytokine receptors were found to be coded by these segments. A custom human oligo array was used to determine methylation by calculating HpaII/MspI cut fragment intensity ratio. All patient samples had a very high level of methylation (range 64–82%, mean 72% ± 8.6%). Expression was found to be significantly decreased for the genes that were methylated (p<.0001, T test) demonstrating the functional relevance of this assay. Analysis of common differentially methylated genes (when compared to normal samples) and their validation are ongoing. Microdeletions and amplifications seen on aCGH did not correlate with changes in global expression of the involved genes. Interestingly, when data from all platforms were combined, methylation of the genes with altered copy number led to significant decreases in gene expression (p=.03, T test). This result suggests pathogenic changes in gene expression in MF result from an interplay between DNA copy number alterations and methylation of the remaining alleles. The high rate of methylation demonstrated in MF suggests that epigenetic silencing of genes may play an important role in pathogenesis and points to the potential utility of hypomethylating agents in this disease.

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