ABSTRACT: We used array-based comparative genomic hybridization (arrayCGH) of 76 hepatocellular carcinomas (HCCs) to search for genetically disrupted genes. Seventy-six HCC clinical specimens were analyzed. Genomic DNA of the tumor sample was labeled with Cy5 and reference normal DNA (Promega) was labeled with Cy3.
<h4>Background & aims</h4>Hepatocellular carcinoma (HCC) is an aggressive malignancy; its mechanisms of development and progression are poorly understood. We used an integrative approach to identify HCC driver genes, defined as genes whose copy numbers associate with gene expression and cancer progression.<h4>Methods</h4>We combined data from high-resolution, array-based comparative genomic hybridization and transcriptome analysis of HCC samples from 76 patients with hepatitis B virus infection ...[more]
Project description:To test the hypothesis that different mechanisms and/or factors might be involved in physiological pigmentary responses of the skin to different types of UV, we used whole human genome microarrays and immunohistochemical analyses to characterize human skin in situ to examine how melanocyte-specific proteins and paracrine melanogenic factors are regulated by repetitive exposure to suberythemal doses of different types of UV (UVA, UVB or SSR). Six volunteers with skin type II-III were irradiated with SSR, UVA or UVB radiation for 2 weeks (5 times per week, 10 times total) after preliminary determination of their MEDs. Biopsies were taken 3 days after the last irradiation.
Project description:Agilent custom designed array comparative genomic hybridization (CGH) was performed on 235 samples with a dual diagnosis of schizophrenia and epilepsy and 80 samples with a dual diagnosis of bipolar and epilpsy. ArrayCGH on 191 psychiatric screened controls was also performed. A common male reference was used for all samples and controls. Samples and controls were obtained from the NIMH cell line repositories. 235 samples with a dual diagnosis of schizophrenia and epilepsy, 80 samples with a dual diagnosis of bipolar and epilepsy, and 191 psychiatric screened controls
Project description:Recent studies of the human transcriptome suggest that many transcripts have short or lack 3' poly(A) ends. In addition, the length of 3' poly(A) ends may vary for some transcript to regulate mRNA translation. Heterogeneous lengths of poly(A) ends may introduce variations in measuring RNA transcripts using current approaches. We hypothesized that affinity purifying Pol II RNAs by their unique 5' m7GpppN cap regardless of their polyadenylation status would add additional information to genomic expression analyses and possibly overcome the variation in signals sometimes observed with analysis of poly(A) selected mRNA. 5' capped and 3' poly(A) RNA were isolated from normal and hepatitis C cirrhotic (HCV) human liver using a high-affinity variant of eIF4E and standard oligo(dT) methods, respectively. Both populations of RNA were analyzed using ENCODE tiling arrays representing 1% of the genome. A total of 64 annotated genes were significantly increased in HCV as compared to normal liver; 27 of these genes were identified by analyzing 5' capped RNA. A total of 31 annotated genes were significantly decreased; 16 of these were identified by analyzing 5' capped RNA. Bioinformatic analysis showed that 5' capped RNA provided a more extensive expression profile of intronic regions and identified Pol II transcriptionally active regions in unannotated regions of the genome that were differentially expressed in normal and disease states. The analysis of 5' capped RNA isolated from biospecimens provides additional gene expression information and identifies novel Pol II transcripts that are differentially expressed. This approach may also be useful in studying of RNAs regulated by 3' polyadenylation or RNA degradation. Four-condition experiment: 5'Cap and 3'Poly(A) isolation in both Normal and HCV Cirrhotic liver. Biological samples: 1 experimental, 1 control. Experimental replicates: 4 of each sample, for a total of 16 samples.
Project description:Histone deacetylase 1 and 2 (HDAC1/2) regulate chromatin structure as the catalytic core of the Sin3A, NuRD and CoREST co-repressor complexes. To better understand the key pathways regulated by HDAC1/2 in the adaptive immune system and inform their exploitation as drug targets, we have generated mice with a T cell specific deletion and performed comparative genomic hybridisation using genomic DNA from HDAC1-/-; HDAC2+/- diseased thymocytes and sample-matched, wild-type tail. A data set from a related transcription-profiling study comparing HDAC1-/-; HDAC2+/- mouse thymus tissue against thymus tissues from wild-type counterparts has also been deposited at ArrayExpress under accession E-MTAB-1432: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1432
Project description:Transcriptional profiling of human peripheral B cell subsets sorted by flow cytometry based on the secretion of IL-10 in response to CpG2006 stimulation. Goal was to identify molecular markers to distinguish IL-10-producing B cells form non-IL-10-producing B cells. Two-condition experiment, non-IL-10-secreting B cells vs. IL-10-secreting B cells. Healthy donors. Biological replicates: 6
Project description:This study aimed to further our understanding of the role that hypermethylatioted in cancer 1 (HIC1) plays in prostate cancer (PCa) development. Microarrays were searched for some genes that had correlated expression with HIC1 mRNA. Our data showed that HIC1 promoter hypermethylation was presented in cell lines, tissues and plasma of PCa patients. According to fold-change screening between restoring expression of HIC1 and its respective control cells, both up-regulated and down-regulated genes were commonly observed in PC3 and C4-2B cells. The restoring expression HIC1 in PCa lines were respectively noted as PC3-HIC1 and C4-2B-HIC1 cells, and the respective controls were noted as C4-2B-GFP and PC3-GFP cells.
Project description:Immunity to Mycobacterium tuberculosis in humans and in mice requires interferon gamma (IFNγ). Wheras IFNγ has been studied extensively for its effects on macrophages in tuberculosis, we determined that protective immunity to tuberculosis also requires IFNγ-responsive non-hematopoietic cells. Bone marrow chimeric mice with IFNγ-unresponsive lung epithelial and endothelial cells exhibited earlier mortality and higher bacterial burdens than control mice, under-expressed indoleamine-2,3-dioxygenase (Ido1) in lung endothelium and epithelium and over-expressed interleukin-17 (IL-17) with massive neutrophilic inflammation in the lungs. We also found that the products of IDO catabolism of tryptophan selectively inhibit IL-17 production by Th17 cells, by inhibiting the action of IL-23. These results reveal a previously-unsuspected role for IFNγ responsiveness in non-hematopoietic cells in regulation of immunity to M. tuberculosis, and reveal a mechanism for IDO inhibition of Th17 cell responses. Bone marrow chimera were created by γ-irradiation (10 Gy) of recipient mice, Ifngr+/+ (W) or Ifngr-/- (K), and reconstitution by i.v. injection of Ifngr+/+ (W) bone marrow cells. After 6 weeks, the two groups of chimera W→W and W→K were infected via the aerosol route with 100 colony forming units of Mycobacterium tuberculosis strain H37Rv. At 63 days post-infection, 4 W→W mice and 4 W→K mice were euthanized, their lung left lobe removed and processed for total RNA isolation and microarray. The 4 samples from the W→W mice were pooled together and used as control sample whereas the 4 samples from the W→K mice were pooled together and used as experimental sample. The same harvest and sample processing was conducted on day 97 after infection, using 5 W→W mice and 6 W→K mice.