Histone acetylation and DNA demethylation of T cells result in an anaplastic large cell lymphoma-like phenotype

Abstract

© F e r r a t a S t o r t i F o u n d a t i o ncell characteristic genes. 13 Interestingly, we demonstrated that B-cell characteristic genes such as CD19 and CD79a as well as the B-cell transcription factor PAX5 have additional suppressive trimethylation of histone H3 lysine 27 (H3K27) in cHL which is absent in B cells. 12 Here we show that DNA demethylation and histone acetylation of T-cell lines induced an ALCL-like phenotype, whereas the same treatment of ALCL cells did not restore the expression of T-cell genes and did not switch off the ALCL-associated genes. Furthermore, we demonstrate that the promoters of important T-cell transcription factor genes (GATA3, TCF1 and LEF1) 14 were silenced by H3K27 trimethylation, a finding in harmony with their absence in primary ALCL tissue specimens. Design and Methods Cell cultures)] and four T-cell lymphoma/leukemia cell lines (CCRF-CEM, Jurkat, MOLT-3 and MOLT-4) were employed in this study. The latter four cell lines are designated as "T-cell lines" throughout the manuscript given their immunophenotype of mature T cells and because of their rearranged TCR genes (data not shown). All cell lines were cultured in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum at 37°C and 5% CO 2 . Combined 5-aza-2'-deoxycytidine/trichostatin A treatmentThe four ALCL-derived cell lines and four T-cell lines were treated with 5-aza-2'-deoxycytidine (5-aza-dC) (Sigma-Aldrich, St Louis, MO, USA) at a concentration of 1 μM for 6 days. 5-aza-dC and medium were replaced on days 2 and 5. On day 5 cells were additionally incubated for 24 h with 625 nM trichostatin A (TSA) (Sigma-Aldrich). Cells were harvested on day 6. 11 RNA isolation and microarray analysisFor both microarray analysis and real-time reverse transcriptase polymerase chain reaction (RT-PCR) analysis, total RNA was isolated from untreated and 5-aza-dC/TSA-treated cells using the RNeasy Midi Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. For real-time RT-PCR, total RNA was additionally treated with DNase for 20 min at room temperature. The quality of the RNA was controlled using the Bioanalyzer (Agilent, Santa Clara, CA, USA) and exclusively high quality RNA (RIN≥8) was used for further analysis. Affymetrix GeneChip hybridization (HG-U133A) was performed with 5 μg total RNA according to the manufacturer's recommendations. CEL files of all experiments were generated with the GCOS 1.3 software (Affymetrix) and are available via the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/geo) under accession number GSE26101. Microarray data analysisAnalysis of the microarray data was performed using R and Bioconductor. All arrays were normalized using robust multichip average. 15,16 A moderated t-test was used for statistical evaluation. Probe sets were defined as differentially expressed if they had a fold change of at least 2 and a Benjamini-Hochberg (BH) corrected P-value less than 0.05 (after the moderated t-test)....

Gene alterations in epigenetic modifiers and JAK-STAT signaling are frequent in breast implant-associated ALCL.

“…specified; and extranodal natural killer/T-cell lymphoma. 15,30,31,[36][37][38][39][40] These latter malignancies, however, harbor mutations of the TET2, IDH2, DNMT3, and SETD2 genes, which were either absent or uncommon in our series (see supplemental Figure 7 and supplemental Table 4).…”

Prevalence and Clinical Significance of Supine-Dependent Obstructive Sleep Apnea in Patients Using Oral Appliance Therapy

“…[5][6][7][8] Therefore, it could be of clinical importance to split up the total AHI according to sleep position with the supine AHI (defi ned as the number of apneas and hypopneas per hour of sleep spent in supine position) and the non-supine AHI (defi ned as the number of apneas and hypopneas per hour of sleep spent in the non-supine position). 9 The most frequently and widely used defi nition is a supine AHI ≥ twice as high as the non-supine AHI and was fi rst described by Cartwright et al 5 The prevalence of sdOSA in a general population ranges the literature from 46% to 80%, which was comparable to the prevalence of sdOSA in the general population. 13,16,17 These results, however, do not reveal the evolution of sdOSA once OA m has started, and the prevalence of sdOSA under OA m therapy is still unknown.…”

“…9 The most frequently and widely used defi nition is a supine AHI ≥ twice as high as the non-supine AHI and was fi rst described by Cartwright et al 5 The prevalence of sdOSA in a general population ranges …”

OmixAnalyzer – A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets

“…Sample correspondence over experiments permits even more suffisticated options, such as miRNA to mRNA mapping by target as well as their correlation. The successful use of the OmixAnalyzer manifests in at least two publications [7,14] accrued in the framework of the TRR54.…”

“…For instance, to study complex phenotypes such as cancer [6] and other genetic diseases [1], researchers analyze cellular samples at various levels, such as gene expression, protein expression, epigenetic status of regulatory elements in the genome, presence of differentially spliced protein isoforms, levels of metabolites etc. Managing and analyzing such diverse and heterogeneous data sets is a significant challenge; therein, analysis cannot stop at individual data sets, but needs to intelligently combine data generated by different methods [13].…”