Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging

Abstract Abstract 3730 Poster Board III-666 Background Histone deacetylase (HDAC) inhibition has emerged as a promising therapeutic approach in malignancies. HDAC inhibition has proved to be a particularly effective option in patients with lymphoma. The HDAC inhibitor vorinostat is approved for the treatment of patients with cutaneous T-cell lymphomas and is being tested in patients with B cell lymphomas. More recently, a number of other HDAC inhibitors have entered preclinical and clinical testing. The mechanisms through which HDAC inhibitors exert their downstream effects are currently unknown. As the number of HDAC inhibitors in development increases, it is unclear if they share a class effect or display unique mechanisms of action. Recently, LBH589 has been described as an orally available, highly potent inhibitor of HDAC. We decided to explore whether LBH589 would be an effective therapeutic option for patients with lymphoma. Methods and Results In order to evaluate whether LBH was efficacious and potent in B cell lymphomas, we tested both vorinostat and LBH589 in the same cell line(s). We found that LBH589 was over 10 times more potent than vorinostat (mean IC50 7.4nM versus 830nM). We decided to further test LBH589 in an expanded panel of 18 cell lines derived from 5 different lymphoid malignancies: Burkitt lymphoma, mantle cell lymphoma, Hodgkin lymphoma, multiple myeloma and diffuse large B cell lymphoma. LBH589 was found to be lethal in each of these cell lines at IC50 concentrations varying from 5.6-31.5 nM (mean 11.2nM), suggesting that this drug may be effective at physiologically achievable concentrations. Based on the IC50 cut-off of 10nM, we assigned the treated cell lines to 2 groups: highly sensitive (IC50 < 10nM, N=11) and less sensitive (IC50> 10nM, N=8). We performed gene expression profiling on 12 of these cell lines and compared the gene expression profiles of the highly sensitive versus less sensitive cell lines. Further, we performed time course experiments in which we evaluated the effects of LBH589 at its IC50 on cell lines at 6 and 12 hours post-treatment. Gene expression profiling was performed on the treated cells at each time point. We also engineered resistant cell lines by incremental dose escalation over a period of months to a concentration greater than or equal to the IC50. The resistant cell lines were also profiled for gene expression and compared to the wild type cell lines. The gene expression profiles of LBH589 treated cells at 6 and 12 hours demonstrated a clear and progressive down regulation of genes associated with the NF-KB pathway (Figure 1). Furthermore, cell lines with high expression of genes in the NF-KB pathway were uniformly highly sensitive to LBH589 with IC50<10nM in all cases. Conclusion NF-KB activation is a common feature of many different lymphoma types. Our data suggest that HDAC inhibition using LBH589 could provide a potent method for treating lymphomas and that HDAC inhibitors may exert their effects through the down-regulation of the NF-KB pathway. Our data also suggest a rationale for dual inhibition of HDAC and NF-KB in the treatment of lymphoma. Disclosures: Rizzieri: Merck & Co., Inc.: Consultancy.

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Age-associated different transcriptome profiling in zebrafish and rat: insight into diversity of vertebrate aging

10.1101/478438 ◽

2018 ◽

Author(s):

Yusuke Kijima ◽

Wang Wantong ◽

Yoji Igarashi ◽

Kazutoshi Yoshitake ◽

Shuichi Asakawa ◽

...

Keyword(s):

Gene Expression ◽

Muscle Development ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Model Organisms ◽

Human Beings ◽

Rna Seq ◽

Down Regulation ◽

Circadian Genes ◽

Age Related

AbstractBackgroundAging and death are inevitable for most species and are of intense interest for human beings. Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish provide attractive models because of their unique aging characteristics. First, the lifespan of fish is highly varied and some long-lived fish can live for over 200 years. Second, some fish show anti-aging features and indeterminate growth throughout their life. Because these characteristics are not found in mammalian model organisms, exploring mechanisms of senescence in fish is expected to provide new insights into vertebrate aging. Therefore, we conducted transcriptome analysis for brain, gill, heart, liver and muscle from 2-month-, 7-month-, 16month- and 39-month-old zebrafish. In addition, we downloaded RNA-seq data for sequential age related gene expression in brain, heart, liver and muscle of rat (1). These RNA-seq data from two species were compared, and common and species-specific features of senescence were analyzed.ResultsScreening of differentially expressed genes (DEGs) in all zebrafish tissues examined revealed up-regulation of circadian genes and down-regulation of hmgb3a. Comparative analysis of DEG profiles associated with aging between zebrafish and rat showed both conserved and clearly different aging phenomena. Furthermore, up-regulation of circadian genes with aging and down-regulation of collagen genes were observed in both species. On the other hand, in zebrafish, up-regulation of autophagy related genes in muscle and atf3 in various tissues suggested fish-specific anti- aging characteristics. Consistent with our knowledge of mammalian aging, a tissue deterioration-related DEG profile was observed in rat. We also detected aging-associated down-regulation of muscle development and ATP metabolism-related genes in zebrafish gill. Correspondingly, hypoxia-related genes were systemically up-regulated in aged zebrafish, suggesting age-related hypoxia as a senescence modulator in fish.ConclusionsOur results indicate both common and different aging profiles between fish and mammals. Gene expression profiles specific to fish will provide new insight for future translational research.

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Using 2D Principal Component Analysis to Reduce Dimensionality of Gene Expression Profiles for Tumor Classification

Bio-Inspired Computing and Applications - Lecture Notes in Computer Science ◽

10.1007/978-3-642-24553-4_78 ◽

2012 ◽

pp. 588-595

Author(s):

Shu-Lin Wang ◽

Min Li ◽

Hongqiang Wang

Keyword(s):

Gene Expression ◽

Principal Component Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Principal Component ◽

Component Analysis ◽

Tumor Classification

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NK Cells From CLL Patients Exhibit Down-Regulation Of Interferon Response Genes That Can Be Reversed With Lenalidomide

Blood ◽

10.1182/blood.v122.21.4131.4131 ◽

2013 ◽

Vol 122 (21) ◽

pp. 4131-4131

Author(s):

John C. Riches ◽

Ajanthah Sangaralingam ◽

Tracy Chaplin ◽

Fabienne McClanahan ◽

Sameena Iqbal ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Nk Cells ◽

Nk Cell ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Interferon Response ◽

Down Regulation ◽

Inducible Genes ◽

Increased Susceptibility

Abstract Chronic lymphocytic leukemia (CLL) is associated with profound defects in immune function, resulting in failure of anti-tumor immunity and increased susceptibility to infection. We have previously demonstrated alterations in gene expression profiles of T cells from CLL patients, which translate into functional defects in T-cell immune synapse formation, motility and cytotoxicity (Gorgun et al. JCI 2005; Ramsay et al. JCI 2008, Blood 2013). However a comparison of the transcriptome of natural killer (NK) cells from CLL patients and controls has not been investigated. NK cells were isolated from the peripheral blood of patients with CLL and healthy donors, followed by gene expression profiling using the Affymetrix U133Plus2.0 platform. 117 probes showed a >2-fold decrease in expression while only 18 probes showed a >2-fold increase in expression (adjusted p-value < 0.05) in CLL NK cells compared to healthy donor NK cells. Strikingly, 52 out of the 117 significantly down-regulated probes (44.4%) were for interferon-inducible genes including STAT1 (Signal Transducers and Activator 1), SOCS1 (Suppressor of cytokine signaling 1), interferon regulatory factor genes IRF7 and IRF9, and oligoadenylate synthetase genes OAS1, OAS2, and OAS3. The majority of these genes were inducible by both type 1 and type 2 interferons. Many of these genes have been implicated in host immunity to viral infections, and so it is possible that decreased NK-cell responsiveness to interferon contributes to the increased susceptibility of CLL patients to viruses. Notably, there was also altered expression of signaling pathways in common with T cells from CLL patients, with dysregulation of the cytoskeleton genes RAB3GAP1, RAB38, and EPHA1 and down-regulation of JUN mirroring the dysregulated JNK-signaling and the altered actin cytoskeleton pathways we have found in T cells from CLL patients. These changes were not due to differences in the relative frequencies of CD56DIM and CD56BRIGHTNK cells. Lenalidomide has significant clinical activity in CLL. It is not directly toxic to tumor cells in vitro, but instead is thought to activate anti-tumor immunity and block pro-tumor micro-environmental factors. NK-cell proliferation has been shown to correlate with clinical response to lenalidomide in CLL (Chanan Khan et al. BJ Haem 2011). Therefore, we investigated the effect of lenalidomide treatment on the gene expression profiles of NK cells from CLL patients in comparison to healthy controls. PBMCs from CLL patients or healthy controls were cultured in the presence of 1μM lenalidomide or vehicle control for 48 hours, followed by NK-cell isolation, RNA extraction and gene expression profiling. There were striking differences in the effect of lenalidomide on NK cells from CLL patients compared with healthy NK cells. In CLL NK cells, lenalidomide repaired the down-regulation of interferon-inducible genes, by increasing the expression of genes such as OAS3, IFIT1, IFI44L, IFIT3, OAS1, PDK4, and ACTN1. Pathway analysis highlighted the effect of lenalidomide on inducing interferon signaling, showing significant activation of interferon α, γ, and λ as upstream regulators. While many of the interferon-inducible genes were up-regulated >3-fold in CLL NK cells, only OAS3 was significantly up-regulated in healthy NK cells with lenalidomide. Furthermore, the gene for IFNγ, IFNG, was actually significantly down-regulated in healthy NK cells by this agent. Lenalidomide also significantly down-regulated the expression of 5 genes encoding killer-cell immunoglobulin-like receptors (KIRs): KIR2DL1, KIR2DL2, KIR2DS3, KIR2DS4, and KIR3DL2, in healthy NK cells, but did not significantly down-regulate KIR genes in the CLL NK-cell dataset. Lenalidomide treatment did have some overlapping effects on CLL and healthy NK cells, including up-regulation of genes ARL11, CYFIP, and CORO1B that regulate the actin cytoskeleton pathway. In conclusion, NK cells from CLL patients have down-regulation of interferon response genes and pathways known to regulate normal immune function in response to bacteria and viruses. Lenalidomide has a differential effect on CLL and healthy NK cells: in CLL NK cells it repairs defective interferon responses, whereas in healthy NK cells it down-regulates inhibitory pathways. Disclosures: Riches: Celgene: Research Funding. Gribben:Celgene: Research Funding; Pharmacyclics: Honoraria; Roche: Honoraria.

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