Estimating the Parameters of Cyclin-Triggered Gene Expression in Cell Cycle Control Network

AbstractAlthough multiple myeloma (MM) is a unique entity, a marked heterogeneity is actually observed among the patients, which has been first related to immunoglobulin (Ig) types and light chain subtypes and more recently to chromosomal abnormalities. To further investigate this genetic heterogeneity, we analyzed gene expression profiles of 92 primary tumors according to their Ig types and light chain subtypes with DNA microarrays. Several clusters of genes involved in various biologic functions such as immune response, cell cycle control, signaling, apoptosis, cell adhesion, and structure significantly discriminated IgA- from IgG-MM. Genes associated with inhibition of differentiation and apoptosis induction were up-regulated while genes associated with immune response, cell cycle control, and apoptosis were down-regulated in IgA-MM. According to the expression of the 61 most discriminating genes, BJ-MM represented a separate subgroup that did not express either the genes characteristic of IgG-MM or those of IgA-MM at a high level. This suggests that transcriptional programs associated to the switch could be maintained up to plasma cell differentiation. Several genes whose products are known to stimulate bone remodeling discriminate between κ- and λ-MM. One of these genes, Mip-1α, was overexpressed in the κ subgroup. In addition, we established a strong association (P = .0001) between κ subgroup expressing high levels of Mip-1α and active myeloma bone disease. This study shows that DNA microarrays enable us to perform a molecular dissection of the bioclinical diversity of MM and provide new molecular tools to investigate the pathogenesis of malignant plasma cells.

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Inhibition of the Epigenetic Modifier EZH2 Upregulates Cell Cycle Control Genes to Inhibit Myeloma Cell Growth and Overcome High-Risk Disease Features

Blood ◽

10.1182/blood.v128.22.3289.3289 ◽

2016 ◽

Vol 128 (22) ◽

pp. 3289-3289 ◽

Cited By ~ 2

Author(s):

Charlotte Pawlyn ◽

Michael Bright ◽

Amy Buros ◽

Caleb K. Stein ◽

Zoe Walters ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

High Risk ◽

Cell Lines ◽

Research Funding ◽

Cell Cycle Control ◽

Myeloma Cell ◽

Expression Arrays ◽

Molecular Features ◽

High Risk Disease

Abstract Introduction High expression of the H3K27 histone methyltransferase EZH2 mRNA in myeloma (MM) patient samples is associated with molecular features of high risk disease, including increased proliferation, and adverse outcomes (1). Mutations or deletions in the H3K27 demethylase KDM6A are associated with similar findings (2) and would be expected to have the same epigenetic effect, increasing H3K27me3 levels, a mark associated with repression of gene expression. We, therefore, sought to identify the role EZH2 plays in controlling myeloma cell proliferation. Methods A panel of MM cell lines and primary patient samples (CD138 selected from bone marrow with consent) representing a variety of different MM molecular subgroups were used. Cell viability (WST-1), cell cycle (PI) and apoptosis (AnnexinV/PI, Caspase-Glo 3/7) assays were performed. Affymetrix gene expression arrays followed by validation with RT-PCR were used to identify patterns of gene expression change with EZH2i. Western blotting confirmed changes at the protein level and Chip-PCR was performed using a validated antibody and isotype control to identify H3K27me3 changes at the relevant gene promotors. Affymetrix gene expression data for 1213 patients enrolled in the Total Therapy studies were used to investigate the relevance of our findings in myeloma patient samples. Results We confirmed a reduction in viability following EZH2i using two chemically distinct, specific small molecule inhibitors (EPZ005687 and UNC1999) and the negative control compound UNC2400. There was a reduction in viability in 6/8 cell lines and 5/6 patient samples. Response to inhibition was not related to molecular subgroup or the presence of high-risk molecular features including del17p. Global levels of H3K27me3 measured by Western blot were reduced in all cell lines regardless of response to EZH2i. In responding cell lines EZH2i induced cell cycle arrest at G1/S followed by induction of apoptosis. Gene expression arrays performed using mRNA from KMS11 and KMM1 cell lines highlighted a change in expression of cell cycle control genes associated with EZH2i. This finding was validated using qRT-PCR, which demonstrated upregulation of the cyclin dependent kinase inhibitors CDKN2B, CDKN1A or both. These findings were confirmed at the protein level by Western blotting. Chip-PCR experiment using cell lysates from KMS11 cells following incubation with EZH2i over 6 days identified changes in H3K27me3 at the promoter and transcriptional start site (PROM/TSS) regions of the CDKN2B and CDKN1A genes. The most specific changes occurred at the CDKN1A PROM/TSS, which were more heavily marked with H3K27me3 at baseline compared to a region approx. 5KB upstream. Given these results, which suggest that CDKN1A expression may be controlled by changes in H3K27me3, we explored the effect of CDKN1A mRNA expression in our patient datasets. We found the expression of EZH2 and CDKN1A to be inversely correlated (R=-0.170, p<0.0001) and that low expression of CDKN1A was associated with a significantly shorter progression free and overall survival (p<0.001). In order to confirm whether these gene expression changes could be used as a potential biomarker of response we looked at our panel of cell lines with variable responses to EZH2i. We identified a consistent increase in expression of CDKN1A only in responding cell lines suggesting it could be used as a biomarker of efficacy in the clinic. Conclusions These data support the hypothesis that CDKN1A expression is suppressed by increased H3K27me3, due to high expression of EZH2 and that this can be reversed with pharmacological EZH2 inhibition leading to a reduction in proliferation of myeloma cells. We provide data which supports the investigation of EZH2i in clinical trials of myeloma patients, which has the potential to be an effective therapeutic strategy even for those with high-risk disease, for whom current treatment approaches are ineffective.Pawlyn et al, EZH2 Overexpression in Myeloma Patients Shortens Survival and in-vitro Data Supports a Potential New Targeted Treatment Strategy. AACR and IMW abstracts, 2015Pawlyn et al, The Spectrum and Clinical Impact of Epigenetic Modifier Mutations in Myeloma. Clinical Cancer Research, 2016 Disclosures Pawlyn: Celgene: Consultancy, Honoraria, Other: Travel Support; Takeda Oncology: Consultancy. Kaiser:Celgene: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; BMS: Consultancy, Other: Travel Support; Takeda: Consultancy, Other: Travel Support; Chugai: Consultancy. Jones:Celgene: Honoraria, Research Funding. Jackson:Amgen: Consultancy, Honoraria, Speakers Bureau; Roche: Consultancy, Honoraria, Speakers Bureau; MSD: Consultancy, Honoraria, Speakers Bureau; Janssen: Consultancy, Honoraria, Speakers Bureau; Celgene: Consultancy, Honoraria, Other: Travel support, Research Funding, Speakers Bureau; Takeda: Consultancy, Honoraria, Other: Travel support, Research Funding, Speakers Bureau. Bergsagel:Novartis: Research Funding; Amgen, BMS, Novartis, Incyte: Consultancy. Morgan:Univ of AR for Medical Sciences: Employment; Janssen: Research Funding; Bristol Meyers: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding. Davies:Celgene: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Janssen: Consultancy, Honoraria.

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Continued withdrawal from the cell cycle and regulation of cellular genes in mouse erythroleukemia cells blocked in differentiation by the c-myc oncogene.

Molecular and Cellular Biology ◽

10.1128/mcb.9.4.1714 ◽

1989 ◽

Vol 9 (4) ◽

pp. 1714-1720 ◽

Cited By ~ 15

Author(s):

J A Coppola ◽

J M Parker ◽

G D Schuler ◽

M D Cole

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Cell Cycle Control ◽

Regulation Of Gene Expression ◽

Constitutive Expression ◽

Housekeeping Genes ◽

Cell System ◽

Myc Oncogene ◽

Temporary Decrease ◽

Mouse Erythroleukemia

Constitutive expression of the c-myc oncogene blocks dimethyl sulfoxide (DMSO)-induced differentiation of mouse erythroleukemia (MEL) cells. During the first 12 h of treatment with DMSO, MEL cells undergo a temporary decrease in the level of c-myc mRNA, followed by a temporary withdrawal from the cell cycle. We found the same shutoff of DNA synthesis during the first 12 to 30 h after DMSO induction in normal MEL cells (which differentiate) and in c-myc-transfected MEL cells (which do not differentiate). We also examined whether deregulated c-myc expression grossly interfered with the regulation of gene expression during MEL cell differentiation. We used run-on transcription assays to monitor the rate of transcription of four oncogenes (c-myc, c-myb, c-fos, and c-K-ras); all except c-K-ras showed a rapid but temporary decrease in transcription after induction in both c-myc-transfected and control cells. Finally, we found the same regulation of cytoplasmic mRNA expression in both types of cells for four oncogenes and three housekeeping genes associated with growth. We conclude that in the MEL cell system, the effects of deregulated c-myc expression do not occur through a disruption of cell cycle control early in induction, nor do they occur through gross deregulation of gene expression.

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Radiofrequency radiation (900 MHz) induces Egr-1 gene expression and affects cell-cycle control in human neuroblastoma cells

Journal of Cellular Physiology ◽

10.1002/jcp.21146 ◽

2007 ◽

Vol 213 (3) ◽

pp. 759-767 ◽

Cited By ~ 65

Author(s):

M. Buttiglione ◽

L. Roca ◽

E. Montemurno ◽

F. Vitiello ◽

V. Capozzi ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Cell Cycle Control ◽

Neuroblastoma Cells ◽

Human Neuroblastoma Cells ◽

Human Neuroblastoma ◽

Radiofrequency Radiation

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Gene Expression Analysis Uncovers Similarity and Differences Among Burkitt Lymphoma Subtypes

Blood ◽

10.1182/blood.v116.21.2494.2494 ◽

2010 ◽

Vol 116 (21) ◽

pp. 2494-2494

Author(s):

Pier Paolo Piccaluga ◽

Giulia De Falco ◽

Manjunat Kustagi ◽

Anna Gazzola ◽

Annalisa Astolfi ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

B Cell ◽

Burkitt Lymphoma ◽

Who Classification ◽

Cell Cycle Control ◽

B Cell Lymphomas ◽

Over Expression

Abstract Abstract 2494 Background. Burkitt lymphoma (BL) is currently listed in the WHO classification of lymphoid tumors as a single genetic and morphological entity with variation in clinical presentation. In particular, three clinical subsets of BL are recognized: endemic (eBL), sporadic (sBL) and immunodeficiency associated (ID-BL). Each affects different populations and can present with different features. So far, possible differences in their gene expression profiles (GEP) have not been investigated. In this study we aimed to 1) assess whether BL subtypes present with differences in their GEP; 2) investigate the relationship of the different BL subtypes with the non-neoplastic cellular counterparts; 3) Identify genes and programs specifically deregulated in BLs and possibly contributing to the malignant phenotype. Methods. We studied by GEP 128 cases of B-cell derived malignancies and 20 samples of normal B-cell subpopulations GEP analysis. In particular, we included 40 BLs (13 eBLs, 21 sBLs 6 HIV-BLs), 40 follicular lymphomas, 10 chronic lymphocytic leukemias, 10 GCB-type diffuse large B-cell lymphomas, 10 ABC-type DLBCL, 5 primary mediastinal B-cell lymphomas, 13 HIV-related DLBCL, as well as 10 germinal center (GC), 5 naïve and 5 memory cells samples. GEP results were confirmed by dividing BL cases into training and test subgroups. In addition, as further validation, we performed immunohistochemistry (IHC) on tissue microarrays containing 85 BL cases as well as functional assays in vitro and in vivo, by focusing on the role of RBL2, a tumor suppressor gene involved in cell cycle control and mutated in eBL. Specifically, we used cell transfection and shRNAs (for mimicking MYC over-expression and RBL2 silencing), soft agar and invasion capability assays, and xenografted mouse models. Results. First, we found that BLs constitute a unique molecular entity, with a relatively homogeneous GEP, distinct from other B-cell malignancies. Indeed, by unsupervised analysis all BLs clearly clustered apart of other lymphomas. However, by supervised analysis, we found that BL subtypes presented slight differences in their GEPs. Particularly, eBLs and ID-BLs appeared to be almost identical, diverging from sBLs. Specifically, they varied for genes involved in cell cycle control, BCR-signaling, and TNF/NFKB-pathways. Of note, eBLs and ID-BLs on one hand, and sBLs on the other (roughly corresponding to EBV+ vs. EBV− cases) also differed for genes target of mi-R127a, which is altered in EBV+ cases as a direct consequence of viral integration. To further investigate cell cycle regulation in BLs, we inferred a network of RBL2-depending genes by reverse engineering, by uncovering possible RBL2 transcriptional targets. Interestingly, we found that eBL and sBL diverged for genes belonging to such network. Notably, we provided evidences that RBL2 can cooperate with MYC in inducing a neoplastic phenotype in vitro and in vivo. In particular, lymphoblastoid cells engineered to carry both MYC over-expression and RBL2 silencing presented with increased colony formation and matrix invasion capabilities, and higher efficiency in inducing tumor formation in nude mice if compared to single transfectants (MYC+ or RBL2−). Moreover, as the present WHO classification does not definitely identify the counterpart of eBL, we compared BLs GEP to those of normal B-cells. We found that all BL subtypes were intimately related to GC cells (by showing an early stage GC differentiation arrest), differing from them for molecules specially involved in cell proliferation, immune response, and signal transduction. Finally, as further validation of GEP, we studied by IHC the expression of SPARC and CYR61, two molecules involved in human tumorigenesis. Indeed, they turned out to be consistently expressed by neoplastic elements in all instances, as indicated by GEP analysis. Conclusions. Our study provided substantial insights on the pathobiology of BLs, by offering novel evidences which may be relevant for its classification and possibly future treatment. Disclosures: No relevant conflicts of interest to declare.

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