Inhibitor of DNA Binding 2 (ID2) Plays a Key Tumor Suppressor Role in Promoting Oncogenic Transformation in Multiple Myeloma

Abstract Dysregulation of transcriptional control is a common phenomenon associated with oncogenesis. Inhibitors of DNA binding (ID) proteins are critical actors in lymphopoiesis, acting as regulators of transcription through a helix-loop-helix (HLH) domain which enables heterodimerization with basic HLH (bHLH) proteins inhibiting their binding to DNA. ID proteins have been implicated in malignant transformation, but their role in multiple myeloma (MM) is unknown. Here, we evaluated the role of ID proteins in biology and transcriptional dysregulation in MM. We first evaluated the expression of the four ID proteins in normal and malignant plasma cells using RNA sequencing data from a cohort of 360 newly diagnosed MM patients and 16 normal plasma cells. We observed significant downregulation of ID2 in primary patient MM cells in comparison to normal plasma cells (p 0.0013). To study ID2 function in MM cells, we next overexpressed ID2 in 2 MM cell lines (MM1S and NCIH929) and observed a significant decrease in proliferation rate, together with G0/G1 phase cell cycle arrest. We performed RNA-sequencing to evaluate the transcriptomic changes following ID2 overexpression. Gene set enrichment analysis (GSEA) revealed significant downregulation of genes involved in E2F pathway and significant changes in pathways related to immune response, regulation of cell death and cell proliferation. In addition, analysis of upstream cis-regulatory motifs of genes significantly dysregulated in both cell lines (>1.5 fold change) showed a highly significant enrichment for bHLH class I transcription factors (E proteins) binding motifs. Conversely, stable ID2 knockdown in 4 MM cell lines (MM1S, NCIH929, RPMI8226 and KMS11) expressing intermediate levels of ID2, showed an increased proliferation rate, assessed by cell counting, H3-thymidine incorporation and ATP production. RNA-sequencing after ID2 knockdown in MM1S and NCIH929 cells showed 600 common genes upregulated in both cell lines (>1.5 fold change). GSEA revealed upregulation of pathways involved in inflammatory response and epithelial-to-mesenchymal transition, while upstream cis regulatory motifs analysis showed a highly significant enrichment for binding motifs of bHLH class I transcription factors E proteins, in particular Tcf3 (p <0.0001). Next, we sought to investigate the mechanisms involved in ID2 downregulation in MM. Since the role of the microenvironment is critical in myelomagenesis, we evaluated the impact of BM microenvironment on ID2 expression in a co-culture system. Using bone marrow stromal cells (BMSC) derived from MM patients and stromal cell line (HS5) in co-culture with various MM cell lines, we observed that both cell-cell interactions and soluble factors secreted by BMSC or HS5 were able to significantly downregulate ID2 expression at the RNA and protein level. Furthermore, ID2 overexpression in MM cell lines (MM1S and NCIH929) abrogated the impact of BMSC on MM cell proliferation. Next, we evaluated ID2 promoter methylation profile and binding motifs using Sequenom mass array and the assay for transposase-accessible chromatin sequencing (ATAC-seq), respectively. While we didn't observe any increase in methylation of CpG islands located in ID2 promoter in co-culture, explaining ID2 downregulation, we identified several binding motifs corresponding to known driver transcription factors in MM. Especially, we identified SP1 binding motif and we confirmed SP1 binding to ID2 promoter by ChIP-sequencing in MM1S, NCIH929 and U266. These data demonstrate that in MM, ID2 acts as a tumor suppressor by promoting major transcriptomic changes and cell cycle arrest. Bone marrow stromal cells further induce significant downregulation of ID2 in myeloma cells suggesting that ID2/bHLH axis and other ID2 related pathways represent a potential new therapeutic target in myeloma. Disclosures Anderson: Gilead: Membership on an entity's Board of Directors or advisory committees; Bristol Myers Squibb: Consultancy; Celgene: Consultancy; C4 Therapeutics: Equity Ownership, Other: Scientific founder; OncoPep: Equity Ownership, Other: Scientific founder; Millennium Takeda: Consultancy. Munshi:OncoPep: Other: Board of director.

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Epigenetic silencing of the immunoglobulin heavy-chain gene in classical Hodgkin lymphoma-derived cell lines contributes to the loss of immunoglobulin expression

Blood ◽

10.1182/blood-2003-04-1197 ◽

2004 ◽

Vol 104 (10) ◽

pp. 3326-3334 ◽

Cited By ~ 67

Author(s):

Alexey Ushmorov ◽

Olga Ritz ◽

Michael Hummel ◽

Frank Leithäuser ◽

Peter Möller ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

B Cell ◽

Hodgkin Lymphoma ◽

Cell Lines ◽

Epigenetic Silencing ◽

Chain Gene ◽

Classical Hodgkin Lymphoma ◽

Regulatory Regions ◽

The Impact

Abstract Immunoglobulin production is impaired in Hodgkin and Reed-Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) in spite of functional clonal rearrangements. The presence of “crippling” mutations in coding and regulatory regions, as well as down-regulation of B-cell-specific transcription factors, has been suggested as a potential reason for the lack of immunoglobulin (Ig) chain gene transcription. We have investigated the impact of epigenetic silencing in suppressing Ig heavy (H)-chain expression. Chromatin immunoprecipitation (ChIP) was used to analyze transcription factor binding to octamer motifs present in the IgH regulatory regions. Transcription factors were bound to these motifs in control cell lines, however, they were absent in the cHL-derived cell lines KMH2, L1236, and L428. Ectopic expression of octamer-binding transcription factor (Oct2) and/or B-cell Oct binding protein/Oct-binding factor (BOB.1/OBF.1) did not result in any measurable binding to these sites. Increased histone 3 Lysine 9 (H3-K9) methylation was observed in the promoter region of the IgH locus in L428 and L1236 cells. This is a typical feature of heterochromatic, transcriptionally silent regions. Treatment of cHL-derived cell lines with the DNA demethylating agent 5-aza-2′-deoxycytidine (5-aza-dC) partially reactivated IgH transcription and affected chromatin modifications. Our results suggest an important role of epigenetic silencing in the inhibition of IgH transcription in HRS cells. (Blood. 2004;104:3326-3334)

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Activation of the Endoplasmic Reticulum (ER) Unfolded Protein Response (UPR) in Aggressive B-Cell Lymphomas.

Blood ◽

10.1182/blood.v108.11.2038.2038 ◽

2006 ◽

Vol 108 (11) ◽

pp. 2038-2038

Author(s):

Olga Balague ◽

Luis Colomo ◽

Armando Lopez-Guillermo ◽

Elias Campo ◽

Antonio Martinez

Keyword(s):

Endoplasmic Reticulum ◽

Transcription Factors ◽

Western Blot ◽

Er Stress ◽

B Cell ◽

Cell Lines ◽

Plasma Cell ◽

Plasma Cells ◽

Lymphoid Tissues ◽

B Cell Lymphomas

Abstract BACKGROUND The UPR is a prosurvival pathway activated in cells under ER stress induced by the accumulation of unfolded proteins. UPR activation in B cells normally occurs during the differentiation to antibody secreting plasma cells and requires XBP1activation. XBP-1 is a member of the TREB family of transcription factors that exists in the endoplasmic reticulum (ER) as a 33kDa protein, and in the nucleus as an active 50kDa transcription factor. The UPR stimulates two different ER proteins, ATF-6 and Ire-1, to increase XBP-1 transcription and XBP-1 mRNA splicing resulting in the accumulation of the active 50kDa nuclear protein. Moreover XBP1 is a target of proteosome inhibitors and is related to the aggressive behaviour of some carcinomas. The role of the activation of XBP-1 in lymphomas is still unknown. DESIGN: Reactive lymphoid tissues and 25 neoplastic human B-cell lines representing different stages of B-cell development were studied for XBP-1 expression by western blot and XBP-1, PAX-5, Blimp-1/prdm1, MUM-1/IRF-4 and ICSBP1/IRF-8 by immunohistochemistry. XBP-1 activation was assessed in 225 B-cell lymphomas from the archives of the laboratory of pathology by western blot, RT-PCR and immunohistochemistry . To further evaluate whether XBP-1 activation was related to the plasmacytic program or to ER stress signals we analyzed the cell lines by Western blot for XBP-1 and ATF-6 expression. RESULTS We characterize XBP-1 expression in reactive lymphoid tissues, 25 human cell lines and 225 B-cell tumors. In nearly all tonsillar lymphoid cells XBP-1 was detected as a cytoplasmic protein with a paranuclear dot pattern. Nuclear positivity was observed only in scattered centrocytes in the light zone of the germinal centers and in plasma cells, always coexpressed with plasma cell related transcription factors as MUM-1/IRF-4 and Blimp1/prdm1. Active p50XBP-1 was found in 24/25 cell lines by western blot regardless ATF-6 expression and confirmed by immunohistochemistry . Moreover p50XBP1 was found in 27/31(87%) plasmacytomas, 36/64(56%) DLBCL-ABC and in 3/10(30%) DLBCL-GCB and 22/43(51%) plasmablastic lymphomas. Intriguingly, p50XBP1 was detected also in 2/11(18%)BL and 4/25(16%)MCL with blastic features. CONCLUSIONS.XBP-1 is activated in a subset of follicular centre cells committed to plasma cell differentiation and in plasma cells.UPR prosurvival pathways in the neoplastic cell lines are activated independently of the extent of the ATF-6 activation.p50XBP1 is mostly activated in aggressive B-cell lymphomas regardless to the plasmacytic differentiation of the tumours. Thus, p50XBP-1 may be a new molecular target in the treatment of aggressive B-cell malignancies.

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C/EBPβ Is a Critical Factor for Proliferation and Apoptosis in MM Cells by Controlling Transcription Factors Like IRF-4, PAX5 and Blimp1.

Blood ◽

10.1182/blood.v110.11.1506.1506 ◽

2007 ◽

Vol 110 (11) ◽

pp. 1506-1506

Author(s):

Rekha Pal ◽

Martin Janz ◽

Deborah Galson ◽

Suzanne Lentzsch

Keyword(s):

Transcription Factors ◽

Western Blot ◽

Cell Lines ◽

Plasma Cells ◽

Annexin V ◽

Critical Factor ◽

Myeloma Cell ◽

Down Regulation ◽

Protein Levels ◽

Rpmi 8226

Abstract The development and maturation of plasma cells is dictated by multiple interacting transcription factors (TFs). C/EBPb (NF-IL6) is a TF regulated by IL-6 and has profound effects on the regulation of growth, survival and differentiation of B-cells. Mice deficient in C/EBPb show impaired generation of B lymphocytes suggesting that C/EBPb plays an important role in B lymphopoiesis. In this study we delineated the effect of C/EBPb on transcription factors critical for myeloma cell proliferation by over-expressing and inhibiting C/EBPb in myeloma cells. Multiple myeloma (MM) cell lines MM.1S, RPMI-8226 and H929 were transiently transfected with GFP, C/EBPb (pcNF-IL6), and truncated C/EBPb with a deletion of the internal spII-spII fragment [pcmNF-IL6(Dspl)] by using Bio-Rad Gene Pulser Xcell, followed by G418 selection. A pool of transfected cells was selected and subjected to thymidine incorporation, flow cytometry and western blot analysis. We found that transfection of a truncated form of C/EBPb induced a down-regulation of C/EBPb in MM cell lines (MM.1S, RPMI-8226 and H929) as measured by western blot. Down-regulation of C/EBPβ significantly inhibited proliferation and induced apoptosis of MM cell lines analyzed by annexin V-FITC/PI staining. This was accompanied by a complete down-regulation of the anti-apoptotic protein BCL-2. Further, inhibition of C/EBPb completely decreased IRF-4 expression. In contrast, over-expression of C/EBPb increased protein levels of IRF-4 suggesting that IRF-4 is under control of C/EBPb. IRF-4, which was over-expressed in all our tested MM cells lines, is an essential TF for the generation of plasma cells by regulating TFs like Blimp-1 and PAX-5, which are critical for plasma cell differentiation. Our studies showed that down-regulation of IRF-4 resulted in a complete abrogation of Blimp-1 and PAX-5 suggesting that the expression of these factors is C/EBPb/IRF-4 dependent. In conclusion, our data indicate that C/EBPb is an important key regulator for survival and growth of MM cells. We show for the first time that C/EBPb is a critical regulator upstream of IRF-4. Down-regulation of the C/EBPb and consequently IRF-4 results in complete disruption of the network of TFs necessary for MM growth and survival. Targeting C/EBPb may provide a novel therapeutic approach in the treatment of MM.

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Augmenting E Protein Activity Impairs cDC2 Differentiation at the Pre-cDC Stage

Frontiers in Immunology ◽

10.3389/fimmu.2020.577718 ◽

2020 ◽

Vol 11 ◽

Author(s):

Sandra Bajana ◽

Kevin Thomas ◽

Constantin Georgescu ◽

Ying Zhao ◽

Jonathan D. Wren ◽

...

Keyword(s):

Transcription Factors ◽

Protein Function ◽

Loss Of Function ◽

Protein Activity ◽

E Proteins ◽

Aberrant Expression ◽

Precise Control ◽

Helix Loop Helix ◽

Id Proteins ◽

E Protein

Dendritic cell (DC) specification and differentiation are controlled by a circuit of transcription factors, which regulate the expression of DC effector genes as well as the transcription factors themselves. E proteins are a widely expressed basic helix-loop-helix family of transcription factors whose activity is suppressed by their inhibitors, ID proteins. Loss-of-function studies have demonstrated the essential role of both E and ID proteins in different aspects of DC development. In this study, we employed a gain-of-function approach to illustrate the importance of the temporal control of E protein function in maintaining balanced differentiation of conventional DC (cDC) subsets, cDC1 and cDC2. We expressed an E protein mutant, ET2, which dimerizes with endogenous E proteins to overcome inhibition by ID proteins and activate the transcription of E protein targets. Induction of ET2 expression at the hematopoietic progenitor stage led to a dramatic reduction in cDC2 precursors (pre-cDC2s) with little impact on pre-cDC1s. Consequently, we observed decreased numbers of cDC2s in the spleen and lung, as well as in FLT3L-driven bone marrow-derived DC cultures. Furthermore, in mice bearing ET2, we detected increased expression of the IRF8 transcription factor in cDC2s, in which IRF8 is normally down-regulated and IRF4 up-regulated. This aberrant expression of IRF8 induced by ET2 may contribute to the impairment of cDC2 differentiation. In addition, analyses of the transcriptomes of splenic cDC1s and cDC2s revealed that ET2 expression led to a shift, at least in part, of the transcriptional profile characteristic of cDC2s to that of cDC1. Together, these results suggest that a precise control of E protein activity is crucial for balanced DC differentiation.

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Transcriptional Deregulation Mediated By ID2-TCF3 Axis Supports MM Cell Growth and Proliferation in the Context of the Bone Marrow Milieu

Blood ◽

10.1182/blood-2021-152526 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 2686-2686

Author(s):

Yao Yao ◽

Tommaso Perini ◽

Mehmet K. Samur ◽

Raphael Szalat ◽

Moritz Binder ◽

...

Keyword(s):

Bone Marrow ◽

Cell Growth ◽

Dna Binding ◽

Board Of Directors ◽

Cell Lines ◽

Plasma Cells ◽

Open Chromatin ◽

E Proteins ◽

Advisory Committees ◽

A Cell

Abstract Multiple myeloma (MM) is a complex and heterogenous disease which is dependent on the surrounding microenvironment for growth and survival. In MM, dysregulation of transcriptional control is a major driver of tumor transformation and progression. To evaluate transcriptional programs activated in MM cells in the context of the bone marrow milieu, we have performed extensive transcriptomic analysis by RNA-seq and ATAC-seq using bone marrow stromal cells (BMSC) derived from MM patients and stromal cell line (HS5) in co-culture with various MM cell lines. We observed that both cell-cell interactions and soluble factors secreted by BMSC or HS5 cells significantly downregulated expression of Inhibitor of DNA Binding 2 (ID2), while footprint analysis of the open chromatin regions in MM cells upon interaction with BMSC revealed enrichment for binding motifs of the TCF family of transcription factors (E proteins). Inhibitors of DNA binding (ID) proteins control crucial transcriptional programs in B cell maturation via their heterodimerization with E proteins which are members of the basic helix-loop-helix (bHLH) class I family of transcription factors, repressing their DNA binding and therefore transcriptional activity. We found that ID2 expression is significantly lower in primary CD138+ MM cells from patients compared to normal plasma cells (NPCs). Moreover, we have previously implicated the B-cell factor TCF3 as a novel MM dependency. Using MM cell lines and primary samples, we observed elevated enhancer activity at TCF3 locus in primary malignant plasma cells compared to NPCs, which resulted in significant upregulation of TCF3 expression in MM patients. We also showed that TCF3 is regulated by a large proximal enhancer that is bound by MYC and is highly sensitive to chemical perturbation of enhancer co-activators such as BRD4. Genetic perturbation of TCF3 confirmed its critical role on MM cell growth and viability especially in IgH MYC translocated MM cell lines. We here further explored the role of ID2-TCF3 axis and the hypothesis that lower expression of ID2 drives higher TCF3 activity in MM cells, which is further enhanced in presence of the bone marrow microenvironment. Genetic modulation of ID2 significantly affected MM cell viability, with MM cells ectopically expressing ID2 displaying a cell growth arrest even in the presence of the supportive BM milieu. To define the mechanism of the observed oncosuppressive role of ID2 in MM, which is in line with preliminary observations in other hematological malignancy but in contrast with the pro-tumoral role described in solid tumors, we first performed immunoprecipitation of ID2 followed by mass spectrometry in 3 MM cell lines, and identified a very consistent and specific interaction with E proteins TCF3 and TCF12. Next, to explore the transcriptional programs dependent on ID2 we performed RNA-seq of 2 MM cell lines after ID2 overexpression. In line with our in vitro data, gene ontology and gene set enrichment analysis showed a significant downregulation of genes involved in E2F pathway, cell cycle progression and regulation of gene transcription. Interestingly, among the known TCF3 targets in B cells, only XBP-1 was significantly downregulated in MM cells after ID2 overexpression, suggesting the existence of a cell-specific TCF3 dependent transcriptional program in MM. Indeed, ATAC-seq experiments revealed ID2 overexpression led to a significant decrease of TCF3 binding motifs in open chromatin regions, confirming the relevance of ID2 in regulating TCF3 transcriptional activity in MM. In conclusion, while both E and ID proteins have been implicated in malignant transformation, their role in supporting MM transcriptional deregulation and tumor growth in the context of the microenvironment is being defined. Here, we have identified ID2 as a major regulator of the TCF3 dependent transcriptional program in MM, whose downregulation is essential to maintain MM proliferation and to mediate the benefits induced by MM-stroma interaction. Disclosures Anderson: Millenium-Takeda: Membership on an entity's Board of Directors or advisory committees; Sanofi-Aventis: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Scientific Founder of Oncopep and C4 Therapeutics: Current equity holder in publicly-traded company, Current holder of individual stocks in a privately-held company; AstraZeneca: Membership on an entity's Board of Directors or advisory committees; Mana Therapeutics: Membership on an entity's Board of Directors or advisory committees. Munshi: Janssen: Consultancy; Amgen: Consultancy; Takeda: Consultancy; Abbvie: Consultancy; Oncopep: Consultancy, Current equity holder in publicly-traded company, Other: scientific founder, Patents & Royalties; Celgene: Consultancy; Karyopharm: Consultancy; Adaptive Biotechnology: Consultancy; Novartis: Consultancy; Legend: Consultancy; Pfizer: Consultancy; Bristol-Myers Squibb: Consultancy.

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Long Non-Coding RNA MALAT1 Is Associated with the Progression of Multiple Myeloma and Induced By Cellular Stress

Blood ◽

10.1182/blood.v126.23.1759.1759 ◽

2015 ◽

Vol 126 (23) ◽

pp. 1759-1759

Author(s):

Yuko Kuroda ◽

Kei Kimura ◽

Yuta Masuda ◽

Arito Yamane ◽

Hikaru Hattori ◽

...

Keyword(s):

Multiple Myeloma ◽

Cell Motility ◽

Rna Sequencing ◽

Cell Lines ◽

Plasma Cells ◽

Extramedullary Plasmacytoma ◽

Expression Levels ◽

Non Coding Rna ◽

Long Non Coding Rna

Abstract Background: Recent transcriptome-wide analyses have revealed an overwhelming amount of transcribed, but not translated, non-coding RNAs capable of influencing diverse cellular processes such as proliferation, apoptosis, and motility. Long non-coding RNA (lncRNAs), which are commonly defined as transcripts >200 nt in length, have emerged as a class of key regulatory RNA. LncRNAs are deregulated in diverse human cancers and associated with disease progression; however, little is known about its role in multiple myeloma (MM). To elucidate the role of lncRNAs in MM, we studied the expression patterns of several well-known lncRNAs in the plasma cells of MM, MGUS and plasmacytoma patients and the function in MM cell lines in vitro. Moreover, to reveal the distinct lncRNA signature comprehensively, we performed next-generation sequencing-based RNA sequencing. Methods: CD138+ plasma cells from bone marrow (BM) mononuclear cells were obtained from 110 MM patients, 48 MGUS patients, 19 control subjects and 1 patient with extramedullary plasmacytoma of the liver and analyzed after obtaining informed consent from all the patients. The expression levels of lncRNAs MALAT1, ANRIL, HOTAIR, HOTTIP, and XIST were determined by a RQ-PCR analysis. RNase H-activating LNA™ GapmeR antisense oligonucleotides were used to knockdown lncRNA in vitro in MM cell lines. The cell lines were then treated with bortezomib, MG132, doxorubicin and hypoxic conditions to evaluate the effects of cytotoxic stress on the lncRNA expression. This study was approved by the IRB of Gunma University Hospital in accordance with the Declaration of Helsinki. Results: A significant higher level of MALAT1 expression was observed in BM plasma cells of MM patients (4.49) compared to MGUS patients (1.51) and control subjects (0.55) (p<0.001). Strikingly, MALAT1 expression in extramedullary plasmacytoma of the liver was 140-fold higher compared with BM plasma cells obtained at the same time of sampling (433.7 vs 3.21). MALAT1 expression was higher in MM patients with t(4;14) and del 17p (10.05 vs 3.90, p=0.049; 5.22 vs 2.76, p=0.03, respectively), but no difference was observed between stages according to the International Staging System (ISS) (p=0.87). Neither the overall survival nor the progression-free survival differed between patients with high and low MALAT1 expression. ANRIL expression levels were diverse according to the patients (range, 0 to 294.3), however, the median expression was significantly higher in MM patients (p<0.001). HOTAIR and HOTTIP expression levels were not detected in most samples, and XIST expression was found only in female patient samples as expected. Interestingly, the MM cell lines KMS12PE, OPM2, KMS11 treated with bortezomib showed elevated MALAT1 expression by 4.3 -21.8 fold and ANRIL by 2.2-4.7 fold; however, this increase was not observed in bortezomib-resistant cell lines. Another proteasome inhibitor, MG132, and a low dose of the cytotoxic drug doxorubicin also elevated both lncRNAs in the cell lines. Hypoxic stress, which has been shown to induce MALAT1 in vascular cells, did not increase either lncRNA. MALAT1 knockdown by GapmeR did not affect cell proliferation. It has been shown that MALAT1 enhances cell motility of lung adenocarcinoma cells by influencing cell motility associated genes; however, the expression of previously reported affected genes, such as HMMR, CTHRC1 and ROD1, was not altered in the MALAT1 knockdown MM cell lines. Although t(4;14) was associated with a high MALAT1 expression in the patient samples, MMSET knockdown by siRNA did not change the MALAT1 expression in the cell lines, thus MMSET was not a regulator of MALAT1. RNA sequencing of MM and MGUS samples revealed a distinct lncRNA expression signature as well as protein coding genes. Conclusion: Significant upregulation of lncRNAs MALAT1 and ANRIL might be associated with MM progression. Given that MALAT1 is associated with lung cancer metastasis, MALAT1 might be strongly associated with extramedullary plasmacytoma formation due to its high expression in liver plasmacytoma. Genotoxic and ER stress induced by therapeutic drugs might upregulate MALAT1 expression, leading to extramedullary extension, which is a recent problem in MM treatment. Determining the distinct lncRNA signature of MM is a current important issue to clarify the molecular mechanisms underlying MM progression for the development of novel therapies. Disclosures No relevant conflicts of interest to declare.

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A High-Throughput Drug Screen Reveals a Novel Compound Class That Significantly Depletes IRF4 Expression in Multiple Myeloma

Blood ◽

10.1182/blood-2019-130910 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 5545-5545 ◽

Cited By ~ 1

Author(s):

Elizabeth D. Lightbody ◽

Mairead Reidy ◽

Michael P. Agius ◽

Salma El-Behaedi ◽

Romanos Sklavenitis-Pistofidis ◽

...

Keyword(s):

Multiple Myeloma ◽

Transcription Factor ◽

Transcription Factors ◽

Western Blot ◽

Cell Lines ◽

High Throughput ◽

Standard Of Care ◽

Drug Screen ◽

Dependent Manner ◽

The Impact

Introduction Multiple myeloma (MM) is an incurable hematological malignancy characterized by the clonal expansion of malignant plasma cells (PCs) within the bone marrow. MM is genetically heterogeneous with aberrations including hyperdiploidy and chromosomal translocations commonly involving the immunoglobulin heavy chain (IgH) region. Many transcription factors can revoke their normal processes and act as oncogenes when they are brought under the control of IgH regulatory regions by a chromosomal translocation. Interferon Regulatory Factor 4 (IRF4) is a transcription factor which controls plasma cell differentiation and possesses many regulatory roles including interferon response, immune cell response, cell proliferation, apoptosis, and metabolism. IRF4 has proven to be a genetic vulnerability in MM as silencing studies in a large panel of MM cell lines with various genetic etiologies have demonstrated IRF4 expression is essential for MM cell survival. Standard of care treatments that indirectly suppress IRF4 including Proteasome inhibitors and Cereblon modulators have provided the greatest clinical outcomes for patients. However, like many other transcription factors, IRF4 has been notoriously difficult to target due to the protein's lack of amenable binding pockets favored for small molecule inhibitor development. Thus, identifying novel mechanisms and compounds to target IRF4 (directly or indirectly) can provide significant clinical impacts for MM patients. Methods To discover compounds capable of depleting IRF4 levels, we performed a high-throughput drug screen utilizing the Selleckchem Drug Repurposing Library on a widely accepted IRF4-dependent cell line. This library consists of over 2,000 diverse compounds that have well validated mechanisms of actions and have additionally passed clinical phase 1 safety trials for accelerated translational use. MM.1S cells were treated for 48 hours in duplicate (n = 2) with 10 μM compound. Following treatment, the cells were fixed, permeabilized, and stained for viability and IRF4 levels. IRF4 expression and viability was acquired by using flow cytometry, with high dose lenalidomide and shRNA for IRF4 as positive controls. Compounds that reduced IRF4 levels and cell viability across both experimental runs were ranked and selected with a cutoff of 40% as promising candidate compounds for further validation. Results Our drug screen results revealed 20 compounds (undisclosed) which met our cutoff of a decrease of IRF4 levels by 40% or greater. Ten hits were selected as having greater or equal to IRF4 depleting properties of lenalidomide and moved forward to be validated by western blot. Six drugs were shown to deplete IRF4 by western blot in MM.1S and KMS-18 cells at 10 μM doses. Interestingly, 4 out of the 10 hits all belong to same compound class that selectively bind to the same target receptor (undisclosed). Additional experiments confirmed these class of compounds deplete IRF4 levels in a dose dependent manner (EC50 = 1 μM). A time course revealed that IRF4 levels decrease shortly after the binding of these drugs to their widely reported target receptor, suggesting this is a selective drug/target receptor-mediated mechanism directly altering levels of IRF4. In vitro studies demonstrated the ability to both halt cell growth and decrease the viability of a panel of 8 MM cell lines, with IC50's ranging from 1.6 - 8.5 μM. Synergy studies with Lenolidomide and Bortezomib are underway to determine any synergistic combinations with standard of care therapies. In vivo studies and RNA-sequencing are also currently underway to determine the impact of these compounds on MM tumor growth and overall survival, as well as better define the mechanism of action driving this novel class of IRF4 targeting compounds. Conclusions Despite knowledge that IRF4 is a biologically potent target in MM there have been no extensive studies highlighting drugs capable of targeting this transcription factor and its oncogenic signaling network. This screen has revealed novel compounds, some of which are clinically used, that are capable of depleting a highly dependent gene in MM. Notably, these compounds are able to deplete IRF4 in a novel mechanism which is capable of affecting survival of MM cell lines that represent the heterogeneity of myeloma, and thus holds potential for significant clinical impact. Disclosures Ghobrial: Amgen: Consultancy; Janssen: Consultancy; Celgene: Consultancy; Takeda: Consultancy; Sanofi: Consultancy; BMS: Consultancy.

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Hundreds of motif pairs may facilitate enhancer-promoter interactions

10.1101/2020.12.29.424656 ◽

2020 ◽

Author(s):

Saidi Wang ◽

Haiyan Hu ◽

Xiaoman Li

Keyword(s):

Transcription Factors ◽

Cell Lines ◽

Human Cell ◽

Human Cell Lines ◽

Binding Motifs ◽

Limited Knowledge ◽

Link Type ◽

Physical Interactions

AbstractPrevious studies have shown that pairs of interacting transcription factors (TFs) bind to enhancers and promoters and contribute to their physical interactions. However, to date, we have limited knowledge about these interacting TF pairs. To identify such TF pairs, we systematically studied the co-occurrence of TF-binding motifs in interacting enhancer-promoter (EP) pairs in seven human cell lines. We discovered hundreds of motif pairs that significantly co-occur in enhancers and promoters of interacting EP pairs. We demonstrated that these motif pairs are biologically meaningful and significantly enriched with motif pairs of known interacting TF pairs. We also showed that the identified motif pairs facilitated the discovery of the interacting EP pairs. The predicted motifs and motif pairs are available at http://www.cs.ucf.edu/~xiaoman/ET/EPmotif/.

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EPCO-21. CORE REGULATORY CIRCUIT TRANSCRIPTION FACTORS DRIVE EXPRESSION FROM HIGH LEVEL AMPLICONS IN PEDIATRIC HIGH-GRADE GLIOMAS

Neuro-Oncology ◽

10.1093/neuonc/noab196.020 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi6-vi6

Author(s):

Davy Deng ◽

Frank Dubois ◽

Alexander Crane ◽

Ashot Harutyunyan ◽

Rameen Beroukhim ◽

...

Keyword(s):

Transcription Factors ◽

Cell Lines ◽

Whole Genome Sequencing Data ◽

High Grade ◽

Sequencing Data ◽

Rtk Signaling ◽

Regulatory Circuit ◽

Significant Enrichment ◽

High Grade Gliomas ◽

High Level

Abstract BACKGROUND Pediatric High-Grade Gliomas (pHGGs) show recurrent high-level amplifications around the oncogenes MET, MYCN and EGFR. However what drives expression of the oncogenes from these amplicons remains unclear. We aim to discover enhancers on these amplicons that are responsible for oncogene expressions and the core regulatory transcription factors (TFs) they bind. METHOD Using RNA-seq from 12 pHGG cell lines, we identified groups of high and low-expressing pHGG lines for MET, MYCN and EGFR. We then compared the H3K27Ac ChIP-seq between the two groups using diffbind. This allowed us to identify statistically significant peaks that are differentially activated in the oncogene-high v.s. oncogene-low expressing groups. Additionally, we overlapped the positions of these candidate oncogene enhancers with the regions that are recurrently incorporated into high-level amplicons based on published whole genome sequencing data. Using a previously defined set of core regulatory TFs we determined which TF binds the amplified oncogene enhancers and could be driving oncogenic expressions of MET, MYCN and EGFR in pHGGs. RESULTS We identify 3 cell lines for both the high- and low-expressing groups for each oncogene. Cell lines with high expression of the oncogene showed distinct enhancers with significant enrichment in H3K27Ac compared to the cell lines with low expression for each oncogene. Of all enhancers with enrichment high oncogene expression groups those with binding sites for known pHGG core regulatory circuit TF were preferentially incorporated into the high-level amplicons of the oncogene. We also identified core TFs that bind enhancers for MYCN, EGFR and MET as well as core TFs that are unique to a single oncogene. CONCLUSION We identified candidate core transcription factor that drives expression of multiple oncogenes in pHGG. These could serve as a potential novel therapeutic target for pHGGs with addiction to MYCN or RTK signaling.

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The long non-coding RNA SAMMSON is essential for uveal melanoma cell survival

10.1101/2021.01.18.427176 ◽

2021 ◽

Author(s):

Shanna Dewaele ◽

Louis Delhaye ◽

Boel De Paepe ◽

Eric De Bony ◽

Jilke De Wilde ◽

...

Keyword(s):

Cell Survival ◽

Rna Sequencing ◽

Cell Lines ◽

Uveal Melanoma ◽

Melanoma Cell ◽

Cancer Type ◽

Uveal Melanoma Cell ◽

Interaction Partners ◽

The Impact ◽

Pdx Models

AbstractPurposeLong non-coding RNAs (lncRNAs) can exhibit cell-type and cancer-type specific expression profiles, making them highly attractive as therapeutic targets. Pan-cancer RNA sequencing data revealed broad expression of the SAMMSON lncRNA in uveal melanoma (UM), the most common primary intraocular malignancy in adults. Currently, there are no effective treatments for UM patients with metastatic disease, resulting in a median survival time of 6-12 months. We aimed to investigate the therapeutic potential of SAMMSON inhibition in UM.Experimental DesignThe impact of antisense oligonucleotide (ASO)-mediated SAMMSON inhibition was evaluated in a panel of UM cell lines and patient derived xenograft (PDX) models. Cell proliferation and apoptosis were quantified in vitro and in vivo and complemented with molecular profiles established through RNA-sequencing. SAMMSON interaction partners were identified using ChIRP-MS.ResultsSAMMSON inhibition impaired the growth and viability of a genetically diverse panel of uveal melanoma cell lines. These effects were accompanied by an induction of apoptosis and were recapitulated in two uveal melanoma PDX models through subcutaneous ASO delivery. SAMMSON pulldown revealed several candidate interaction partners, including various proteins involved in mitochondrial translation. Consequently, inhibition of SAMMSON impaired global protein translation levels and mitochondrial function in uveal melanoma cells.ConclusionSAMMSON expression is essential for uveal melanoma cell survival. ASO-mediated silencing of SAMMSON may provide an effective treatment strategy to treat primary and metastatic uveal melanoma patients.

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