scholarly journals Combinatorial Genetics Uncovers Novel Targets for the Treatment of Npm1/Cohesin Mutated AML

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2598-2598
Author(s):  
Alison E Meyer ◽  
Cary Stelloh ◽  
Joseph B Fisher ◽  
Kirthi Pulakanti ◽  
George S. Vassiliou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Research Funding ◽  
Double Mutant ◽  
Cancer Genome ◽  
Cohesin Complex ◽  
Self Renewal ◽  
Cancer Genome Atlas ◽  
Equity Ownership ◽  
Genome Atlas

Abstract Current precision medicine approaches typically target a single genetic mutation. However, adult acute myeloid leukemia (AML) is difficult to treat due to its genetic complexity. Approximately 30 somatic mutations have been found to be recurrent, with an average of 5-15 mutations present per patient (Cancer Genome Atlas 2013). Therefore, combinatorial genetic approaches have the power to uncover novel gene targets that can be used to tailor therapies to an individual's unique mutational spectrum. Mutations in NPM1 commonly occur in in AML. Approximately 25-30% of patients harbor a specific variant of the NPM1 mutation referred to as NPM1cA, which results in mislocalization of the Npm1 protein from the nucleus to the cytoplasm (Cancer Genome Atlas 2013; Falini 2005). While NPM1cA is considered to be a driver of AML development, mice with this mutation develop AML with a long latency (18 months) and with incomplete penetrance (Vassiliou 2011). In addition, those mice that do develop AML acquire additional genetic mutations, suggesting that NPM1cA cooperates with serially acquired mutations to drive AML development (Dovey 2017). It was recently discovered that mutations in the cohesin complex (consisting of the genes STAG2, SMC1A, SMC3, and RAD21) are also common in AML, with mutation in any of the four components resulting in haploinsufficiency (Cancer Genome Atlas 2013). Cohesin haploinsufficiency is enriched in patients with NPM1 mutations. Although cohesin mutations alone are insufficient to generate AML in mice (Viny 2015), they do result in increased hematopoietic stem and progenitor cell (HSPC) self-renewal (Mazumdar 2015; Fisher 2017). As the cohesin complex has known roles in chromosomal organization and the regulation of gene expression, we hypothesized that cohesin mutations would cooperate with NPM1cA to uniquely alter gene expression, resulting in AML. We crossed inducible NPM1cAflox/+ and SMC3flox/+ mouse models to examine this genetic interaction. Our current data show that the double mutant mice develop AML with increased penetrance compared with the Npm1cA/+ mice alone, with a trend toward decreased latency. The double mutant HSPCs also exhibit increased self-renewal in vitro compared to the Npm1cA/+ or SmcΔ/+ single mutants. To examine changes in gene expression, we performed RNA sequencing on lineage-depleted bone marrow in 3 mice from each genotype (WT, Npm1cA/+, Smc3Δ/+, and double) 4 weeks post excision. Consistent with our hypothesis, additive changes in gene expression were not observed. Instead, a unique set of genes were found to be deregulated in Npm1cA/+; Smc3Δ/+ marrow. In an effort to specifically target Npm1cA/+; Smc3Δ/+ mutant AML, we screened our list of uniquely-affected genes for those associated with AML. We found DOCK1 to be overexpressed in the double, but not Npm1cA/+ single, cells. High expression of this gene has been correlated with decreased overall and disease-free survival in AML patients (Lee 2017). To determine if DOCK1 contributes to the enhanced cell growth observed in vitro in our leukemic lines, we used an inhibitor that targets Dock1. This inhibitor induced apoptosis in our double leukemic cell lines but was less effective in our NPM1 single mutant or WT cells. Additionally, no effect was observed with a genetically unrelated AML line, MLL-AF9. Similarly, shRNA-mediated knockdown of Dock1 resulted in decreased cell viability in Npm1cA/+; Smc3Δ/+ leukemic lines but not in Npm1cA/+ only lines. We thus hypothesize that Dock1 represents a unique target for the treatment of patients harboring the Npm1/Cohesin mutational combination. Our results provide validity to the concept that combinatorial genetics can be used to target the unique genetic landscape of an individual patient. Future studies will focus on the impact of Dock1 inhibition in human Npm1/Cohesion mutated AML cell lines. Disclosures Vassiliou: KYMAB: Consultancy, Equity Ownership; Celgene: Research Funding. Levine:Isoplexis: Equity Ownership; Epizyme: Patents & Royalties; Imago: Equity Ownership; Loxo: Consultancy, Equity Ownership; Janssen: Consultancy, Honoraria; Gilead: Honoraria; Prelude: Research Funding; Novartis: Consultancy; Celgene: Consultancy, Research Funding; Roche: Consultancy, Research Funding; C4 Therapeutics: Equity Ownership; Qiagen: Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

scholarly journals Role of INSL4 Signaling in Sustaining the Growth and Viability of LKB1-Inactivated Lung Cancer

2018 ◽  
Vol 111 (7) ◽  
pp. 664-674 ◽  
Author(s):  
Rongqiang Yang ◽  
Steven W Li ◽  
Zirong Chen ◽  
Xin Zhou ◽  
Wei Ni ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Transcriptome Profiling ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Growth And Survival ◽  
Cancer Genome Atlas ◽  
Lung Adenocarcinomas ◽  
Genome Atlas

Abstract Background The LKB1 tumor suppressor gene is commonly inactivated in non-small cell lung carcinomas (NSCLC), a major form of lung cancer. Targeted therapies for LKB1-inactivated lung cancer are currently unavailable. Identification of critical signaling components downstream of LKB1 inactivation has the potential to uncover rational therapeutic targets. Here we investigated the role of INSL4, a member of the insulin/IGF/relaxin superfamily, in LKB1-inactivated NSCLCs. Methods INSL4 expression was analyzed using global transcriptome profiling, quantitative reverse transcription PCR, western blotting, enzyme-linked immunosorbent assay, and RNA in situ hybridization in human NSCLC cell lines and tumor specimens. INSL4 gene expression and clinical data from The Cancer Genome Atlas lung adenocarcinomas (n = 515) were analyzed using log-rank and Fisher exact tests. INSL4 functions were studied using short hairpin RNA (shRNA) knockdown, overexpression, transcriptome profiling, cell growth, and survival assays in vitro and in vivo. All statistical tests were two-sided. Results INSL4 was identified as a novel downstream target of LKB1 deficiency and its expression was induced through aberrant CRTC-CREB activation. INSL4 was highly induced in LKB1-deficient NSCLC cells (up to 543-fold) and 9 of 41 primary tumors, although undetectable in all normal tissues except the placenta. Lung adenocarcinomas from The Cancer Genome Atlas with high and low INSL4 expression (with the top 10th percentile as cutoff) showed statistically significant differences for advanced tumor stage (P < .001), lymph node metastasis (P = .001), and tumor size (P = .01). The INSL4-high group showed worse survival than the INSL4-low group (P < .001). Sustained INSL4 expression was required for the growth and viability of LKB1-inactivated NSCLC cells in vitro and in a mouse xenograft model (n = 5 mice per group). Expression profiling revealed INSL4 as a critical regulator of cell cycle, growth, and survival. Conclusions LKB1 deficiency induces an autocrine INSL4 signaling that critically supports the growth and survival of lung cancer cells. Therefore, aberrant INSL4 signaling is a promising therapeutic target for LKB1-deficient lung cancers.

scholarly journals The JAK1/2 Inhibitor Ruxolitinib Downregulates the Immune Checkpoint Protein B7-H3 in Multiple Myeloma

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1824-1824
Author(s):  
Ning Xu ◽  
Nicole Ng ◽  
Mingjie Li ◽  
Erin Yu ◽  
Eric Sanchez ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Immune Checkpoint ◽  
Research Funding ◽  
Flow Cytometric Analysis ◽  
Cell Activity ◽  
Cytokine Signaling ◽  
Checkpoint Protein ◽  
Equity Ownership

Introduction: The JAKSTAT pathway plays a critical role in the regulation of hematopoietic pathways and immunological cytokine signaling. The JAK pathway is also involved in tumor cell proliferation and drug resistance in multiple myeloma (MM). Thus, inhibition of the JAK pathway should be a potentially effective strategy for treating MM patients. B7-H3 is an immune checkpoint protein in the B7 superfamily and has been shown overexpressed in several tumors. Immune checkpoint blockade may suppress tumor progression or enhance anti-tumor immune responses. In this study, we investigated the effects of the JAK1/2 inhibitor ruxolitinib (Rux) on B7-H3 in MM. Materials and Methods: Bone marrow mononuclear cells (BMMCs) were collected from MM patients after obtaining IRB approval. Single-cell suspensions were prepared from human MM LAGλ-1A xenografts which had been grown in severe combined immunodeficient mice. HS-5 stromal and SUP-T1 T cells were purchased from ATCC. The cells were cultured and treated with or without RUX and then subjected to qRT-PCR, flow cytometric analysis, and western blot analysis. For qRT-PCR, total RNA was extracted and applied to cDNA synthesis, followed by qPCR. Gene expression was analyzed in MM BMMCs alone or co-cultured with stromal cells or T cells with or without Rux treatment (1μM) in vitro. Results: We identified increased B7-H3 expression in MMBMMCs from patients with progressive disease (PD) patients compared to those in complete remission (CR). Rux significantly reduced B7-H3 expression in MMBMMCs in patients with PD, MM cells (U266), and BM from patients in PD when co-cultured with stromal cells (HS-5) after 48-72 hours. Rux decreased B7H3 expression in the human MM xenograft model LAGλ-1A when cultured ex vivo. In addition, Rux suppressed B7-H3 at protein levels as shown with flow cytometric analysis and western blotting, consistent with the gene expression results. Next, we tested whether B7-H3 blockade by Rux could potentially restore exhausted T cell activity against myeloma cells in MMBM. We found that Rux can increase IL-2 and CD8 gene expression in MMBM with lower plasma percentages (< 30%) but not among those with higher plasma cell percentages (>70%). Rux also elevated IL-2 and CD8 gene expression in BM when it was cocultured with T cells (SUP-T1), suggesting Rux may mediate immunological cytokine signaling. B7-H3-neutralizing antibody increased CD8 gene expression in MMBM in vitro, suggesting that one of the mechanisms through which Rux upregulates CD8 T cells in MMBM may be via downregulation of B7-H3. Conclusion: The immune checkpoint protein B7-H3 is overexpressed in MMBM in PD compared to CR patients. The JAK1/2 inhibitor Rux can decrease B7-H3 expression and increase IL-2 and CD8 expression in BM in vitro. Our results provide evidence for Rux inhibiting the immune checkpoint protein B7-H3 which may potentially restore exhausted T-cell activity in the MMBM tumoral microenvironment. Disclosures Chen: Oncotraker Inc: Equity Ownership. Berenson:Amgen: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau; Sanofi: Consultancy; Sanofi: Consultancy; Amag: Consultancy, Speakers Bureau; Amag: Consultancy, Speakers Bureau; Janssen: Consultancy, Speakers Bureau; OncoTracker: Equity Ownership, Other: Officer; OncoTracker: Equity Ownership, Other: Officer; Bristol-Myers Squibb: Honoraria, Research Funding; Bristol-Myers Squibb: Honoraria, Research Funding; Incyte Corporation.: Consultancy, Research Funding; Incyte Corporation.: Consultancy, Research Funding; Takeda: Consultancy, Speakers Bureau; Takeda: Consultancy, Speakers Bureau; Janssen: Consultancy, Speakers Bureau.

Leukemia Stem Cell Potential of Different Progenitor Subpopulations in Myeloid Blast Phase CML

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3489-3489
Author(s):  
Ross Kinstrie ◽  
Dimitris Karamitros ◽  
Nicolas Goardon ◽  
Heather Morrison ◽  
Richard E Clark ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Research Funding ◽  
Cell Populations ◽  
Novel Therapies ◽  
Blast Phase ◽  
Self Renewal ◽  
Stem Cell Populations

Abstract Blast phase (BP)-CML remains the most critical area of unmet clinical need in the management of CML and novel, targeted therapeutic strategies are urgently needed. In the tyrosine kinase inhibitor (TKI) era, the rate of progression to BP is 1 to 1.5% per annum in the first few years after diagnosis, falling sharply when major molecular response is obtained. Around 10% of patients present with de novo BP-CML and despite the use of TKIs, median survival after the diagnosis of BP-CML is between 6.5 and 11 months.Therefore, improved understanding of the biology of BP-CML and novel therapies to prolong therapeutic responses are urgently sought. Studies of myeloid malignancies show that acquisition of tumor-associated mutations occurs principally in a step-wise manner. Initiating mutations usually originate in an hematopoietic stem cell (HSC) to give rise to preleukemic stem cell populations that expand through clonal advantage. Further mutation acquisition and/or epigenetic changes then lead to blast transformation and disruption of the normal immunophenotypic and functional hematopoietic hierarchy. At this stage, multiple leukemic stem cell (LSC) populations (also termed leukemia initiating cell populations) can be identified. We previously showed, in AML, that the CD34+ LSC populations were most closely related to normal progenitor populations, rather than stem cell populations, but had co-opted elements of a normal stem cell expression signature to acquire abnormal self-renewal potential (Goardon et al, Cancer Cell, 2011). CD34+CD38- LSCs were most commonly similar to an early multi-potent progenitor population with lympho-myeloid potential (the lymphoid-primed multi-potential progenitor [LMPP]). In contrast, the CD34+CD38+ LSCs were most closely related to the more restricted granulocyte-macrophage progenitor (GMP). In chronic phase CML, the leukemia-propagating population is the HSC, and the progenitor subpopulations do not have stem cell characteristics. To date, studies to isolate LSC populations in BP-CML have been limited, identifying the GMP subpopulation only as a possible LSC source (Jamieson et al, NEJM, 2004). Furthermore, in vivo LSC activity has not been assessed. We therefore set out to assess the LSC characteristics of different primitive progenitor subpopulations in myeloid BP-CML both in vitro and in vivo. We isolated different stem and progenitor cell subpopulations using FACS; HSC (Lin-CD34+CD38-CD90+ CD45RA-), multipotent progenitor (MPP; Lin-CD34+CD38-CD90-CD45RA-), LMPP (Lin-CD34+CD38-CD90-CD45RA+), common myeloid progenitor (CMP; Lin-CD34+CD38+CD45RA-CD123+), GMP (Lin-CD34+CD38+CD45RA+CD123+) and megakaryocyte erythroid progenitor (MEP; Lin-CD34+CD38+CD45RA-CD123-). The functional potential of these purified populations was examined in 13 patients by: (i) serial CFC replating assays to study progenitor self-renewal (n=10); (ii) In vivo xenograft studies using NSG mice with serial transplantation to identify populations with LSC potential (n=6). Our data conclusively demonstrate that functional LSCs are present in multiple immunophenotypic stem/progenitor subpopulations in myeloid BP-CML, including HSC, MPP, LMPP, CMP and GMP subpopulations. There was inter-patient variability in terms of both in vitro and in vivo functional properties. Fluorescence in situ hybridisation (FISH) was used to assess clonality in the different progenitor subpopulations and identify which populations contained cells with additional cytogenetic abnormalities (ACAs) with a view to improving our understanding of the clonal hierarchy. Interestingly, there were no significant differences in ACAs in the different progenitor subpopulations in the majority of samples studied, suggesting that clonal evolution tends to occur in the HSC compartment in myeloid BP-CML. Preliminary gene expression profiling studies of the different progenitor subpopulations, using Affymetrix Human Gene 1.0 ST Arrays, demonstrated highly variable gene expression, supporting the functional heterogeneity seen. Taken together, our results demonstrate that myeloid BP-CML is a very heterogeneous disorder with variable LSC populations. Further interrogation of these populations will likely identify novel therapies which will specifically target the LSC. Disclosures Copland: Bristol-Myers Squibb: Consultancy, Honoraria, Other, Research Funding; Novartis: Consultancy, Honoraria, Other; Ariad: Consultancy, Honoraria, Research Funding.

scholarly journals Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas

2018 ◽  
Author(s):  
SR Rosario ◽  
MD Long ◽  
HC Affronti ◽  
AM Rowsam ◽  
KH Eng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Flux ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Targeted Therapeutics ◽  
Bioinformatics Pipeline ◽  
Metabolic Dysregulation ◽  
Pathway Gene ◽  
Cancer Genome Atlas ◽  
Genome Atlas

AbstractUnderstanding the levels of metabolic dysregulation in different disease settings is vital for the safe and effective incorporation of metabolism-targeted therapeutics in the clinic. Using transcriptomic data from 10,704 tumor and normal samples from The Cancer Genome Atlas, across 26 disease sites, we developed a novel bioinformatics pipeline that distinguishes tumor from normal tissues, based on differential gene expression for 114 metabolic pathways. This pathway dysregulation was confirmed in separate patient populations, further demonstrating the robustness of this approach. A bootstrapping simulation was then applied to assess whether these alterations were biologically meaningful, rather than expected by chance. We provide distinct examples of the types of analysis that can be accomplished with this tool to understand cancer specific metabolic dysregulation, highlighting novel pathways of interest in both common and rare disease sites. Utilizing a pathway mapping approach to understand patterns of metabolic flux, differential drug sensitivity, can accurately be predicted. Further, the identification of Master Metabolic Transcriptional Regulators, whose expression was highly correlated with pathway gene expression, explains why metabolic differences exist in different disease sites. We demonstrate these also have the ability to segregate patient populations and predict responders to different metabolism-targeted therapeutics.

scholarly journals METTL3-Mediated m6A mRNA Modification of FBXW7 Suppresses Lung Adenocarcinoma

2020 ◽  
Author(s):  
Yingtong Wu ◽  
Ning Chang ◽  
Yong Zhang ◽  
Xinxin Zhang ◽  
Leidi Xu ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Cell Model ◽  
Biological Effects ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Luciferase Reporter ◽  
Rna Immunoprecipitation ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Abstract BackgroundFBXW7 m6A modification plays an important role in lung adenocarcinoma (LUAD) progression; however, the underlying mechanisms remain unclear.MethodsThe correlation between FBXW7 and various genes related to m6A modification was analyzed using The Cancer Genome Atlas database. The regulatory effects of METTL3 on FBXW7 mRNA m6A modification were examined in a cell model, and the underlying mechanism was determined by methylated RNA immunoprecipitation, RNA immunoprecipitation, luciferase reporter, and mutagenesis assays. In vitro experiments were performed to further explore the biological effects of METTL3-mediated FBXW7 m6A modification on LUAD development.ResultsDecreased FBXW7 expression was accompanied by downregulated METTL3 expression in human LUAD tissues and was associated with a worse prognosis for LUAD in The Cancer Genome Atlas database. m6A was highly enriched in METTL3-mediated FBXW7 transcripts, and increased m6A modification in the coding sequence region increased its translation. Functionally, METTL3 overexpression or knockdown affected the apoptosis and proliferation phenotype of LUAD cells by regulating FBXW7 m6A modification and expression. Furthermore, FBXW7 overexpression in METTL3-depleted cells partially restored the suppression of LUAD cells in vitro and in vivo.ConclusionsOur findings reveal that METTL3 positively regulates FBXW7 expression and confirm the tumor-suppressive role of m6A-modified FBXW7, thus providing insight into its epigenetic regulatory mechanisms in LUAD initiation and development.

scholarly journals The role of miR-92b in cholangiocarcinoma patients

2018 ◽  
Vol 33 (3) ◽  
pp. 293-300 ◽  
Author(s):  
Min-hang Zhou ◽  
Hong-wei Zhou ◽  
Mo Liu ◽  
Jun-zhong Sun
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Gene Expression Omnibus ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Positive Regulation ◽  
Cancer Genome Atlas ◽  
High Level ◽  
Genome Atlas

Purpose: The role of microRNA (miRNA) in cholangiocarcinoma was not clear. The aim of this study was to find the potential diagnostic and prognostic miRNA in cholangiocarcinoma patients. Methods: The miRNA expression profiles in cholangiocarcinoma patients from The Cancer Genome Atlas and Gene Expression Omnibus (GSE53870) were analyzed. The comparison of overall survival was performed using the Kaplan–Meier method. The targeted genes of prognostic miRNA were identified in miRanda, PicTar, or TargetScan, and their cell signaling pathways were analyzed by the Database for Annotation, Visualization and Integrated Discovery. Results: In The Cancer Genome Atlas and the Gene Expression Omnibus miRNA dataset, miR-92b and miR-99a were found with concordant directionality, up-regulated and down-regulated, respectively. In The Cancer Genome Atlas survival data, patients with the high level of miR-99b had obviously shorter overall survival time ( P=0.038). However, the level of miR-99a was not found to be significant. The 17 shared target genes of miR-92b were identified, such as DAB21IP, BCL21L11, SPHK2, PER2, and TSC1. The related pathways included positive regulation of transcription, positive regulation of cellular biosynthetic process, regulation of programmed cell death, etc. Conclusion: miR-92b was up-regulated in cholangiocarcinoma compared with normal controls. The high level of miR-92b was associated with adverse outcomes in cholangiocarcinoma patients, which might be partly explained by the targeted genes of miR-92b and their signaling pathways.

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