SUZ12 Loss Amplifies the Ras/ERK Pathway by Activating Adenylate Cyclase 1 in NF1-Associated Neurofibromas

Patients with germline neurofibromatosis type 1 (NF1) microdeletions frequently exhibit hereditary syndromes such as cardiovascular anomalies and have an increased risk of malignant peripheral nerve sheath tumors (MPNSTs). This study aimed to identify the genes codeleted with SUZ12 that are related to MPNST. We used differential gene expression and enrichment analyses to analyze the SUZ12-mutant and SUZ12-wild-type gene expression profiles in the GSE118186 and GSE66743 datasets in Gene Expression Omnibus (GEO). PPI network analysis combined with MPNST patient survival analysis was used to identify ADCY1, which catalyzes the conversion of ATP to cAMP, as a key gene. Moreover, chromatin immunoprecipitation sequencing (ChIP-Seq) showed that the distribution of H3K27me3 in the ADCY1 promoter region and gene body was significantly reduced in SUZ12-mutant cells. To verify the role of ADCY1 in SUZ12 mutation, we used RNA interference and plasmid transfection to interfere with SUZ12 expression in plexiform neurofibroma (pNF) and MPNST cell lines and then treated the cells with forskolin, IBMX and H89. ERK phosphorylation was accelerated and prolonged after siRNA transfection, especially in ipNF05.5 cells, and the intensity and duration of ERK activation were reduced after SUZ12 overexpression. Importantly, the level of p-ERK was consistent with that of Rap1-GTP. Moreover, H89 completely blocked Rap1 activation and the changes in the p-ERK level after SUZ12 siRNA transfection. In conclusion, our findings suggested that SUZ12 loss potentiates the effects of NF1 mutations by amplifying Ras signaling through the ADCY1/cAMP/Rap1/ERK pathway and that SUZ12 may serve as a therapeutic and prognostic biomarker in NF1-associated neurofibromas.

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A novel association between GSTM1 null variant and anthracycline-induced cardiac dysfunction (ACD) in childhood cancer survivors (CCS): A COG ALTE03N1 report.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.10030 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. 10030-10030

Author(s):

Purnima Singh ◽

Xuexia Wang ◽

Lindsey Hageman ◽

Yanjun Chen ◽

Tarek Magdy ◽

...

Keyword(s):

Gene Expression ◽

Cancer Survivors ◽

Childhood Cancer ◽

Expression Profiles ◽

Conditional Logistic Regression ◽

Gene Expression Profiles ◽

Childhood Cancer Survivors ◽

Differentially Expressed ◽

Gstm1 Null Genotype ◽

Increased Risk

10030 Background: ACD is a leading cause of mortality in CCS. Previous studies have identified genomic variants that moderate the ACD risk. An agnostic evaluation of differential gene expression between those with and without ACD has not been explored, and could provide insights into the mechanism of cardiotoxicity. Methods: Gene expression profiles in leukocyte RNA from anthracycline-exposed non-Hispanic white (NHW) CCS (20 with ACD [cases]; 20 without ACD [controls]) used Illumina HumanHT-12 v4.0 Expression Beadchips. Gene expression profiles in h uman iPSC-derived cardiomyocytes (hiPSC-CMs – Day 30) from 6 childhood cancer patients (3 each with and without CD) treated with 1μM doxorubicin or vehicle for 24 h, used RNA-seq. Genotyping in leukocyte DNA from anthracycline-exposed NHW CCS (65 cases; 76 controls) to determine if the differentially-expressed genes mapped to genetic variants that modified ACD risk, used conditional logistic regression analysis adjusted for sex, age at cancer diagnosis, chest radiation and anthracycline dose. Patient characteristics are in Table. Results: Gene-expression in survivors:Glutathione S transferase mu 1 ( GSTM1) was differentially-expressed; RT q-PCR showed significant downregulation of GSTM1 in cases (0.67±0.57 vs. 1.33±1.33, p=0.049). hiPSC-CMs gene expression: GSTM1 was downregulated in patients with ACD (logFC = -1.4). Genotyping: Using PCR for GSTM1 null, we observed a significant association between CD risk and GSTM1 null genotype (OR=3.0; 95%CI, 1.4-6.2, p=0.003). Conclusions: We report an association between GSTM1 null genotype and ACD, previously unreported likely because GWAS studies did not examined gene deletions. GSTM1 is involved in detoxification of anthracyclines. This finding could facilitate identification of childhood cancer survivors at increased risk of ACD. [Table: see text]

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Naproxen chemoprevention promotes immune activation in Lynch syndrome colorectal mucosa

Gut ◽

10.1136/gutjnl-2020-320946 ◽

2020 ◽

pp. gutjnl-2020-320946

Author(s):

Laura Reyes-Uribe ◽

Wenhui Wu ◽

Ozkan Gelincik ◽

Prashant V Bommi ◽

Alejandro Francisco-Cruz ◽

...

Keyword(s):

Gene Expression ◽

Clinical Trial ◽

Lynch Syndrome ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Predictive Biomarkers ◽

Colorectal Mucosa ◽

Genetically Engineered Mouse Model ◽

Increased Risk

ObjectivePatients with Lynch syndrome (LS) are at markedly increased risk for colorectal cancer. It is being increasingly recognised that the immune system plays an essential role in LS tumour development, thus making an ideal target for cancer prevention. Our objective was to evaluate the safety, assess the activity and discover novel molecular pathways involved in the activity of naproxen as primary and secondary chemoprevention in patients with LS.DesignWe conducted a Phase Ib, placebo-controlled, randomised clinical trial of two dose levels of naproxen sodium (440 and 220 mg) administered daily for 6 months to 80 participants with LS, and a co-clinical trial using a genetically engineered mouse model of LS and patient-derived organoids (PDOs).ResultsOverall, the total number of adverse events was not different across treatment arms with excellent tolerance of the intervention. The level of prostaglandin E2 in the colorectal mucosa was significantly decreased after treatment with naproxen when compared with placebo. Naproxen activated different resident immune cell types without any increase in lymphoid cellularity, and changed the expression patterns of the intestinal crypt towards epithelial differentiation and stem cell regulation. Naproxen demonstrated robust chemopreventive activity in a mouse co-clinical trial and gene expression profiles induced by naproxen in humans showed perfect discrimination of mice specimens with LS and PDOs treated with naproxen and control.ConclusionsNaproxen is a promising strategy for immune interception in LS. We have discovered naproxen-induced gene expression profiles for their potential use as predictive biomarkers of drug activity.Trial registration numbergov Identifier: NCT02052908

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Comparison and Identification of Estrogen-Receptor Related Gene Expression Profiles in Breast Cancer of Different Ethnic Origins

Breast Cancer Basic and Clinical Research ◽

10.4137/bcbcr.s626 ◽

2008 ◽

Vol 1 ◽

pp. BCBCR.S626 ◽

Cited By ~ 1

Author(s):

Hsiao-Wei Chen ◽

Hsuan-Cheng Huang ◽

Yi-Shing Lin ◽

King-Jen Chang ◽

Wen-Hung Kuo ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Estrogen Receptor ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Microarray Experiment ◽

Breast Cancer Patients ◽

Related Gene ◽

Increased Risk ◽

Ethnic Origins

The interactions between genetic variants in estrogen receptor (ER) have been identified to be associated with an increased risk of breast cancer. Available evidence indicates that genetic variance within a population plays a crucial role in the occurrence of breast cancer. Thus, the comparison and identification of ER-related gene expression profiles in breast cancer of different ethnic origins could be useful for the development of genetic variant cancer therapy. In this study, we performed microarray experiment to measure the gene expression profiles of 59 Taiwanese breast cancer patients; and through comparative bioinformatics analysis against published U.K. datasets, we revealed estrogen-receptor (ER) related gene expression between Taiwanese and British patients. In addition, SNP databases and statistical analysis were used to elucidate the SNPs associated with ER status. Our microarray results indicate that the expression pattern of the 65 genes in ER+ patients was dissimilar from that of the ER- patients. Seventeen mutually exclusive genes in ER-related breast cancer of the two populations with more than one statistically significant SNP in genotype and allele frequency were identified. These 17 genes and their related SNPs may be important in population-specific ER regulation of breast cancer. This study provides a global and feasible approach to study population-unique SNPs in breast cancer of different ethnic origins.

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Clinical, genomic, and imaging predictors of malignancy: Analysis of the first U.S. cooperative group prospective clinical trial in asymptomatic monoclonal gammopathies (SWOG S0120).

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.8515 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. 8515-8515

Author(s):

Madhav V. Dhodapkar ◽

Rachel Sexton ◽

Sarah Waheed ◽

Saad Zafar Usmani ◽

Xenofon Dimitrios Papanikolaou ◽

...

Keyword(s):

Gene Expression ◽

Clinical Trial ◽

Tumor Cells ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cooperative Group ◽

Precursor Phase ◽

Increased Risk ◽

Risk Of Progression ◽

Clinical Genomic

8515 Background: Asymptomatic monoclonal gammopathies (AMG) are the most common plasma cell dyscrasia classified as either monoclonal gammopathy of undetermined significance (MGUS) or asymptomatic multiple myeloma (AMM). Clinical outcome in AMGs can be highly variable and there is an unmet need to identify newer clinical, genomic and imaging parameters from prospective studies to guide patient management. Methods: We analyzed clinical, genomic and imaging data from AMG patients (n=334) enrolled in a prospective observational clinical trial (S0120) conducted under the auspices of SWOG. Baseline data from clinical variables, as well as gene expression profiles of purified tumor cells and the findings on magnetic resonance imaging (MRI) were correlated with the risk of progression to symptomatic myeloma (MM) requiring therapy. Results: In addition to serum M spike, percent bone marrow plasma cells and the ratio of involved/uninvolved serum free light chains, the level of serum beta-2-microglobulin was associated with an increased risk of progression to clinical myeloma requiring therapy. Gene expression profiles (GEP) of purified tumor cells revealed that all of the known molecular GEP subtypes of human MM are also represented in the precursor phase. An increased risk score (> - 0.26) based on a 70-gene signature (GEP70) was an independent predictor of the risk of progression to clinical MM requiring therapy. The presence of focal lesions on MRI also conferred an increased risk of disease progression but was not independent of other clinical and genomic features. Conclusions: These data represent the first comprehensive evaluation of clinical, genomic and imaging features of AMGs in the context of a prospective US-cooperative group trial, and demonstrate that while all genetic subtypes of MM have a precursor phase, genetic signatures previously associated with high risk myeloma also predict the risk of progression to clinical malignancy requiring therapy. These findings suggest the need to integrate both clinical assessment of tumor bulk and genomic properties of tumor cells in the clinical management of these patients. Clinical trial information: NCT00900263.

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Using Gene Expression Profiles to Identify a Clinically Distinct ARDS Phenotype Associated with Increased Risk of Long-Term Disability

10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2611 ◽

2020 ◽

Author(s):

J.A. Howrylak ◽

M. Moll ◽

V. Walter ◽

T. Dolinay ◽

L. Schultz ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Increased Risk

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Dissection of Clinical and Gene Expression Signatures of Familial versus Multifactorial Chylomicronemia

Journal of the Endocrine Society ◽

10.1210/jendso/bvaa056 ◽

2020 ◽

Vol 4 (6) ◽

Author(s):

Karine Tremblay ◽

Daniel Gaudet ◽

Etienne Khoury ◽

Diane Brisson

Keyword(s):

Gene Expression ◽

Roc Curve ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Poor Response ◽

Postprandial Metabolism ◽

Increased Risk ◽

Gene Expression Analyses ◽

Eruptive Xanthomas ◽

New Treatments

Abstract Familial chylomicronemia syndrome (FCS) is a rare disorder associated with chylomicronemia (CM) and an increased risk of pancreatitis. Most individuals with CM do not have FCS but exhibit multifactorial CM (MCM), which differs from FCS in terms of risk and disease management. This study aimed to investigate clinical and gene expression profiles of FCS and MCM patients. Anthropometrics, clinical, and biochemical variables were analyzed in 57 FCS and 353 MCM patients. Gene expression analyses were performed in a subsample of 19 FCS, 28 MCM, and 15 normolipidemic controls. Receiver operating characteristic (ROC) curve analyses were performed to analyze the capacity of variables to discriminate FCS from MCM. Sustained fasting triglycerides ≥20 mmol/L (>15 mmol/L with eruptive xanthomas), history of pancreatitis, poor response to fibrates, diagnosis of CM at childhood, body mass index <22 kg/m2, and delipidated apolipoprotein B or glycerol levels <0.9 g/L and <0.05 mmol/L, respectively, had an area under the ROC curve ≥0.7. Gene expression analyses identified 142 probes differentially expressed in FCS and 32 in MCM compared with controls. Among them, 13 probes are shared between FCS and MCM; 63 are specific to FCS and 2 to MCM. Most FCS-specific or shared biomarkers are involved in inflammatory, immune, circadian, postprandial metabolism, signaling, docking systems, or receptor-mediated clearance mechanisms. This study reveals differential signatures of FCS and MCM. It opens the door to the identification of key mechanisms of CM expression and potential targets for the development of new treatments.

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Activated Ral and Mutated RAS Are Independent Drivers of Multiple Myeloma Cell Survival.

Blood ◽

10.1182/blood-2018-99-119804 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 3217-3217

Author(s):

Marcel Seibold ◽

Thorsten Stuehmer ◽

Anja Mottok ◽

Claus J Scholz ◽

Manik Chatterjee ◽

...

Keyword(s):

Gene Expression ◽

Mass Spectrometry ◽

Multiple Myeloma ◽

Cell Survival ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Ras Signaling ◽

Functional Link ◽

Oncogenic Ras ◽

Interaction Partners

Abstract Introduction RAS-associated pathways are promising therapeutic targets in RAS-driven tumors because oncogenic RAS itself is not druggable. Alongside the pathways via PI3K/AKT and RAF/MAPK, the small GTPase RAL is considered to represent a third route for oncogenic RAS signaling, which mediates malignant transformation and tumor cell survival. We performed shRNA-mediated knockdown studies in multiple myeloma (MM) cells to investigate the functional role of RAL activity and to analyze the putative functional link between oncogenic RAS and RAL. Moreover, we used screening approaches to identify possible RAL effectors and interacting partners. Methods First, we analyzed expression of the isoforms RALA and RALB in bone marrow biopsies (n=24) and in CD138+ selected primary MM cell samples (n=10) by immunohistochemistry and Western blotting, respectively. Next, we generated two isoform-specific shRNA expression vectors for each of the RAL isoforms to perform RNAi-mediated RAL knockdown and to analyze the functional consequences of RAL abrogation. Experiments were also carried out in combination with clinical anti-myeloma drugs. Furthermore, we treated MM cells with a recently developed pharmacological RAL inhibitor. MM cell survival and apoptotic cells were measured by flow cytometry with annexin V/propidium iodide staining. Changes in RAF/MAPK, PI3K/AKT or RAL pathway activation were detected by Western analysis. We then combined RAL pulldown and knockdown of mutated RAS to investigate the functional link between RAL activation and oncogenic RAS signaling. In addition, we compared RAS- and RAL-mediated gene expression profiles by RNA sequencing. Last, we used mass spectrometry to identify potential RAL effectors and interaction partners. Results RAL protein was detected in all MM cells tested, with RALA showing ubiquitously strong expression and RALB showing more heterogeneous stainings. In contrast, RALA and RALB expression was weak or absent in MGUS or normal plasma cells. MM cell survival was strongly impaired by shRNA-mediated RALA or RALB knockdown, with cell survival rates of 25% or 40 % in L-363 cells and 32% or 52% in MM.1S cells, respectively. No cross-activation between RAL and PI3K/AKT or RAF/MAPK pathways could be detected in MM cell lines. Pharmacological RAL inhibition was achieved in an MM subgroup at concentrations of 20 µM. Combining RAL knockdown and treatment with carfilzomib, pomalidomide, or ixazomib led to enhanced cell death induction. Of note, knockdown of oncogenic RAS also strongly reduced MM cell survival, but did not change constitutive RAL activation as detected by pulldown assay. Moreover, RNA sequencing after RAS or RAL knockdown produced differential gene expression profiles (1473 KRAS-regulated genes versus 771 RALA-regulated genes, with an overlap of 235 genes), again suggesting that both targets represent distinct signaling pathways. Using mass spectrometry, we identified novel RAL interaction partners which are currently being evaluated. Conclusion Our data indicate that the RAL signaling pathway constitutes a promising therapeutic target in MM and mediates MM cell survival and apoptosis independently of oncogenic RAS. Clinical translation of novel pharmacological RAL inhibitors may therefore be a future therapeutic strategy to tackle MM. Disclosures No relevant conflicts of interest to declare.

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Gene expression profiles of esophageal squamous cell cancers in Hodgkin lymphoma survivors versus sporadic cases

PLoS ONE ◽

10.1371/journal.pone.0243178 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243178

Author(s):

Berbel L. M. Ykema ◽

Sanne J. M. Hoefnagel ◽

Lisanne S. Rigter ◽

Liudmila L. Kodach ◽

Gerrit A. Meijer ◽

...

Keyword(s):

Gene Expression ◽

Hodgkin Lymphoma ◽

Rna Sequencing ◽

Squamous Cell ◽

Expression Profiles ◽

Cell Cancer ◽

Gene Expression Profiles ◽

Second Primary ◽

Increased Risk ◽

Sporadic Cases

Hodgkin lymphoma (HL) survivors are at increased risk of developing second primary esophageal squamous cell cancer (ESCC). We aimed to gain insight in the driving events of ESCC in HL survivors (hESCC) by using RNA sequencing and NanoString profiling. Objectives were to investigate differences in RNA signaling between hESCC and sporadic ESCC (sESCC), and to look for early malignant changes in non-neoplastic esophageal tissue of HL survivors (hNN-tissue). We analyzed material of 26 hESCC cases, identified via the Dutch pathology registry (PALGA) and 17 sESCC cases from one academic institute and RNA sequencing data of 44 sESCC cases from TCGA. Gene expression profiles for the NanoString panel PanCancer IO 360 were obtained from 16/26 hESCC and four hNN-tissue, while non-neoplastic squamous tissue of four sporadic cases (sNN-tissue) served as reference profile. Hierarchical clustering, differential expression and pathway analyses were performed. Overall, the molecular profiles of hESCC and sESCC were similar. There was increased immune, HMGB1 and ILK signaling compared to sNN-tissue. The profiles of hNN-tissue were distinct from sNN-tissue, indicating early field effects in the esophagus of HL survivors. The BRCA1 pathway was upregulated in hESCC tissue, compared to hNN tissue. Analysis of expression profiles reveals overlap between hESCC and sESCC, and differences between hESCC and its surrounding hNN-tissue. Further research is required to validate our results and to investigate whether the changes observed in hNN-tissue are already detectable before development of hESCC. In the future, our findings could be used to improve hESCC patient management.

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