Including Tumor Suppressor Genes Research Articles

Molecular detection of exosomal miRNAs of blood serum for prognosis of colorectal cancer

Colorectal cancer (CRC) is the third most common cancer affecting people. The discovery of new, non-invasive, specific, and sensitive molecular biomarkers for CRC may assist in the diagnosis and support therapeutic decision making. Exosomal miRNAs have been demonstrated in carcinogenesis and CRC development, which makes these miRNAs strong biomarkers for CRC. Deep sequencing allows a robust high-throughput informatics investigation of the types and abundance of exosomal miRNAs. Thus, exosomal miRNAs can be efficiently examined as diagnostic biomarkers for disease screening. In the present study, a number of 660 mature miRNAs were detected in patients diagnosed with CRC at different stages. Of which, 29 miRNAs were differentially expressed in CRC patients compared with healthy controls. Twenty-nine miRNAs with high abundance levels were further selected for subsequent analysis. These miRNAs were either highly up-regulated (e.g., let-7a-5p, let-7c-5p, let-7f-5p, let-7d-3p, miR-423-5p, miR-3184-5p, and miR-584) or down-regulated (e.g., miR-30a-5p, miR-99-5p, miR-150-5p, miR-26-5p and miR-204-5p). These miRNAs influence critical genes in CRC, leading to either tumor growth or suppression. Most of the reported diagnostic exosomal miRNAs were shown to be circulating in blood serum. The latter is a novel miRNA that was found in exosomal profile of blood serum. Some of the predicted target genes of highly expressed miRNAs participate in several cancer pathways, including CRC pathway. These target genes include tumor suppressor genes, oncogenes and DNA repair genes. Main focus was given to multiple critical signaling cross-talking pathways including transforming growth factor β (TGFβ) signaling pathways that are directly linked to CRC. In conclusion, we recommend further analysis in order to experimentally confirm exact relationships between selected differentially expressed miRNAs and their predicted target genes and downstream functional consequences.

Abstract 7007: 5hmc-sequencing identifies candidate genes in Puerto Rican Hispanic/Latino men with aggressive prostate cancer

Abstract Introduction: Puerto Rican (PR) Hispanic/Latino (H/L) men are an understudied population which has the highest prostate cancer (PCa) specific mortality when compared with other Hispanic populations. According to the recent PR Cancer Registry data, PCa is the leading cancer type in terms of incidence (38% of all cancer cases) and mortality (16% of all cancer deaths) in PR H/L men. PR H/L men also have significantly higher PCa-specific mortality than non-Hispanic Whites (NHW) and non-Hispanic Blacks (NHB). So far, little is known about higher mortality in PR H/L men. It is believed that epigenetic changes of key genes play a critical role in aggressive tumors. Therefore, our study was aimed to identify key 5-hydroxymethylcytosine (5hmC) changes in PR H/L men with aggressive PCa. Methods: We prepared sequencing libraries using the enriched 5hmC DNA from 42 prostate tumor and 44 adjacent normal FFPE samples. We performed sequencing on an Illumina NextSeq 500 with 75bp single end. We used DESeq2 package to identify differentially methylated genes (DMGs). We also downloaded additional 5hmC data (Database: EGAS00001004942) of 51 localized PCa and 7 adjacent normal for confirmation analysis. We used Gleason score (GS) as a cut-off to identify DMGs in aggressive PCa patients (GS- 7 (3+4) or less, Non-aggressive; GS- 7 (4+3) and above, Aggressive). Results: We identified 808 DMGs in tumors compared to adjacent normal tissues (FDR<0.05, log2FC>|0.4|). Pathway analysis of DMGs demonstrated that cell-cycle, cell division, and DNA repair related pathways were most upregulated in tumors. Since 5hmC abundance is highly correlated with gene expression levels, we further investigated 808 DMGs with TCGA prostate cancer gene expression data. This analysis identified 59/73 DMGs (80.1%, (FDR<0.05, delta>|1|) with significant 5hmC and gene expression changes in the same direction. We also performed differential methylation analysis in another dataset and observed that 129 DMGs were common with our results. Finally, we demonstrated 111 DMGs (p<0.05) in aggressive tumors (n=7) compared to non-aggressive tumors (n=15). These 111 DMGs include important 5hmC hypomethylated genes (BCCIP and KLK10) and hypermethylated genes (COX6C, ARMC2, PVT1) in aggressive PCa patients. Conclusions: Our study identifies 59 genes having coordinated epigenetic and transcriptomic changes in PR H/L men and 111 DMGs in aggressive tumors. The coordinated 59 genes include tumor suppressor genes such as DKK3 and PRDM8 with downregulated 5hmC and gene expression levels. Also, previous studies reported downregulation of BCCIP and KLK10 and upregulation of COX6C, ARMC2, PVT1 expression in PCa. The coordinated changes in 5hmC could be critical in aggressive PCa biology, hence in future, these genes will be validated as candidate biomarkers and targets for aggressive PCa among PR H/L men. Citation Format: Manishkumar S. Patel, Muosa Almubarak, Jaime Matta, Carmen Ortiz-Sánchez, Jarline Encarnacion, Gilberto Ruiz-Deya, Julie Dutil, Jasreman Dhillon, Kosj Yamoah, Anders Berglund, Hyun Park, Liang Wang, Jong Y. Park. 5hmc-sequencing identifies candidate genes in Puerto Rican Hispanic/Latino men with aggressive prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7007.

Mechanisms of action and resistance in histone methylation-targeted therapy

Epigenomes enable the rectification of disordered cancer gene expression, thereby providing new targets for pharmacological interventions. The clinical utility of targeting histone H3 lysine trimethylation (H3K27me3) as an epigenetic hallmark has been demonstrated1–7. However, in actual therapeutic settings, the mechanism by which H3K27me3-targeting therapies exert their effects and the response of tumour cells remain unclear. Here we show the potency and mechanisms of action and resistance of the EZH1–EZH2 dual inhibitor valemetostat in clinical trials of patients with adult T cell leukaemia/lymphoma. Administration of valemetostat reduced tumour size and demonstrated durable clinical response in aggressive lymphomas with multiple genetic mutations. Integrative single-cell analyses showed that valemetostat abolishes the highly condensed chromatin structure formed by the plastic H3K27me3 and neutralizes multiple gene loci, including tumour suppressor genes. Nevertheless, subsequent long-term treatment encounters the emergence of resistant clones with reconstructed aggregate chromatin that closely resemble the pre-dose state. Acquired mutations at the PRC2–compound interface result in the propagation of clones with increased H3K27me3 expression. In patients free of PRC2 mutations, TET2 mutation or elevated DNMT3A expression causes similar chromatin recondensation through de novo DNA methylation in the H3K27me3-associated regions. We identified subpopulations with distinct metabolic and gene translation characteristics implicated in primary susceptibility until the acquisition of the heritable (epi)mutations. Targeting epigenetic drivers and chromatin homeostasis may provide opportunities for further sustained epigenetic cancer therapies.

Abstract 6271: Discovery of BR1733 for the treatment of SWI/SNF deficient or highly vascularized solid tumor

Abstract Polycomb repressive complex 2 (PRC2) catalyze the writing of H3K27me3 epigenetic marker and suppresses the expression of genes including tumor suppressors. Activation mutation of EZH2, the catalytic subunit of the PRC2 complex, drives the progression of tumors such as DLBCL. The embryonic ectoderm development (EED) protein acts as the scaffolding and H3K27me3-binding subunit of PRC2 and is essential for its activity. We have developed potent, selective, and orally bioavailable EED inhibitor BR1733. BR1733 blocks the interaction between EED and H3K27me3, and inhibits catalytic activity of PRC2. BR1733 showed superior PK profile across species and exhibited tumor growth inhibition against several B cell lymphoma CDX models. Indication expansion studies demonstrated that BR1733 could inhibit solid tumors with SWI/SNF loss-of-function mutation only when both CDKN2A and TET1 are expressed. BR1733 also inhibited tumor angiogenesis and showed tumor growth inhibition in several CDX models of highly vascularized solid tumors such as HCC and RCC. BR1733 is currently in Phase I clinical trials. Citation Format: Xinghao Wang, Shichao Ma, Min (Bella) Xie, Lele Wang, Yajun Wang, Song Zhang, Sheng Chen, Lynette Zhang, Yongqi Zhou, Mengxi Zhao, Dandan Li, Guobin Li, Xiao Fan, Hailong Zhang. Discovery of BR1733 for the treatment of SWI/SNF deficient or highly vascularized solid tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6271.

Abstract B013: Suppression of TET1 expression down-regulates p16 and contributes to the resistance of SWI/SNF LOF tumors to PRC2 inhibition

Abstract Polycomb repressive complex 2 (PRC2) drives the expansion of H3K27me3 epigenetic marker and suppress the expression of target genes including tumor suppressors. Activation mutations of EZH2, the catalytic subunit of the PRC2 complex, are thought to be the driver for certain malignancies such as diffused large B cell lymphoma (DLBCL). The SWI/SNF complex remodels nucleosomes to modulate transcription, they are generally considered as tumor suppressors and loss-of-function (LOF) mutations are frequently found across a wide variety of cancers. Many studies suggest that PRC2 is important for the proliferation of tumor cells with SWI/SNF LOF mutations, indeed, EZH2 inhibitor tazemetostat was approved by FDA for epithelioid sarcoma with SWI/SNF subunit SMARCB1 deletion. While not all SWI/SNF LOF tumors respond to PRC2 inhibition, we would like to know what subset of these tumors are sensitive to PRC2 inhibition. In this study, we have developed a potent and selective PRC2 inhibitor BR1763 which blocks the interaction of EED with tri-methylated histone H3 at Lys 27 (H3K27me3) and inhibits cellular H3K27me3 levels. By analyzing the gene expression patterns of BR1763 treated cells, we found that up-regulation of CDKN2A/p16 and down-regulation of E2F downstream gene are essential for cellular response to PRC2 inhibition. Further studies also confirmed that PRC2 inhibition caused P16 up-regulation and induced cell senescence for the sensitive cells. Importantly, suppression of TET1 expression contributes to the resistance to PRC2 inhibition in SWI/SNF LOF tumors, which may be caused by PcG hypermethylation on p16 promoters. TET1 expression, together with SWI/SNF LOF mutation status, can largely predict the sensitivity of tumor cells to PRC2 inhibition. Citation Format: Hailong Zhang. Suppression of TET1 expression down-regulates p16 and contributes to the resistance of SWI/SNF LOF tumors to PRC2 inhibition. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B013.

The Potential Role of Apigenin in Cancer Prevention and Treatment.

Cancer is the leading cause of death worldwide. In spite of advances in the treatment of cancer, currently used treatment modules including chemotherapy, hormone therapy, radiation therapy and targeted therapy causes adverse effects and kills the normal cells. Therefore, the goal of more effective and less side effects-based cancer treatment approaches is still at the primary position of present research. Medicinal plants or their bioactive ingredients act as dynamic sources of drugs due to their having less side effects and also shows the role in reduction of resistance against cancer therapy. Apigenin is an edible plant-derived flavonoid that has received significant scientific consideration for its health-promoting potential through modulation of inflammation, oxidative stress and various other biological activities. Moreover, the anti-cancer potential of apigenin is confirmed through its ability to modulate various cell signalling pathways, including tumor suppressor genes, angiogenesis, apoptosis, cell cycle, inflammation, apoptosis, PI3K/AKT, NF-κB, MAPK/ERK and STAT3 pathways. The current review mainly emphases the potential role of apigenin in different types of cancer through the modulation of various cell signaling pathways. Further studies based on clinical trials are needed to explore the role of apigenin in cancer management and explain the possible potential mechanisms of action in this vista.

Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer.

Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.

ASB2 is a direct target of FLI1 that sustains NF-\u03baB pathway activation in germinal center-derived diffuse large B-cell lymphoma

BackgroundDiffuse large B-cell lymphoma (DLBCL) comprises at least two main biologically distinct entities: germinal center B-cell (GCB) and activated B-cell (ABC) subtype. Albeit sharing common lesions, GCB and ABC DLBCL present subtype-specific oncogenic pathway perturbations. ABC DLBCL is typically characterized by a constitutively active NF-kB. However, the latter is seen in also 30% of GCB DLBCL. Another recurrent lesion in DLBCL is an 11q24.3 gain, associated with the overexpression of two ETS transcription factors, ETS1 and FLI1. Here, we showed that FLI1 is more expressed in GCB than ABC DLBCL and we characterized its transcriptional network.MethodsGene expression data were obtained from public datasets GSE98588, phs001444.v2.p1, GSE95013 and GSE10846. ChIP-Seq for FLI1 paired with transcriptome analysis (RNA-Seq) after FLI1 silencing (siRNAs) was performed. Sequencing was carried out using the NextSeq 500 (Illumina). Detection of peaks was done using HOMER (v2.6); differential expressed genes were identified using moderated t-test (limma R-package) and functionally annotated with g:Profiler. ChIP-Seq and RNA-Seq data from GCB DLBCL cell lines after FLI1 downregulation were integrated to identify putative direct targets of FLI1.ResultsAnalysis of clinical DLBCL specimens showed that FLI1 gene was more frequently expressed at higher levels in GCB than in ABC DLBCL and its protein levels were higher in GCB than in ABC DLBCL cell lines. Genes negatively regulated by FLI1 included tumor suppressor genes involved in negative regulation of cell cycle and hypoxia. Among positively regulated targets of FLI1, we found genes annotated for immune response, MYC targets, NF-κB and BCR signaling and NOTCH pathway genes. Of note, direct targets of FLI1 overlapped with genes regulated by ETS1, the other transcription factor gained at the 11q24.3 locus in DLBCL, suggesting a functional convergence within the ETS family. Positive targets of FLI1 included the NF-κB-associated ASB2, a putative essential gene for DLBCL cell survival. ASB2 gene downregulation was toxic in GCB DLBCL cell lines and induced NF-κB inhibition via downregulation of RelB and increased IκBα. Additionally, downregulation of FLI1, but not ASB2, caused reduction of NF-κB1 and RelA protein levels.ConclusionsWe conclude that FLI1 directly regulates a network of biologically crucial genes and processes in GCB DLBCL. FLI1 regulates both the classical NF-κB pathway at the transcriptional level, and the alternative NF-κB pathway, via ASB2. FLI1 and ASB2 inhibition represents a potential novel therapeutic approach for GCB DLBCL.

Regulation of CDK inhibitor p27 by microRNA 222 in breast cancer patients

BackgroundBreast cancer is the most common of all cancers and the second leading cause of cancer-related deaths among women worldwide. MicroRNAs regulate at least 60% of the human genes, including tumor suppressor genes and oncogenes, and can thereby affect cancer risk. In this study, the prognostic values of the CDK inhibitor p27 and miR-222 as biomarkers for breast cancer were evaluated. MethodsThe real-time quantitative polymerase chain reaction method was employed to measure the expression level of miR-222, whereas the serum levels of the CDK inhibitor p27 were measured via enzyme-linked immunosorbent assay. The levels were determined in sera from 110 participants representing three different groups. ResultsPatients with breast cancer exhibited significantly higher expression levels of miR-222 and lower levels of CDK inhibitor p27 than the control group. In addition, a statistically significant inverse correlation between miR-222 and the CDK inhibitor p27 was observed. The receiver operating characteristic curves plotted for serum p27 and miR-222 helped in significantly differentiating between breast cancer patients and controls but could not discriminate between those with stage II and stage III cancer. ConclusionThus, a significant upregulation in the serum miR-222 levels was observed in cancer patients, and a significant inverse correlation was noted between the miR-222 and CDK inhibitor p27 expression levels. These findings indicate that miR-222 may be used as a useful noninvasive screening biomarker for human breast cancer. MicroabstractNovel biomarkers for prognosis, prediction, and therapeutic purposes are essential as the prognosis and therapeutic targets of breast cancer are dependent on traditional markers, such as the tumor stage and hormonal receptor status. This study aimed to evaluate the diagnostic and prognostic values of the CDK inhibitor p27 and miR-222 in breast cancer. Our results indicated that miR-222 and the CDK inhibitor p27 may be used as noninvasive biomarkers to screen for human breast cancer but cannot discriminate between patients with early breast cancer and patients with advanced breast cancer.

Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer

Tumor development involves alterations in DNA methylation patterns, which include both gains (hypermethylation) and losses (hypomethylation) in different genomic regions. The mechanisms underlying these two opposite, yet co-existing, alterations in tumors remain unclear. While studying the human MAGEA6/GABRA3 gene locus, we observed that DNA hypomethylation in tumor cells can lead to the activation of a long transcript (CT-GABRA3) that overlaps downstream promoters (GABRQ and GABRA3) and triggers their hypermethylation. Overlapped promoters displayed increases in H3K36me3, a histone mark deposited during transcriptional elongation and known to stimulate de novo DNA methylation. Consistent with such a processive mechanism, increases in H3K36me3 and DNA methylation were observed over the entire region covered by the CT-GABRA3 overlapping transcript. Importantly, experimental induction of CT-GABRA3 by depletion of DNMT1 DNA methyltransferase, resulted in a similar pattern of regional DNA hypermethylation. Bioinformatics analyses in lung cancer datasets identified other genomic loci displaying this process of coupled DNA hypo/hypermethylation, and some of these included tumor suppressor genes, e.g. RERG and PTPRO. Together, our work reveals that focal DNA hypomethylation in tumors can indirectly contribute to hypermethylation of nearby promoters through activation of overlapping transcription, and establishes therefore an unsuspected connection between these two opposite epigenetic alterations.

Catalytic Space Engineering as a Strategy to Activate C-H Oxidation on 5-Methylcytosine in Mammalian Genome.

Conditional remodeling of enzyme catalysis is a formidable challenge in protein engineering. Herein, we have undertaken a unique active site engineering tactic to command catalytic outcomes. With ten-eleven translocation (TET) enzyme as a paradigm, we show that variants with an expanded active site significantly enhance multistep C-H oxidation in 5-methylcytosine (5mC), whereas a crowded cavity leads to a single-step catalytic apparatus. We further identify an evolutionarily conserved residue in the TET family with a remarkable catalysis-directing ability. The activating variant demonstrated its prowess to oxidize 5mC in chromosomal DNA for potentiating expression of genes including tumor suppressors.

Abstract 2081: Transcriptional silencing of CDK18 in BRG1 mutant lung cancer

Abstract In ~10% of lung cancers, the BRG1 gene is mutated often causing a loss of function (LOF). BRG1 is a tumor suppressor that encodes a protein (SMARCA4), which is one of the mutually exclusive ATPase subunits of the Switch/Sucrose Non-fermentable (SWI/SNF) complex. The SWI/SNF complex functions to regulate transcription of many genes including tumor suppressor genes, through mediating chromatin remodeling and nucleosome repositioning by maintaining open chromatin and actively evicting polycomb repressive complexes (PRCs) from target genes and regions. Our previous research showed that BRG1 mutation occurs in approximately 9% of lung adenocarcinomas in smokers and 11% in smokers delineating BRG1 as a clinically relevant mutation. The goal of these studies is to elucidate the downstream effects of BRG1 LOF on gene expression. RNA sequencing of isogenic BRG1 wild type (WT) and knock out (KO) clones from malignant and transformed cell lines identified cell cycle control and chromosomal replication as the most significantly affected pathway. qRT-PCR was used to validate expression changes in 17 genes from this pathway in the WT and KO clones as well as wild type and mutant tumors lines. CDK18 was the most significantly affected target exhibiting a 78% reduction in expression (p<0.001) comparing wild type to mutant cell lines. Ongoing studies are investigating the epigenetic mechanisms leading to transcriptional repression of CDK18 that include cytosine DNA methylation and histone methylation of H3K27. In addition, functional assays (e.g., soft agar, cell migration) are evaluating the role of epigenetically repressed CDK18 in lung carcinogenesis and cell cycle control through siRNA knock down of CDK18 in wild type BRG1 cell lines and carcinogen transformed human bronchial epithelial cells. Together, these studies will provide new insight into the role of LOF of CDK18 in BRG1 mutant cancer. (Supported by P30 CA11800). Citation Format: Loryn Michelle Phillips, Christopher A. Johnston, Steven A. Belinsky, Mathewos Tessema. Transcriptional silencing of CDK18 in BRG1 mutant lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2081.

Preferential In Vitro and In Vivo Induction of Endogenous Retrovirus Transcription from a Monoallelic Chromosome 7q in Decitabine (DAC) Treated AML Blasts

Background: Hypomethylating agents (HMAs) show an encouraging but not yet well-understood activity in AML/MDS patients (pts) with adverse cytogenetics, such as -7/7q-, often embedded in a complex, monosomal karyotype (Lübbert et al., Haematologica 2012). Integrative methylome/transcriptome studies have provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes (TSGs, Kotini et al., Nat. Biotechnol. 2015). Recently, an alternative mechanism of HMA action was described (Roulois et al., Chiappinelli et. al, Cell 2015): induction of silenced endogenous retroviral (ERV) dsRNA transcription, resulting in activation of an interferon-mediated, antitumor immune response (“viral mimicry”). To unravel in vivo HMA activity in different (cyto)genetic backgrounds, we hypothesized that in AML haploinsufficient for 7q, transcriptional repression of monoallelic genes in this region may be preferentially reversed by HMA treatment.Materials and Methods: For identification of genes induced by HMAs, two AML cell lines were selected, ELF-153 (ELF) and UCSD-AML1 (AML1): copy number variations were analyzed by Genome-Wide Human SNP Array 6.0 (Affymetrix), and revealed no monosomies but loss of 7p; in AML1 loss of one entire chromosome 7 was the only numerical aberration. Cells were treated with DAC at equitoxic and -effective concentrations for 4 days, harvested on day 5. Total RNA was depleted of ribosomal RNA (Ribo-Zero rRNA Removal Kit, Illumina) and cDNA libraries (strand-specific, 50 bp) were sequenced with ≥33 million paired-end reads, read quality checked with FastQC (≥95% >Q30). Alignment to the reference genome hg19 was performed with TopHat2, read-counting with HTseq, differential expression testing with DESeq2 (protein-coding transcripts only). Selected target genes were validated by RT-qPCR. Peripheral blood mononuclear cells (PBMC) were collected from 9 AML pts (5 pts with 7q-, 4 cytogenetically normal [CN] pts) treated with DAC (i.v. 20 mg/m2 for 5 days) within the DECIDER trial (NCT00867672). Leukemic blasts before treatment and at day 8 were isolated using automatic magnetic sorting of cells labeled with anti-human CD34 and CD117 MACS microbeads.Results: DAC treatment of AML1 and ELF cells resulted in massive transcriptome changes in both cell lines, with 1,704 genes induced in AML1 (total of 3,583) and 1,206 in ELF (total of 1,867; adjusted FDR <0.01). Comparing DAC-induced expression changes only of genes on 7q, we identified 43 genes significantly differentially expressed only in AML1 cells (up: 15), 24 only in ELF (up: 21), and 19 in both (up: 12). The 15 genes on 7q that were selectively upregulated in AML1 included 3 with TSG features: zyxin (ZYX; up 6.0-fold), homeodomain interacting protein kinase 2 (HIPK2; up 3.8-fold), and high mobility group box transcription factor 1 (HBP1, up 3.1-fold). However, the most heavily upregulated transcripts in AML1 were the endogenous retrovirus 3 group member 1 (ERV3-1 ; up 86.4-fold in AML1 vs 14.3-fold in ELF) and the neighboring zinc finger 117 (ZNF117; up 119.4-fold in AML1vs. 6.5-fold in ELF), both transcribed from the ERV3-1 promoter. ERV3-1 induction was accompanied by induction of the interferon type I response genes retinoic acid inducible gene I (RIG-I) and interferon regulatory factor 7 (IRF7) in both cell lines. Therefore, we next interrogated induction of these genes by DAC in vivo, utilizing serially sorted, matched primary AML blasts (purified before and 3 days after DAC administration). Stronger induction of ERV3-1 and RIG-I mRNA was seen in the 7q- pts compared to the CN pts: By qRT-PCR, median ERV3-1 and RIG-I expression was induced 1.5- and 1.4-fold, respectively, in the pts with 7q- (range: 1.1-2.1 and 1.0-3.2), 1.1- and 0.7-fold, respectively, in the CN pts (range: 0.8-1.7 and 0.3-0.9).Conclusions: We successfully developed an unbiased RNA-seq approach of AML cell lines either mono- or bi-allelic for 7q, demonstrating that DAC treatment preferential upregulates several monoallelic TSGs, and massively activates the ERV3-1 gene (implicated in “viral mimicry”). Induction of ERV3-1 and the dsRNA sensor RIG-I was validated in vivo, and preferentially seen in 7q- AML purified primary blasts. Thus, under clinically established treatment conditions, both the ERV and an interferon response gene can be activated by DAC, supporting a combination with immunotherapy. DisclosuresLübbert:Janssen-Cilag: Other: Travel Funding, Research Funding; Ratiopharm: Other: Study drug valproic acid; Celgene: Other: Travel Funding.

Micro RNA-148a Targets Bcl-2 in Patients with Non-Small Cell Lung Cancer

Objective:Lung cancer is one of the most prevalent cancers and the leading cause of cancer-related deaths worldwide. MicroRNAs regulate more than 60% of human genes, including tumor suppressor genes and oncogenes. Accordingly, they can affect cancer risk. This study aimed to evaluate the role of serum miR-148a as a non-invasive biomarker in non-small cell lung cancer (NSCLC) patients and to assess the correlation between miR-148a and Bcl-2, as one of its target proteins. Materials and Methods:A total of 50 newly diagnosed NSCLC cases and 30 apparently healthy controls were recruited in this study. MiR-148a level was measured by TaqMan- Real time RT-PCR assay and Bcl-2 level was measured by ELISA. Results:Significant lower expression of serum miR-148a and higher serum Bcl-2 levels were observed in NSCLC patients as compared to the control group (p <0.001 each). A statistically significant inverse correlation was also evident between miR-148a and Bcl-2. Lower miR-148a gene expression level and higher Bcl-2 concentration were found to be associated with advanced tumor stage, lymph node involvement and distant metastasis. Conclusion:MiR-148a could be a possible biomarker for NSCLC and by targeting Bcl-2, it may offer a novel approach for treatment.

Epstein–Barr Virus Promotes B Cell Lymphomas by Manipulating the Host Epigenetic Machinery

Simple SummaryEpstein-Barr Virus (EBV)-induced lymphomas have a significant global incidence, given the widespread infection to the human population. EBV adopts several mechanisms to replicate and persist in the host, by hijacking its epigenetic machinery. The main topic of this review details the current insights of EBV interactions with the host epigenetic system, and it will be discussed the potential relationship between the EBV-induced chronic inflammation and the dysregulation of epigenetic modifiers that might lead to tumorigenesis. Promising novel therapies against several types of cancer involve the use of epigenetic modifier inhibitors. To design new therapeutical strategies targeting lymphomas, it is crucial to conduct exhaustive reaserch on the regulation of these enzymes.During the past decade, the rapid development of high-throughput next-generation sequencing technologies has significantly reinforced our understanding of the role of epigenetics in health and disease. Altered functions of epigenetic modifiers lead to the disruption of the host epigenome, ultimately inducing carcinogenesis and disease progression. Epstein–Barr virus (EBV) is an endemic herpesvirus that is associated with several malignant tumours, including B-cell related lymphomas. In EBV-infected cells, the epigenomic landscape is extensively reshaped by viral oncoproteins, which directly interact with epigenetic modifiers and modulate their function. This process is fundamental for the EBV life cycle, particularly for the establishment and maintenance of latency in B cells; however, the alteration of the host epigenetic machinery also contributes to the dysregulated expression of several cellular genes, including tumour suppressor genes, which can drive lymphoma development. This review outlines the molecular mechanisms underlying the epigenetic manipulation induced by EBV that lead to transformed B cells, as well as novel therapeutic interventions to target EBV-associated B-cell lymphomas.

TOP2A and CENPF are synergistic master regulators activated in cervical cancer

BackgroundIdentification of master regulators (MRs) using transcriptome data in cervical cancer (CC) could help us to develop biomarkers and find novel drug targets to fight this disease.MethodsWe performed differential expression (DE) analyses of public microarray and RNA-seq transcriptome data of CC and normal cervical tissues (N). Virtual Inference of Protein activity by Enriched Regulon analysis (VIPER) was used to convert the DE outcomes to differential activity (DA) signature for MRs. Synergy analysis was conducted to study synergistic effect of MR-pairs. TCGA and microarray data were used to test the association of expression of a MR and a clinical feature or a molecular feature (e.g. somatic mutations). Various bioinformatic tools/websites (DAVID, GEPIA2, Oncomine, cBioPortal) were used to analyze the expression of the top MRs and their regulons.ResultsTen DE and 10 DA signatures were generated for CC. Two MRs, DNA topoisomerase II alpha (TOP2A) and centromere protein F (CENPF) were found to be up-regulated, activated and synergistic in CC compared to N across the 10 datasets. The two MRs activate a common set of genes (regulons) with functions in cell cycle, chromosome, DNA damage etc. Higher expression of CENPF was associated with metastasis. High expression of both MRs is associated with somatic mutation of a set of genes including tumor suppressors (TP53, MSH2, RB1) and genes involved in cancer pathways, cell cycle, DNA damage and repair. The magnitude of up-regulation and the absolute expression level of both MRs in CC are significantly higher compared to many other cancer types.ConclusionTOP2A and CENPF are a synergistic pair of MRs that are overexpressed and activated in CC. Their high expression is correlated with some prognosis features (e.g. metastasis) and molecular features (e.g. somatic mutations) and distinctly high in CC vs. many other cancer types. They may be good biomarkers and anticancer drug targets for CC.

Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer

BackgroundIn cancer, mutations of DNA methylation modification genes have crucial roles for epigenetic modifications genome-wide, which lead to the activation or suppression of important genes including tumor suppressor genes. Mutations on the epigenetic modifiers could affect the enzyme activity, which would result in the difference in genome-wide methylation profiles and, activation of downstream genes. Therefore, we investigated the effect of mutations on DNA methylation modification genes such as DNMT1, DNMT3A, MBD1, MBD4, TET1, TET2 and TET3 through a pan-cancer analysis.MethodsFirst, we investigated the effect of mutations in DNA methylation modification genes on genome-wide methylation profiles. We collected 3,644 samples that have both of mRNA and methylation data from 12 major cancer types in The Cancer Genome Atlas (TCGA). The samples were divided into two groups according to the mutational signature. Differentially methylated regions (DMR) that overlapped with the promoter region were selected using minfi and differentially expressed genes (DEG) were identified using EBSeq. By integrating the DMR and DEG results, we constructed a comprehensive DNA methylome profiles on a pan-cancer scale. Second, we investigated the effect of DNA methylations in the promoter regions on downstream genes by comparing the two groups of samples in 11 cancer types. To investigate the effects of promoter methylation on downstream gene activations, we performed clustering analysis of DEGs. Among the DEGs, we selected highly correlated gene set that had differentially methylated promoter regions using graph based sub-network clustering methods.ResultsWe chose an up-regulated DEGs cluster where had hypomethylated promoter in acute myeloid leukemia (LAML) and another down-regulated DEGs cluster where had hypermethylated promoter in colon adenocarcinoma (COAD). To rule out effects of gene regulation by transcription factor (TF), if differentially expressed TFs bound to the promoter of DEGs, that DEGs did not included to the gene set that effected by DNA methylation modifiers. Consequently, we identified 54 hypomethylated promoter DMR up-regulated DEGs in LAML and 45 hypermethylated promoter DMR down-regulated DEGs in COAD.ConclusionsOur study on DNA methylation modification genes in mutated vs. non-mutated groups could provide useful insight into the epigenetic regulation of DEGs in cancer.

Identification of novel quinoline inhibitor for EHMT2/G9a through virtual screening

G9a (also known as EHMT2 - Euchromatin histone methyltransferase 2) is a protein lysine methyltransferase which introduces methylation modification in variety of proteins including histones. G9a catalyzes the dimethylation of lysine 9 on histone 3 (H3K9me2) which is a repressive epigenetic modification. H3K9me2 is associated with the silencing of several genes including tumor suppressor genes in many cancers and hence G9a is a well characterized drug target for cancer therapy. Here, we report the discovery of CSV0C018875 as a novel quinoline based G9a inhibitor through virtual screening strategy from a HTS database. Sub-structure querying based on the known G9a inhibitors, followed by docking based virtual screening, led to the identification of CSV0C018875 as G9a inhibitor. We found that CSV0C018875 inhibits the activity of G9a in both enzyme and cell based assays. Importantly, the toxicity of CSV0C018875 is much lesser than that of the well-studied G9a inhibitor, BIX-01294. Molecular dynamics simulations shows that CSV0C018875 binds deeper inside the active site cavity of G9a, which facilitates the tight binding and also increases the compounds residence time, which in turn reflects better G9a inhibition. The novel quinoline CSV0C018875 could be further optimized to improve the ADME as well pharmacodynamic property.

Hypomethylating Agent Maintenance Therapy after Allogeneic Stem Cell Transplant Improves Transplant Outcome in High Risk Acute Myelogenous Leukemia

Background: Allogeneic hematopoietic stem cell transplant (HSCT) is the only potential curative modality for high risk acute myelogenous leukemia (AML). However, relapse disease remains to be the main reason of failure of allogeneic HSCT. Salvage therapy for relapse AML after allogeneic HSCT is limited and rarely successful. Prognosis is poor with a 2-year survival rate of less than 20%. As majority of relapses occur within first 6 months after transplant, effective preventive intervention given early post allogeneic HSCT may be crucial. An ideal drug for pharmacologic maintenance is difficult to achieve as it should have activity against the disease without excessive myelosuppression or eradication of donor cells, and has minimal or low risk of exacerbation of graft-versus-host disease or additional toxicity. Azacitidine and decitabine are hypomethylating agents (HMAs), which work epigenetically to modulate various genes, including tumor suppressor genes. They have been shown to have benefits in improvement of event free survival and overall survival in relapse AML. Similar benefits have also been reported when low dose azacitadine was given after allogeneic stem cell transplant as a maintenance therapy. Method: This is a single institutional study carried out at the Bone Marrow Transplant Program at the University of Oklahoma Health Science Center. It was started as a case control study in June 2014 when post-transplant azacitadine protocol was initiated, and continues on as a prospective study. Subjects over 18 years old with high risk AML based on cytogenetic and molecular mutation undergoing allogeneic HSCT were enrolled from September 2013 to July 2018. The study is to compare outcome in patients received post-transplant low dose azacitidine at 32mg/m2 on days 1-5 every 28 days for 4 cycles initiating between 6-8 weeks post-transplant versus post-transplant observation. Multivariable cox proportional hazards model was derived to adjust for covariates that differ between the two treatment arms and was used to analyze time to relapse and overall survival in both arms; then our results were graphed using Kaplan Meier Plot. Results: This study included 49 patients undergoing allogeneic HSCT for high risk AML. They were divided into 2 groups with 31 patients received post-transplant azacitidine, and 18 patients did not (prior to initiation of post-transplant azacitadine protocol, control). Our Analysis concluded a greater proportion of deaths among the control group (88.89%) compared to the azacitidine group (25.81%). Majority of deaths in the control group was due to relapse (12 of 16 deaths). Relapse rate was higher in the control group (66.67%) as compared to azacitidine group (25.81%) with statistically significant improvement in time to relapse in the azacitidine group (not reach (NR)) versus 4.1 months in the control arm (log-rank p-value &lt;0.0001) which was described in Figure (1). Median Overall survival was 7.6 months in control arm versus 27.4 months in the 8 patients who relapsed in azacitidine arm (log-rank p-value&lt;0.0001). (Figure 2) Among the 29 subjects from both arms who were relapse-free, overall survival differed between the two treatment groups (log-rank p-value 0.003). Median survival time among those in the control group was 9.8 months. For the azacitidine arm, only 2 events occurred among the 23 relapse-free subjects while the remaining 21 subjects were censored (Figure 3). Among other transplant-related factors, disease status was not differed among the two groups (p=0.411), but conditioning regimen was (p=0.019) with a greater proportion of reduced intensity conditioning (RIC) in the control group (55.56%) than azacitadine group (22.58) (Table 1). After adjusting for conditioning regimen, hazard of relapse was 5.26 (1.99,13.93) times greater (p value&lt;0.001) and death was 5.41 (1.99,13.93) times greater (p value&lt;0.001) in the control group than azacitadine group. In our analysis, cause of death was not statistically significantly different among the two arms (p-value 0.325). Use of azacitidine post-HSCT did not increase the risk of GVHD or infections (table 2). Implications: Low dose azacitidine maintenance therapy after allogeneic stem cell transplant in high risk acute myelogenous leukemia decreases relapse rate, time to relapse and improved overall survival without increasing adverse events and no increased risk of graft-versus-host disease or infections. Disclosures No relevant conflicts of interest to declare.

Alternative Splicing and Intronic Polyadenylation Post-Transcriptionally Regulate CSF3R Via a Cryptic Exon

Increasing evidence suggests that alternative splicing of CSF3R occurs during normal granulopoiesis and is altered in certain pathologic conditions. To further examine CSF3R splicing, Sashimi plots from RNA-seq data were generated from CD34+ cells and neutrophils isolated from healthy donors (Figure 1A). The majority of splicing events were found to follow a pattern of enforced exon order resulting in production of CSF3R-V1, and to a lesser extent production of variants 3 and 4 that arise from alternative splicing of distal exonic sequences. However, a significant number of splicing events also mapped to a region within intron 3 (Figure 1A, black hashed box), suggesting a putative cryptic exon (CE). RT-PCR was performed to amplify the region containing the putative CE and Sanger sequencing of the amplification products confirmed the presence of a 73 base pair CE between exons 3 and 4 (E3 and E4). The CE adds an in-frame stop codon that is far removed from the terminal exon; transcripts containing the CE would be predicted to be degraded by nonsense-mediated decay (NMD). We detected transcripts containing the CE sequence in HL-60 cells as well as in CD34+ cells, neutrophils, and monocytes from healthy donors. Cycloheximide had no appreciable effect on the CE-containing transcript, indicating this transcript does not undergo NMD. One mechanism by which the CSF3R CE-containing transcripts could evade NMD would be through alternative polyadenylation (ApA). ApA commonly occurs in the 3'UTRs of mRNAs and is a mechanism for regulating differential transcript expression. ApA can also occur in introns and lead to production of either non-coding RNA or transcripts that produce truncated proteins. Using RT-PCR with a forward primer positioned across the E3:CE junction and a reverse primer positioned within the intronic sequence following the CE and Sanger sequencing of the amplified product, we detected the ApA transcript. The presence of the ApA transcript was confirmed by custom TaqMan assays capable of identifying each of the two predicted CE-containing CSF3R transcripts (Figure 1B). Transcription of either of the CE-containing transcripts would generate mRNAs with a very short open reading frame, and, hence, a protein of only 28 amino acids that is predicted to be signaling-incompetent. Production of the CE-containing CSF3R transcripts could quantitatively alter the amount of full-length CSF3R (V1) transcripts available for production of CSF3R protein, and therefore alter cellular responses to G-CSF. We next examined cells from patients with AML to determine whether expression of the signaling-incompetent CE-containing CSF3R transcripts was altered. Real-time RT-PCR was performed on total RNA isolated from CD34+ cells from healthy donors and from patients with acute myeloid leukemia (AML) to quantitate "productive" CSF3R transcripts (signaling-competent CSF3R-V1 transcripts arising from correct splicing of E3 to E4) versus "non-productive" CSF3R transcripts (signaling-incompetent CSF3R+CE and CSF3R+CEApA transcripts) arising from inclusion of the CE. Significant changes in the relative amounts of CSF3R-V1, CSF3R+CE, and CSF3R+CEApA, and in overall CSF3R transcription were detected in AML samples compared to normal samples. We are currently investigating the effects of mutations in different splicing genes on the output of "productive" versus "non-productive" CSF3R transcripts. In conclusion, we have identified two additional CSF3R transcripts generated by a CE following exon 3 that are expressed in human CD34+ cells and myeloid cells (Figure 1B). Notably, the expression of both CE-containing transcripts effectively decreases expression of the mature CSF3R mRNA, and by extension, of mature full-length CSF3R protein. Our data support a previously unrecognized mechanism of post-transcriptional regulation of CSF3R expression involving a CE and alternative splicing. Recently, widespread intronic polyadenylation of multiple genes including tumor suppressor genes was detected in cells from patients with CLL that resulted in expression of truncated mRNAs and proteins that functionally mimic somatic mutations, which was proposed as a novel mechanism for tumorigenesis. We suggest a similar mechanism involving CSF3R may play a role in AML. Disclosures Avalos: Best Practice-Br Med J: Patents &amp; Royalties: receives royalties from a coauthored article on evaluation of neutropenia; Juno: Membership on an entity's Board of Directors or advisory committees.