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Supplementary Table 1: List of primers used for quantitative real time PCR. Supplementary Table. 2: List of primers used for construction of pGL2 and pMIR reporter plasmids. Supplementary Table. 3: List of primers used to generate PCR amplicons for pyrosequencing analysis. Supplementary Table. 4: Sequencing primers used for pyrosequencing. Supplementary Table. 5: Primers used for qPCR analysis in ChIP assay.

A subset of primary breast tumors expresses a 308-gene signature that correlated with gene signatures specifically expressed in immune cells.

Triple-negative breast cancer (TNBC) cells are modulated in reaction to tumor-infiltrating lymphocytes. However, their specific responses to this immune pressure are unknown. In order to address this question, we first used mRNA sequencing to compare the immunophenotype of the TNBC cell line MDA-MB-231 and the luminal breast cancer cell line MCF7 after both were cocultured with activated human T cells. Despite similarities in the cytokine-induced immune signatures of the two cell lines, MDA-MD-231 cells were able to transcribe more IDO1 than MCF7 cells. The two cell lines had similar upstream JAK/STAT1 signaling and IDO1 mRNA stability. However, using a series of breast cancer cell lines, IFNγ stimulated IDO1 protein expression and enzymatic activity only in ER−, not ER+, cell lines. Treatment with 5-aza-deoxycytidine reversed the suppression of IDO1 expression in MCF7 cells, suggesting that DNA methylation was potentially involved in IDO1 induction. By analyzing several breast cancer datasets, we discovered subtype-specific mRNA and promoter methylation differences in IDO1, with TNBC/basal subtypes exhibiting lower methylation/higher expression and ER+/luminal subtypes exhibiting higher methylation/lower expression. We confirmed this trend of IDO1 methylation by bisulfite pyrosequencing breast cancer cell lines and an independent cohort of primary breast tumors. Taken together, these findings suggest that IDO1 promoter methylation regulates anti-immune responses in breast cancer subtypes and could be used as a predictive biomarker for IDO1 inhibitor–based immunotherapy. Cancer Immunol Res; 5(4); 330–44. ©2017 AACR.

Figure Legends for Supplementary Figures 1-6

Purpose: Metastasis is the leading cause of death for gastric carcinoma. An epigenetic biomarker panel for predicting gastric carcinoma metastasis could have significant clinical impact on the care of patients with gastric carcinoma. The main purpose of this study is to characterize the methylation differences between gastric carcinomas with and without metastasis.Experimental Design: Genome-wide DNA methylation profiles between 4 metastatic and 4 nonmetastatic gastric carcinomas and their surgical margins (SM) were analyzed using methylated-CpG island amplification with microarray. The methylation states of 73 candidate genes were further analyzed in patients with gastric carcinoma in a discovery cohort (n = 108) using denatured high performance liquid chromatography, bisulfite-sequencing, and MethyLight. The predictive values of potential metastasis-methylation biomarkers were validated in cohorts of patients with gastric carcinoma in China (n = 330), Japan (n = 129), and Korea (n = 153).Results: The gastric carcinoma genome showed significantly higher proportions of hypomethylation in the promoter and exon-1 regions, as well as increased hypermethylation of intragenic fragments when compared with SMs. Significant differential methylation was validated in the CpG islands of 15 genes (P < 0.05) and confirmed using bisulfite sequencing. These genes included BMP3, BNIP3, CDKN2A, ECEL1, ELK1, GFRA1, HOXD10, KCNH1, PSMD10, PTPRT, SIGIRR, SRF, TBX5, TFPI2, and ZNF382. Methylation changes of GFRA1, SRF, and ZNF382 resulted in up- or downregulation of their transcription. Most importantly, the prevalence of GFRA1, SRF, and ZNF382 methylation alterations was consistently and coordinately associated with gastric carcinoma metastasis and the patients' overall survival throughout discovery and validation cohorts in China, Japan, and Korea.Conclusion: Methylation changes of GFRA1, SRF, and ZNF382 may be a potential biomarker set for prediction of gastric carcinoma metastasis. Clin Cancer Res; 20(17); 4598–612. ©2014 AACR.

Supplementary Figure S4. Methylation levels of GFRA1, SRF, and ZNF382 by DHPLC are confirmed by MethyLight and inversely correlated with their transcription levels. (A) Correlation between DNA methylation levels measured by DHPLC and MethyLight. The methylation levels of GFRA1, SRF, and ZNF382 measured by DHPLC positively correlated with the results obtained using MethyLight assay. RCN, relative copy number relative to the reference gene COL2A1 for bisulfite-modified DNA; (B) The methylation levels of these genes were inversely correlated with their mRNA levels. The mRNA levels were determined by quantitative RT-PCR assays in matched GC tissues. Statistically significant correlations were obtained using Spearman test. RCN, relative copy number relative to the reference gene GAPDH.

Aiming at the general integrated scheduling problem of tree-structured complex single-product machining and assembling, a reverse order hierarchical integrated scheduling algorithm (ROHISA) is proposed by considering the dynamic time urgency degree (TUD) of process sequences (PSs). The strategy of process sorting is put forward, and the TUD of PS is defined. The process tree is reversed using leaf alignment, and according to the order from leaf to root, the scheduling order of leaf nodes in the same layer is determined layer by layer according to the TUD values of the PSs to which the leaf nodes belong. In turn, the sorted leaf nodes in each layer are stored in a corresponding layered array (LA). Finally, the elements in each LA are reversed, and the LAs’ arranging order is reversed. A reverse order hierarchical scheduling strategy is proposed. Starting from the root node, every LA is taken as a unit to conduct trial scheduling each time. Under the condition of meeting the craft constraints, a set of quasi-scheduling schemes of same-layer processes (QSSSLP) is obtained, and the one with the minimum end time is selected from it as the scheduling scheme of the same layer processes (SSSLP). If it is not unique, the QSSSLP that machines all the same layer processes (SLP) as early as possible is selected. The research shows that the ROHISA optimizes the integrated scheduling results of single-product manufacturing enterprises and improves its production efficiency.

The presence of polyfunctional CD4(+) T cells is often associated with favorable antitumor immunity. We report here that persistent activation of signal transducer and activator of transcription 5 (STAT5) in tumor-specific CD4(+) T cells drives the development of polyfunctional T cells. We showed that ectopic expression of a constitutively active form of murine STAT5A (CASTAT5) enabled tumor-specific CD4(+) T cells to undergo robust expansion, infiltrate tumors vigorously and elicit antitumor CD8(+) T cell responses in a CD4(+) T-cell adoptive transfer model system. Integrated epigenomic and transcriptomic analysis revealed that CASTAT5 induced genome-wide chromatin remodeling in CD4(+) T cells and established a distinct epigenetic and transcriptional landscape. Single-cell RNA sequencing analysis further identified a subset of CASTAT5-transduced CD4(+) T cells with a molecular signature indicative of progenitor polyfunctional T cells. The therapeutic significance of CASTAT5 came from our finding that adoptive transfer of T cells engineered to co-express CD19-targeting chimeric antigen receptor (CAR) and CASTAT5 gave rise to polyfunctional CD4(+) CAR T cells in a mouse B-cell lymphoma model. Notably, the optimal therapeutic outcome was obtained when both CD4(+) and CD8(+) CAR T cells were transduced with CASTAT5, indicating that CASTAT5 facilitates productive CD4 help to CD8(+) T cells. Furthermore, we provide evidence that CASTAT5 is functional in primary human CD4(+) T cells, underscoring its potential clinical relevance. Our results implicate STAT5 as a valid candidate for T cell engineering to generate polyfunctional, exhaustion-resistant, and tumor-tropic antitumor CD4(+) T cells to potentiate adoptive T-cell therapy for cancer.

DNA methylation is an epigenetic mechanism that regulates gene transcription without changing primary nucleotide sequences. In mammals, DNA methylation involves the covalent addition of a methyl group to the 5-carbon position of cytosine by DNA methyltransferases (DNMTs). The change of DNA methylation and its pathological role in acute kidney injury (AKI) remain largely unknown. Here, we analyzed genome-wide DNA methylation during cisplatin-induced AKI by reduced representation bisulfite sequencing. This technique identified 215 differentially methylated regions between the kidneys of control and cisplatin-treated animals. While most of the differentially methylated regions were in the intergenic, intronic, and coding DNA sequences, some were located in the promoter or promoter-regulatory regions of 15 protein-coding genes. To determine the pathological role of DNA methylation, we initially examined the effects of the DNA methylation inhibitor 5-aza-2'-deoxycytidine and showed it increased cisplatin-induced apoptosis in a rat kidney proximal tubular cell line. We further established a kidney proximal tubule-specific DNMT1 (PT-DNMT1) knockout mouse model, which showed more severe AKI during cisplatin treatment than wild-type mice. Finally, interferon regulatory factor 8 (Irf8), a pro-apoptotic factor, was identified as a hypomethylated gene in cisplatin-induced AKI, and this hypomethylation was associated with a marked induction of Irf8. In the rat kidney proximal tubular cells, the knockdown of Irf8 suppressed cisplatin-induced apoptosis, supporting a pro-death role of Irf8 in renal tubular cells. Thus, DNA methylation plays a protective role in cisplatin-induced AKI by regulating specific genes, such as Irf8.

The characteristic of multi-shop scheduling is that the processing equipment is scattered in multiple workshops in different geographical locations. To solve this problem, a multi-shop comprehensive scheduling algorithm considering migration dual-objective is proposed of migration of a single complex product in multi-shop equipment, and the workpiece is migrated from one device to another during the processing. The algorithm first uses the leaf nodes of the process tree as a set of schedulable operations; second, the pre-scheduled operation set is determined according to the long path first strategy and the short time strategy; third, the actual scheduling set of the same idle equipment is determined according to the same equipment procedure selection strategy in the workshop; finally, considering the migration time and cost of the process to be processed, a two-objective optimization strategy for process shop selection is proposed. The example results show that the algorithm in this paper consumes less time and cost during the migration process, and can obtain a relatively compromised solution of the total time and total cost of product scheduling.

Triple-negative breast cancer (TNBC) cells are modulated in reaction to tumor-infiltrating lymphocytes. However, their specific responses to this immune pressure are unknown. In order to address this question, we first used mRNA sequencing to compare the immunophenotype of the TNBC cell line MDA-MB-231 and the luminal breast cancer cell line MCF7 after both were cocultured with activated human T cells. Despite similarities in the cytokine-induced immune signatures of the two cell lines, MDA-MD-231 cells were able to transcribe more IDO1 than MCF7 cells. The two cell lines had similar upstream JAK/STAT1 signaling and IDO1 mRNA stability. However, using a series of breast cancer cell lines, IFNγ stimulated IDO1 protein expression and enzymatic activity only in ER−, not ER+, cell lines. Treatment with 5-aza-deoxycytidine reversed the suppression of IDO1 expression in MCF7 cells, suggesting that DNA methylation was potentially involved in IDO1 induction. By analyzing several breast cancer datasets, we discovered subtype-specific mRNA and promoter methylation differences in IDO1, with TNBC/basal subtypes exhibiting lower methylation/higher expression and ER+/luminal subtypes exhibiting higher methylation/lower expression. We confirmed this trend of IDO1 methylation by bisulfite pyrosequencing breast cancer cell lines and an independent cohort of primary breast tumors. Taken together, these findings suggest that IDO1 promoter methylation regulates anti-immune responses in breast cancer subtypes and could be used as a predictive biomarker for IDO1 inhibitor–based immunotherapy. Cancer Immunol Res; 5(4); 330–44. ©2017 AACR.

Splicing factor SF3B1 is frequently mutated in chronic lymphocytic leukemia (CLL) patients and has been suggested as a potential therapeutic target. In this study, we demonstrated that SF3B1 modulator sudemycin D6 (SD6) effectively inhibits cell growth and induces apoptosis in CLL cells. RNA sequencing analysis revealed significant increases in global intron retention in SD6-treated CLL cells. Pathway analysis of the genes associated with increased intron retention suggested that B-cell receptor (BCR) and PI3K signaling pathways were among the most important pathways being affected by SD6. The increases in intron retention were inversely correlated with decreases in mRNA and protein levels of the affected BCR/PI3K pathway molecules including BLNK, BTK, AKT, PLCγ2, and PI3Kδ. SD6 treatment also induced a time-dependent exon-skipping event in MCL-1 mRNA and resulted in significant down-regulation of another anti-apoptotic gene TRAF1, thus collectively contributing to the SD6-induced apoptosis. Furthermore, SD6 treatment can overcome the pro-survival and pro-growth signals and synergize with established CLL therapies ibrutinib, idelalisib, and venetoclax to induce apoptosis in primary CLL cells co-cultured with bone marrow stromal cells and T-cell-derived cytokines. Finally, in vivo treatment with SD6 at 10mg/kg/day for 7 days significantly inhibited the growth of xenograft tumors that were established by subcutaneous inoculation of 5×106 MEC1 CLL cells into NOD mice. Collectively, these results provide a strong rationale for the future clinical development of spliceosome modulators and potential combination therapies for the treatment of CLL. Citation Format: Qimei Han, Jianbo Wang, Austin Y. Shull, Fang Shi, Libin Deng, Jeong-Hyeon Choi, Eun-Jeong Park, Shuo Tu, Lirong Pei, Farrukh T. Awan, Roni Bollag, Locke J. Bryan, Hong-bo Xin, Chandraiah Lagisetti, Thomas R. Webb, Victor Jin, Huidong Shi. Modulation of SF3B1 causes global intron retention and downregulation of the B-cell receptor pathway in chronic lymphocytic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5230.

SF3B1 mutation, which occurs in 10-20% of chronic lymphocytic leukemia (CLL) patients, is associated with faster disease progression, shorter overall survival and fludarabine resistance. Mutant SF3B1 utilizes cryptic 3′ splice sites to generate aberrantly spliced mRNAs, half of which may undergo non-sense mediated mRNA decay (NMD), leading to downregulation of the affected genes. To identify potential tumor suppressor genes that are aberrantly spliced and downregulated by mutant SF3B1, we performed RNA-sequencing analysis of SF3B1-mutated primary CLL cells in the presence or absence of cycloheximide (CHX), a translation inhibitor known to inhibit NMD. Our analysis identified PPP2R5A, encoding one of the regulatory subunits of protein phosphatase-2A (PP2A B56α), as one of the key genes that were most consistently affected by an aberrantly spliced junction, and significantly downregulated (>2 fold) in CLL patient samples with various SF3B1 hotspot mutations. Splicing analyses by RT-PCR and Sanger sequencing confirmed that a 13-nucleotides sequence was added before the 5th exon of PPP2R5A via alternative splicing in CLL patients with the SF3B1 mutation. Due to this 13-nucleotides addition, three consecutive premature stop codons were created by frameshift at a position more than 55 bases upstream of an exon-exon junction, which is a canonical feature of the mRNAs degraded through NMD. The down-regulation of PPP2R5A was confirmed by quantitative PCR (p Citation Format: Qimei Han, Libin Deng, Shuo Tu, Lirong Pei, Jeong-Hyeon Choi, Victor Jin, Huidong Shi. SF3B1 mutation promotes c-Myc protein stability through aberrant splicing and downregulation of PP2A B56α subunit in chronic lymphocytic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4493.

A commercial microscope-based reflectometer was modified and a custom measurement protocol and analysis regimen were developed for characterization of coatings around curved surfaces.

Immunosuppression is a prevalent clinical feature in chronic lymphocytic leukemia (CLL) patients, with many patients demonstrating increased susceptibility to infections as well as increased failure of an antitumor immune response. However, much is currently not understood regarding the precise mechanisms that attribute to this immunosuppressive phenotype in CLL. To provide further clarity to this particular phenomenon, we analyzed the T-cell profile of CLL patient samples within a large cohort and observed that patients with an inverted CD4/CD8 ratio had a shorter time to first treatment as well as overall survival. These observations coincided with higher expression of the immune checkpoint receptor PD-1 in CLL patient CD8+ T cells when compared to age-matched healthy donors. Interestingly, we discovered that increased PD-1 expression in CD8+ T cells corresponds with decreased DNA methylation levels in a distal upstream locus of the PD-1 gene PDCD1. Further analysis using luciferase reporter assays suggests that the identified PDCD1 distal upstream region acts as an enhancer for PDCD1 transcription and this region becomes demethylated during activation of naive CD8+ T cells by anti-CD3/anti-CD28 antibodies and IL2. Finally, we conducted a genome-wide DNA methylation analysis comparing CD8+ T cells from CLL patients against healthy donors and identified additional differentially methylated genes with known immune regulatory functions including CCR6 and KLRG1. Taken together, our findings reveal the occurrence of epigenetic reprogramming taking place within CLL patient CD8+ T cells and highlight the potential mechanism of how immunosuppression is accomplished in CLL.

Background: Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults in the Western countries but is relatively rare in East Asia. Mutations in myeloid differentiation primary response gene 88 (MYD88) occur in 2.0-4.4% of Caucasian patients with CLL. However, Asian subjects showed a higher MYD88 mutation frequency of 8% and MYD88 mutations were associated with unfavorable prognosis in Asian CLL patients with mutated IGHV gene. To further explore the molecular and pathological mechanisms of the MYD88 L265P mutation in CLL, we performed a pilot study to investigate the transcriptome-wide differential expression between CLL patients with and without MYD88 L265P mutation. Methods: mRNA sequencing was performed on a cohort of 15 Chinese CLL patients with MYD88 L265P mutation (n=5) or wild-type MYD88 gene (n=10). Differential expression and pathway enrichment analyses were performed based on FPKM values after processing the raw sequencing reads. The alternative splicing events were analyzed using JuncBASE and the differences in splicing patterns were compared between the two groups. The MYD88 L265P and wild-type genes were overexpressed in the MEC-1 cell line using lentiviral vectors, and stable cell lines were established after puromycin selection. Real time quantitative PCR was used to determine the mRNA expression of spliceosome pathway genes. The protein expression of TLR pathway was assessed with Western Blot. The PrestoBlue™ assay was used for determining IC-50 of spliceosome inhibitor-treated CLL cell lines, and flow cytometry was utilized for apoptosis and cell death analyses. Results: mRNA sequencing analysis revealed that 4231 genes showed significant differences in mRNA expression between MYD88 mutant and wild-type CLL patients. Of these genes, 3033 were up regulated and 1198 were down regulated in patients with MYD88 L265P mutation. Pathway analysis demonstrated that tumor necrosis factor (TNF) signaling, cell cycle, spliceosome, ribosome, p53 signaling, and NF-κB signaling pathways were significantly enriched among differentially expressed genes. Interestingly, about two thirds (19 out of 30) of differentially expressed genes in the spliceosome pathway were down regulated in CLL samples with MYD88 mutation. Quantitative RT-PCR confirmed the down regulation of spliceosome genes including SF3A1, SF3A2, SF3B4, SF3B5 and PUF60 in MYD88 mutated samples in an independent CLL patient cohort. Analysis of alternative splicing events revealed a total of 180 genes with inter-group splicing differences, among which differential splicing events were most common in the genes involved in immune system regulation, i. e. CD22, CD79B, CD200 and IKZF1 etc. The MEC1 cells stably overexpressing MYD88 L265P demonstrated decreases in RelA and TRAF6 expression as compared to wild type MYD88-overexpressing cells, which was in agreement with RNA-seq analysis results in CLL patient samples. In addition, we found that overexpression of MYD88 L265P mutant resulted in decreased mRNA expression of several spliceosome genes such as SF3A1, SF3A2, SF3B4, SF3B5 and PUF60 in the stable cell line. Furthermore, MYD88 L265P increased the sensitivity of MEC1 cells to spliceosome inhibitor sudemycin D6 (SD6) by 3 fold, while reducing their sensitivity to Ibrutinib by two fold. Conclusion: We discovered the differential mRNA expression landscapes related to MYD88 mutation status in CLL and their contributions to the progression of CLL through multiple pathways. Of particular interest was the down regulation of spliceosome pathway genes. In a CLL cell line model, we found that, compared with the MYD88 wild-type CLL cell line, CLL cells overexpressing the mutant MYD88 were more sensitive to spliceosome inhibitor SD6, suggesting that inhibiting spliceosome function may be a potential therapeutic target for CLL patients with mutant MYD88 gene. In summary, our findings provide novel insights for further understanding of the molecular and pathological mechanisms of MYD88 mutation in CLL. Disclosures Lagisetti: St. Jude Children's Research Hospital: Patents & Royalties: Chandraiah Lagisetti is listed as inventors on patents assigned to St. Jude Children's Research Hospital covering sudemycin D6 and was employed by SRI Biosciences at the time these experiments were carried out. Webb:St. Jude Children's Research Hospital: Patents & Royalties: Thomas R. Webb is listed as inventors on patents assigned to St. Jude Children's Research Hospital covering sudemycin D6 and was employed by SRI Biosciences at the time these experiments were carried out..

Glioblastoma (GBM) is the most common and most aggressive primary brain tumor in adults. The existence of a small population of stem-like tumor cells that efficiently propagate tumors and resist cytotoxic therapy is one proposed mechanism leading to the resilient behavior of tumor cells and poor prognosis. In this study, we performed an in-depth analysis of the DNA methylation landscape in GBM-derived cancer stem cells (GSCs). Parallel comparisons of primary tumors and GSC lines derived from these tumors with normal controls (a neural stem cell (NSC) line and normal brain tissue) identified groups of hyper- and hypomethylated genes that display a trend of either increasing or decreasing methylation levels in the order of controls, primary GBMs, and their counterpart GSC lines, respectively. Interestingly, concurrent promoter hypermethylation and gene body hypomethylation were observed in a subset of genes including MGMT, AJAP1 and PTPRN2. These unique DNA methylation signatures were also found in primary GBM-derived xenograft tumors indicating that they are not tissue culture-related epigenetic changes. Integration of GSC-specific epigenetic signatures with gene expression analysis further identified candidate tumor suppressor genes that are frequently down-regulated in GBMs such as SPINT2, NEFM and PENK. Forced re-expression of SPINT2 reduced glioma cell proliferative capacity, anchorage independent growth, cell motility, and tumor sphere formation in vitro. The results from this study demonstrate that GSCs possess unique epigenetic signatures that may play important roles in the pathogenesis of GBM.

Chronic lymphocytic leukemia (CLL), the most common adult leukemia, remains incurable despite advancements in treatment regimens over the past decade. Several expression profile studies have been pursued to better understand CLL pathogenesis. However, these large-scale studies only provide information at the transcriptional level. To better comprehend the differential protein changes that take place in CLL, we performed a reverse-phase protein array (RPPA) analysis using 167 different antibodies on B-cell lysates from 18 CLL patients and 6 normal donors. From our analysis, we discovered an enrichment of protein alterations involved with mRNA translation, specifically upregulation of the translation initiator eIF4G and phosphorylation of the cap-dependent translation inhibitor 4E-BP1 at serine 65. Interestingly, 4E-BP1 phosphorylation occurred independently of AKT phosphorylation, suggesting a disconnect between PI3K/AKT pathway activation and 4E-BP1 phosphorylation. Based on these results, we treated primary CLL samples with NVP-BEZ235, a PI3K/mTOR dual inhibitor, and compared its apoptotic-inducing potential against the BTK inhibitor Ibrutinib and the PI3Kδ inhibitor Idelalisib. We demonstrated that treatment with NVP-BEZ235 caused greater apoptosis, greater apoptotic cleavage of eIF4G, and greater dephosphorylation of 4E-BP1 in primary CLL cells. Taken together, these results highlight the potential dependence of eIF4G overexpression and 4E-BP1 phosphorylation in CLL survival.

Tumor infiltrating lymphocytes (TILs) play a critical role in regulating the immunomodulatory properties of triple negative breast cancer (TNBC). However, the specific adaptations that TNBC tumors undergo when challenged by lymphocyte infiltration remain unclear. In order to address this gap in knowledge, we conducted an immuno-phenotype comparison using mRNA sequencing between the TNBC cell line MDA-MB-231 and the luminal breast cancer cell line MCF7 after both were co-cultured with activated human T-cells. Although the cytokine-induced immune signature of the two cell lines were similar, MDA-MD-231 cells were able to transcribe the tryptophan catabolizing enzyme IDO1 at a significantly higher level than MCF7 cells. Stimulation with IFNg was able to differentially induce IDO protein expression and enzymatic activity in ER- cell lines compared to ER+ cell lines, though no differences were observed in upstream JAK/STAT1 signaling or IDO1 mRNA stability between the two cell lines. Further experiments showed that treatment with the demethylating agent 5-aza-deoxycytidine was able to reverse suppression of IDO1 expression in MCF7 cells, suggesting that DNA methylation serves as a potential determinant in IDO1 induction. Analysis of TCGA and other previously published breast cancer datasets revealed subtype-specific mRNA and promoter methylation differences in IDO1, with TNBC/basal-like subtypes exhibiting lower promoter methylation and higher mRNA expression than ER+/luminal subtypes. Bisulfite pyrosequencing validated the subtype-specific association of decreased promoter methylation with increased IDO1 expression in breast cancer cell lines and an independent cohort of primary breast tumors. In addition, decreased IDO1 promoter methylation and elevated IDO1 expression in basal-like breast tumors was found to be associated with increased levels of kynurenine, the metabolic product of IDO1, as well as higher numbers of CD8+ TILs. Furthermore, high kynurenine levels in breast tumors were associated with worse patient survival. Taken together, these findings suggest that subtype-specific IDO1 promoter methylation regulates the ability of breast tumors to escape from antitumor immune responses driven by CD8+ TILs and could be used as a predictive biomarker for IDO inhibitor-based immunotherapy. Citation Format: Gu F, Noonepalle SK, Lee E-J, Choi J-H, Shull AY, Pei L, Sreekumar A, Ambs S, Shi H. Modulation of indoleamine 2, 3-dioxygenase (IDO1) expression in breast cancer cells by activated CD8+ T cells is controlled by DNA promoter methylation [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-02-08.

Purpose: Metastasis is the leading cause of death for gastric carcinoma. An epigenetic biomarker panel for predicting gastric carcinoma metastasis could have significant clinical impact on the care of patients with gastric carcinoma. The main purpose of this study is to characterize the methylation differences between gastric carcinomas with and without metastasis. Experimental Design: Genome-wide DNA methylation profiles between 4 metastatic and 4 nonmetastatic gastric carcinomas and their surgical margins (SM) were analyzed using methylated-CpG island amplification with microarray. The methylation states of 73 candidate genes were further analyzed in patients with gastric carcinoma in a discovery cohort (n = 108) using denatured high performance liquid chromatography, bisulfite-sequencing, and MethyLight. The predictive values of potential metastasis-methylation biomarkers were validated in cohorts of patients with gastric carcinoma in China (n = 330), Japan (n = 129), and Korea (n = 153). Results: The gastric carcinoma genome showed significantly higher proportions of hypomethylation in the promoter and exon-1 regions, as well as increased hypermethylation of intragenic fragments when compared with SMs. Significant differential methylation was validated in the CpG islands of 15 genes (P < 0.05) and confirmed using bisulfite sequencing. These genes included BMP3, BNIP3, CDKN2A, ECEL1, ELK1, GFRA1, HOXD10, KCNH1, PSMD10, PTPRT, SIGIRR, SRF, TBX5, TFPI2, and ZNF382. Methylation changes of GFRA1, SRF, and ZNF382 resulted in up- or downregulation of their transcription. Most importantly, the prevalence of GFRA1, SRF, and ZNF382 methylation alterations was consistently and coordinately associated with gastric carcinoma metastasis and the patients' overall survival throughout discovery and validation cohorts in China, Japan, and Korea. Conclusion: Methylation changes of GFRA1, SRF, and ZNF382 may be a potential biomarker set for prediction of gastric carcinoma metastasis. Clin Cancer Res; 20(17); 4598–612. ©2014 AACR.

Chronic lymphocytic leukemia (CLL), characterized by the progressive and uncontrolled accumulation of CD19+ B cells, currently remains as an incurable malignancy. The difficulties of eliciting curative measures in CLL are partly driven by the adaptability of the transcriptional response mediated by epigenetic mechanisms. In this study, we sought to better characterize the complexities of the CLL transcriptional profile by conducting an integrative analysis between the B cell enhancer and super enhancer signatures defined from 3 B cell H3K27Ac ChIPseq samples (CD19+ B cell, GM12878, and MEC1), the DNA methylation signatures defined from reduced-representation bisulfite sequencing (RRBS) of 42 CLL patient and 8 healthy donor samples, and the mRNA expression signatures defined from RNA sequencing of 47 CLL patient and 5 healthy donor samples. From our analysis, we identified super enhancers (SEs) in each of the ChIPseq profiles (approximately 4% of called enhancers) and discovered 741 SEs in GM12878, 374 SEs in MEC1, and 523 SEs in the CD19+ B cell profiles, respectively. Based on MSigDB gene ontology analysis, many of the genes corresponding with SEs were involved in pathways regulating immune signaling activation (e.g. TNFA_SIGNALING_VIA_NFKB, INFLAMMATORY RESPONSE) or metabolic homeostasis (e.g. MTORC1_SIGNALING, FATTY_ACID_METABOLISM). By further analyzing the corresponding expression level of SE-associated genes in CLL patients, we identified 190 transcripts associated with SEs that were significantly overexpressed in CLL patient B cells (Student's t-test p Disclosures Awan: Innate Pharma: Research Funding; Pharmacyclics: Consultancy; Novartis Oncology: Consultancy.

In this study we performed a systematic evaluation of functional miRNA-mRNA interactions associated with the invasiveness of breast cancer cells using a combination of integrated miRNA and mRNA expression profiling, bioinformatics prediction, and functional assays. Analysis of the miRNA expression identified 11 miRNAs that were differentially expressed, including 7 down-regulated (miR-200c, miR-205, miR-203, miR-141, miR-34a, miR-183, and miR-375) and 4 up-regulated miRNAs (miR-146a, miR-138, miR-125b1 and miR-100), in invasive cell lines when compared to normal and less invasive cell lines. Transfection of miR-200c, miR-205, and miR-375 mimics into MDA-MB-231 cells led to the inhibition of in vitro cell migration and invasion. The integrated analysis of miRNA and mRNA expression identified 35 known and novel target genes of miR-200c, miR-205, and mir-375, including CFL2, LAMC1, TIMP2, ZEB1, CDH11, PRKCA, PTPRJ, PTPRM, LDHB, and SEC23A. Surprisingly, the majority of these genes (27 genes) were target genes of miR-200c, suggesting that miR-200c plays a pivotal role in regulating the invasiveness of breast cancer cells. We characterized one of the target genes of miR-200c, CFL2, and demonstrated that CFL2 is overexpressed in aggressive breast cancer cell lines and can be significantly down-regulated by exogenous miR-200c. Tissue microarray analysis further revealed that CFL2 expression in primary breast cancer tissue correlated with tumor grade. The results obtained from this study may improve our understanding of the role of these candidate miRNAs and their target genes in relation to breast cancer invasiveness and ultimately lead to the identification of novel biomarkers associated with prognosis.

Chronic lymphocytic leukemia (CLL) is a malignancy characterized by the progressive accumulation of CD19+ B-cells capable of overcoming their regulated life cycle. Because this disease is highly heterogeneous and utilizes several mechanisms to resist apoptotic death, CLL currently remains incurable. Based on the ongoing efforts to interpret the transcriptional dynamics of CLL pathogenicity as well as prior reports demonstrating the efficacy of cyclin-dependent kinase (CDK) transcriptional inhibitors, we sought to characterize the molecular response of CLL cells treated with the covalent CDK7 inhibitor THZ1 and determine the therapeutic potential of CDK7 inhibition in CLL. We first observed that THZ1 was able to inhibit growth in malignant B-cell lines MEC1 and MEC2 in both a dose dependent (IC50: .045uM & .030uM, respectively) and time dependent manner. The inhibition in cell growth corresponded with both G1-mediated cell cycle arrest as well as apoptosis in the respective cell lines. We also observed dose-dependent reduction in cell viability through apoptosis in patient-derived CLL B-cells after 24 hours. Because of the observed outcomes of THZ1-treated CLL cells, we then wanted to determine the specific transcriptional targets significantly suppressed by THZ1 treatment. To identify the THZ1-sensitive transcripts, we performed a time course RNAseq expression analysis in both MEC1 and MEC2 treated with 50nM THZ1. Based on the incremental reduction of covered reads over a 12-hour period, we determined that the top 50 transcripts greatly diminished in both MEC1 and MEC2 contain significant enrichment in genes attributed to glycolytic metabolism (ex: ALDOC, SLC2A1, TPI1, GAPDH, ENO2). Along with the overlapping comparison between the two cell lines, we next compared the downregulated transcripts from the treated cell lines against the RNAseq expression profile of 47 CLL patients and 5 healthy donors. We observed that THZ1 was able to suppress transcripts upregulated in CLL patient samples including ENO2, FGR, WNT10A, and CBX7 in MEC1 and ENO2, MALAT1, CCR7, and PLCG1 in MEC2. Finally, we performed H3K27Ac ChIPseq in MEC1 to identify super enhancers that may overlap with THZ1-sensitive transcripts. From this comparison, we determined that super enhancers exist within reported oncogenic drivers CBX7, WNT10A, and FGR. Overall, we observe that THZ1 can effectively overcome the anti-apoptotic phenotype of CLL B-cells as well as directly suppress transcription of genes that can drive CLL malignancy. With the addition of CDK7 ChIPseq, our ultimate goal is to provide clarity regarding CDK7-mediated transcriptional regulation in CLL and demonstrate the molecular consequences of therapeutic CDK7 inhibition in CLL. Citation Format: Austin Young Shull, Jeong-Hyeon Choi, Jordan Bauer, Lirong Pei, Farrukh T. Awan, Huidong Shi. The covalent CDK7 inhibitor THZ1 can counteract apoptotic resistance and suppress the transcription of genes attributed to chronic lymphocytic leukemia malignancy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4697.

We conducted a genome-wide DNA methylation analysis in CD19 (+) B-cells from chronic lymphocytic leukemia (CLL) patients and normal control samples using reduced representation bisulfite sequencing (RRBS). The methylation status of 1.8-2.3 million CpGs in the CLL genome was determined; about 45% of these CpGs were located in more than 23,000 CpG islands (CGIs). While global CpG methylation was similar between CLL and normal B-cells, 1764 gene promoters were identified as being differentially methylated in at least one CLL sample when compared with normal B-cell samples. Nineteen percent of the differentially methylated genes were involved in transcriptional regulation. Aberrant hypermethylation was found in all HOX gene clusters and a significant number of WNT signaling pathway genes. Hypomethylation occurred more frequently in the gene body including introns, exons, and 3'-UTRs in CLL. The NFATc1 P2 promoter and first intron was found to be hypomethylated and correlated with upregulation of both NFATc1 RNA and protein expression levels in CLL suggesting that an epigenetic mechanism is involved in the constitutive activation of NFAT activity in CLL cells. This comprehensive DNA methylation analysis will further our understanding of the epigenetic contribution to cellular dysfunction in CLL.

The majority of meningiomas are benign tumors associated with favorable outcomes; however, the less common aggressive variants with unfavorable outcomes often recur and may be due to subpopulations of less-differentiated cells residing within the tumor. These subpopulations of tumor cells have tumor-initiating properties and may be isolated from heterogeneous tumors when sorted or cultured in defined medium. We report the isolation and characterization of a population of tumor-initiating cells derived from an atypical meningioma. We identify a tumor-initiating population from an atypical meningioma, termed meningioma-initiating cells (MICs). These MICs self-renew, differentiate, and can recapitulate the histological characteristics of the parental tumor when transplanted at 1000 cells into the flank regions of athymic nude mice. Immunohistochemistry reveals stem-like protein expression patterns similar to neural stem and progenitor cells (NSPCs) while genomic profiling verified the isolation of cancer cells (with defined meningioma chromosomal aberrations) from the bulk tumor. Microarray and pathway analysis identifies biochemical processes and gene networks related to aberrant cell cycle progression, particularly the loss of heterozygosity of tumor suppressor genes CDKN2A (p16(INK4A)), p14(ARF), and CDKN2B (p15(INK4B)). Flow cytometric analysis revealed the expression of CD44 and activated leukocyte adhesion molecule (ALCAM/CD166); these may prove to be markers able to identify this cell type. The isolation and identification of a tumor-initiating cell population capable of forming meningiomas demonstrates a useful model for understanding meningioma development. This meningioma model may be used to study the cell hierarchy of meningioma tumorogenesis and provide increased understanding of malignant progression.

Background Follicular lymphoma (FL) is a form of non-Hodgkin's lymphoma (NHL) that arises from germinal center (GC) B-cells. Despite the significant advances in immunotherapy, FL is still not curable. Beyond transcriptional profiling and genomics datasets, there currently is no epigenome-scale dataset or integrative biology approach that can adequately model this disease and therefore identify novel mechanisms and targets for successful prevention and treatment of FL. Methodology/Principal Findings We performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19+ B-cells using 454 sequencing technology. The methylated DNA fragments were enriched with methyl-binding proteins, treated with bisulfite, and sequenced using the Roche-454 GS FLX sequencer. The total number of bases covered in the human genome was 18.2 and 49.3 million including 726,003 and 1.3 million CpGs in FL and CD19+ B-cells, respectively. 11,971 and 7,882 methylated regions of interest (MRIs) were identified respectively. The genome-wide distribution of these MRIs displayed significant differences between FL and normal B-cells. A reverse trend in the distribution of MRIs between the promoter and the gene body was observed in FL and CD19+ B-cells. The MRIs identified in FL cells also correlated well with transcriptomic data and ChIP-on-Chip analyses of genome-wide histone modifications such as tri-methyl-H3K27, and tri-methyl-H3K4, indicating a concerted epigenetic alteration in FL cells. Conclusions/Significance This study is the first to provide a large scale and comprehensive analysis of the DNA methylation sequence composition and distribution in the FL epigenome. These integrated approaches have led to the discovery of novel and frequent targets of aberrant epigenetic alterations. The genome-wide bisulfite sequencing approach developed here can be a useful tool for profiling DNA methylation in clinical samples.

The pile-up of arsenic at the Si/SiO2 interface after As implantation and annealing was investigated by high resolution Z-contrast imaging, electron energy-loss spectroscopy (EELS), grazing incidence x-ray fluorescence spectroscopy (GI-XRF), secondary ion mass spectrometry, x-ray photoelectron spectroscopy, Rutherford backscattering spectrometry, as well as Hall mobility and four-point probe resistivity measurements. After properly taking into account their respective artifacts, the results of all methods are compatible with each other, with EELS and GI-XRF combined with etching providing similar spatial resolution on the nanometer scale for the dopant profile. The sheet concentration of the piled-up As at the interface was found to be similar to 1 x 10(15) cm(-2) for an implanted dose of I X 1016 cm-2 with a maximum concentration of similar to 10 at. %. The strain observed in the Z-contrast images also suggests a significant concentration of local distortions within 3 nm from the interface, which, however, do not seem to involve intrinsic point defects. (C) 2008 American Institute of Physics.

The segregation of As atoms at the Si/SiO2 interface during annealing was investigated by grazing incidence X-ray fluorescence spectroscopy in combination with successive removal of silicon layers by etching with thicknesses on the order of a nanometer. With this method it is possible to clearly distinguish between the segregated atoms and the As atoms in the bulk over a large range of implantation doses from 3·12 cm−2 to 1·16 cm−2. The samples were annealed at 900 °C and 1000 °C, respectively, for times sufficiently long to ensure that the segregation reflects an equilibrium effect. The results were confirmed by medium energy ion scattering, Z-contrast measurements and electron energy loss spectroscopy.

Indoleamine 2, 3-dioxygenase 1, encoded by IDO1, is a key immunosuppressive enzyme that catabolizes essential amino acid tryptophan to kynurenine in the tumor microenvironment. Severe depletion of tryptophan by IDO1 affects proliferation of T cells and tryptophan metabolites cause T-cell anergy and induce apoptosis. In this study, we investigated the epigenetic regulation of IDO1 expression by DNA methylation in breast cancer cells. Bisulfite pyrosequencing analysis of IDO1 promoter methylation performed on a panel of 10 breast cancer cell lines revealed that triple negative breast cancer (TNBC) cell lines (i.e. MDA-MB-231, Hs578t, SUM159) are hypomethylated compared to estrogen receptor positive (ER+) cell lines (i.e. MCF7, BT474, T47D). The same analysis was extended to 30 primary breast tumor and normal control samples and the results demonstrated that TNBC tumors had lower IDO1 promoter methylation compared to ER+ tumors. RT-PCR analysis showed that IDO1 mRNA expression is higher in TNBC cell lines than ER+ cell lines. This inverse correlation between IDO1 promoter methylation and mRNA expression can also be observed in TCGA 450K methylation and RNA-seq data sets in which promoter is hypomethylated and mRNA is up-regulated in basal-like molecular subtypes as compared to other breast cancer subtypes. IDO1 promoter is relatively CpG poor with most CpG sites concentrated near interferon γ (IFNg) responsive GAS and ISRE transcription factor binding sites. To investigate the role of CpG methylation in regulating IDO1 induction by IFNg, we cloned either methylated or unmethylated IDO1 promoter DNA into a luciferase reporter plasmid. Methylated promoter reporter exhibited significantly lower luciferase activity at basal or with IFNg stimulation compared to unmethylated reporter plasmid when transfected into MCF-7 or MDA-MB-231 cell lines. Treatment with a demethylating agent, 5-aza-deoxycytidine, synergistically up-regulated IDO1 mRNA expression with IFNg in MCF7 cells which have hypermethylated IDO1 promoter further supporting the influence of CpG methylation on IDO1 expression. IFNg stimulation or co-culture with activated T-cells significantly induced IDO1 protein expression in MDA-MB-231 cells, but not in MCF7 cells. We found no difference in IDO1 mRNA stability and IFNg induced JAK/STAT signaling pathway between MDA-MB-231 and MCF7 cell lines except promoter methylation. Furthermore, RNA-seq analysis of MDA-MB-231 and MCF7 cell lines co-cultured with activated T-cells revealed an active immune signaling mediated through JAK/STAT pathway shared by both cell lines, but also differential induction of IDO1 transcription between these two cell lines. These findings indicate IDO1 promoter methylation status as an important factor that regulates anti-immune responses by tumor cells towards tumor infiltrating lymphocytes and it could be used as a useful biomarker for IDO inhibitor based immunotherapy. Citation Format: Satish Kumar Reddy Noonepalle, Eun Joon Lee, Maria Ouzounova, Jaejik Kim, Jeong-Hyeon Choi, Austin Shull, Lirong Pei, Ravindra Kolhe, Pei-Yin Hsu, Nagireddy Putluri, Tim Hui-Ming Huang, Arun Sreekumar, Hasan Korkaya, David Munn, Huidong Shi. Promoter methylation regulates interferon-γ induced indoleamine 2,3-dioxygenase expression in breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4060. doi:10.1158/1538-7445.AM2015-4060

Mammary stem/progenitor cells (MaSCs) maintain self-renewal of the mammary epithelium during puberty and pregnancy. DNA methylation provides a potential epigenetic mechanism for maintaining cellular memory during self-renewal. Although DNA methyltransferases (DNMTs) are dispensable for embryonic stem cell maintenance, their role in maintaining MaSCs and cancer stem cells (CSCs) in constantly replenishing mammary epithelium is unclear. Here we show that DNMT1 is indispensable for MaSC maintenance. Furthermore, we find that DNMT1 expression is elevated in mammary tumours, and mammary gland-specific DNMT1 deletion protects mice from mammary tumorigenesis by limiting the CSC pool. Through genome-scale methylation studies, we identify ISL1 as a direct DNMT1 target, hypermethylated and downregulated in mammary tumours and CSCs. DNMT inhibition or ISL1 expression in breast cancer cells limits CSC population. Altogether, our studies uncover an essential role for DNMT1 in MaSC and CSC maintenance and identify DNMT1-ISL1 axis as a potential therapeutic target for breast cancer treatment.

Background CD8+ T cells from chronic lymphocytic leukemia (CLL) patients have been demonstrated to exhibit a number of alterations in global gene expression profiles when compared with healthy controls. It has been shown that CD8+ T cells from CLL patients have increased expression of T-cell exhaustion markers like PD-1. CLL-induced functional defects in T cells are thought to directly contribute to the failure of antitumor immunity and are considered a hallmark of this disease. Nevertheless, the molecular regulation of T-cell dysfunction in CLL patients still remains poorly understood. Methods In the present study, CD8+ T cells were isolated from peripheral blood mononuclear cells (PBMCs) of patients with CLL (n=10) and healthy donors (n=5), and analyzed by genome-wide DNA methylation profiling using Illumina Infinium 450K methylation array. The differentially methylated genes (KLRG1, CCR6 and TCRA) identified by the 450K array analysis were validated by bisulfite pyrosequencing in additional CLL and healthy control samples. DNA methylation in the first intron, distal upstream, and proximal promoter regions of PD-1 was also examined by pyrosequencing. Luciferase reporter assays were used to determine the effects of DNA methylation on the enhancer activity of a PD-1 upstream sequence. To investigate whether CLL cells can directly alter the methylation of the candidate genes in CD8+ T cells, healthy PBMCs were cultured alone or co-cultured with purified allogeneic CLL cells for 72 hours. In parallel, healthy PBMCs were cultured in CD3mAb-coated plates containing CD28mAb or treated with PMA/ionomycin for 72 hours. Cultured PBMCs were then harvested for flow cytometrc analysis and CD8+ T cells purification. Multicolor flow cytometry was used to characterize T-cell subsets and expression of PD-1, KLRG1 and TCRα/β. Bisulfite pyrosequencing was used to determine the methylation changes of KLRG1, CCR6, TCRA, and PD-1 in CD8+ T cells after co-culture with CLL cells or after T-cell activation. Results The Illumina 450K methylation array analysis identified 312 differentially methylated CpG sites (Student t-test, p0.25) between CD8+ T cells from CLL and healthy controls with 199 hypermethyated and 113 hypomethylated CpG sites that are associated with 206 genes. Interestingly, 4 out of the 7 most significant CpG sites (FDR Conclusion For the first time, our investigation demonstrates the genome-wide DNA methylation profiles of CD8+ T cells isolated from CLL patients and determined that recurrent epigenetic changes in PD-1, KLRG1, CCR6, and TCRA in CD8+ T cells occur in CLL patients. Our methylation data suggest that the exhaustion phenotype observed in CLL patient CD8+ T cells maybe associated with altered DNA methylation profiles, an event previously seen in antigen-specific CD8+ T cells that undergo chronic viral infection-induced epigenetic changes. Disclosures Awan: Boehringer Ingelheim: Consultancy; Lymphoma Research Foundation: Research Funding. Wang:NIH/NIMHD: Research Funding. Shi:NIH/NCI: Research Funding; Georgia Research Alliance: Research Funding.

Metastasis is the leading cause of caner-related death for solid tumors including gastric carcinoma (GC). An epigenetic biomarker panel for prediction GC metastasis will have clinical impact on the care of GC patients. In order to characterize the methylation differences between GCs with and without metastasis, genome-wide DNA methylation profiles were compared between 4 metastatic and 4 non-metastatic GCs and their surgical margins (SM). The GC genome showed significantly higher proportions of hypomethylation in the promoter and exon-1 regions, as well as increased hypermethylation of intragenic fragments when compared to SMs. From the list of differentially methylated CpG islands (CGIs), 63 candidate genes and 10 known tumor-related genes were selected for further analysis based on their known functions. Significant differential methylation was validated in the CGIs of 15 genes (Ps Citation Format: Zhaojun Liu, Jun Zhang, Yanhong Gao, Lirong Pei, Naoko Hattori, Budong Zhu, Jiafu Ji, Yasuhito Yuasa, Wooho Kim, Toshikazu Ushijima, Huidong Shi, Dajun Deng. Large-scale characterization of DNA methylation changes in human gastric carcinomas with and without metastasis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4012. doi:10.1158/1538-7445.AM2014-4012

Glioblastoma (GBM) is the most common and most aggressive brain tumor in adults. Its frequent recurrence after resection and dismal prognosis are thought to be due to a small population of stem-like tumor cells that efficiently propagate tumors and resist cytotoxic therapy. In this study, we performed an in depth analysis of the DNA methylation landscape in GBM-derived cancer stem cells (GSCs). Parallel comparisons of primary GBM tumors and GSC lines derived from these tumors with normal controls (a neural stem cell (NSC) line and normal brain tissue) identified two groups hyper- and hypomethylated of genes that display a trend of either increasing or decreasing methylation levels in the order of controls, primary GBMs, and their counterpart GSC lines, respectively. Interestingly, concurrent promoter hypermethylation and gene body hypomethylation were observed in a subset of genes including MGMT, AJAP1 and PTPRN2. These unique DNA methylation signatures were also be found in primary GBM-derived xenograft tumors suggesting that they were not tissue culture-related epigenetic changes. Integration of GSC-specific epigenetic signatures with gene expression analysis further identified candidate tumor suppressor genes that are frequently down regulated in GBMs such as SPINT2, NEFM, and PENK. The comparison between the NSC line and the normal brain tissue sample leads to the identification of a group of NSC-specific differentially methylated regions (nsDMRs). Cluster analysis using nsDMRs revealed the presence of stem cell-specific DNA methylation signatures in both primary GBM and GSC lines. Higher expression of genes associated with stem cell-specific DNA methylation signatures such as DNMT3A, STAT5A, CSTB, PMEPA1 and G6PD in GBM patients was found to be associated with poor patient survival. The results from this study demonstrate the utility of using cancer stem cell models for advancing understanding of the pathobiology of gliomas. Citation Format: Eun Joon Lee, Prakash Rath, Jimei Liu, Dungsheng Ryu, Alan Free, Lirong Pei, Douglas C Anthony, Suash Sharma, Mark D Kirk, John J. Laterra, Duck Hwan Ryu, Jeong-Hyeon Choi, Huidong Shi, Douglas C. Miller, N. Scott Litofsky, Qi Feng. Identification of global DNA methylation signatures in glioblastoma-derived cancer stem cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1379. doi:10.1158/1538-7445.AM2014-1379

Chronic lymphocytic leukemia (CLL) is a cancer in which B-lymphocytes proliferate in an unchecked manner and escape normal apoptotic death. It is one of the most common leukemias in the Western world, and currently, there is no cure for CLL due to the heterogeneous ways in which it can proliferate. Due to the dynamics of how CLL can develop, it is very critical to investigate the oncogenic mechanisms that allow particular clinical CLL subtypes to expand, as well as discovering potential underlying mechanisms that are common among all CLL patients. With this comprehensive goal in mind, we investigated the gene expression landscape in CLL by performing whole transcriptome analysis via RNA sequencing in 47 CLL patients and 5 normal CD19+ B-cell donors to determine differential expression and isoform patterns in CLL. Between CLL and normal CD19+ B-cells, there were 725 differentially expressed genes (FDR p Citation Format: Austin Y. Shull, Junfeng Luo, Jeong-Hyeon Choi, Lirong Pei, Farrukh T. Awan, Eun-Joon Lee, Jimei Liu, Phillip J. Buckhaults, Xiao-Jie Yan, Nicholas Chiorazzi, Huidong Shi. Identifying differential gene expression and splicing events in chronic lymphocytic leukemia patients through whole transcriptome profiling. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5182. doi:10.1158/1538-7445.AM2014-5182

Abstract 3504 Programmed Death-1 (PD-1) is an inhibitory cell surface receptor of the immunoglobulin superfamily expressed on activated lymphocytes, monocytes and dendritic cells. Although PD-1 function is best characterized in T-cells, it is known that PD-1 also suppresses the immune response of B lymphocytes through protein phosphatase recruitment and dephosphorylation of signaling molecules downstream of the B-cell receptor (BCR). Recent studies have found that PD-1 expression is elevated at the mRNA as well as the protein levels in B cells obtained from chronic lymphocytic leukemia (CLL) patients compared to those from healthy controls. Using genome-wide DNA methylation sequencing, we identified PD-1 as one of the significantly hypomethylated genes in CLL compared to normal B-cell samples. Three differentially methylated regions (DMRs) were discovered in the first intron, proximal promoter and up-stream enhancer regions. We validated these DMRs in 43 CLL and 7 normal control samples using bisulfite pyrosequencing. The pyrosequencing analysis further confirmed that all three regions were significantly hypomethylated in CLL patient samples (p Disclosures: No relevant conflicts of interest to declare.

Abstract 526 Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). We conducted a genome-wide DNA methylation analysis in CD19+ B-cells from a group of 43 CLL patients using reduced representation bisulfite sequencing (RRBS). Using base-pair resolution methylation sequencing, 2323 differentially methylated regions between CLL and normal B cells (CLL-specific DMRs) and 569 between M-CLL and U-CLL samples (IGHV-specific DMRs) were identified in the CLL genomes. The IGHV-specific DMRs are mostly unique when compared to the CLL-specific DMRs. Less than 10% of the IGHV-specific DMRs are located in promoter regions; however, more than half of these overlap with known DNase I hypersensitive sites, enhancer regions marked by histone modification (H3K4Me1 and H3K27Ac), and transcription factor binding sites in the ENCODE datasets, which indicates that these DMRs contain regulatory sequences. Distinctive DNA methylation patterns were observed in M-CLL and U-CLL samples. Overall, U-CLL was found to contain 50% more hypermethylated regions than M-CLL samples. The hypermethylated loci observed in the U-CLL samples also appear to be hypermethylated in normal naïve B cells as compared memory B cells, suggesting that M-CLL and U-CLL differ in differentiation status corresponding to normal B cell differentiation stages. RNA-seq analysis performed using matched samples (n=34), in which both DNA methylation and gene expression data were available, demonstrated excellent correlation between DNA methylation and gene expression. Several genes whose expression status was previously shown to be associated with CLL prognosis such as ZAP70, CRY1, LDOC1, SEPT10, LAG3, and LPL were differentially methylated in the promoter regions between M-CLL and U-CLL samples indicating that DNA methylation plays an important role in defining the gene expression patterns of these prognostic genes. We further validated 9 genes with IGHV-specific DMRs in the promoter regions using bisulfite pyrosequencing, and the results demonstrated excellent correlation between differential methylation and IGHV mutation status. These novel differentially methylated genes could be developed into biomarkers for CLL prognosis. In addition, DNA hypomethylation was observed in a significant number of genes involved in lymphocyte activation such as PDCD1, NFATc1, and CD5. DNA hypomethylation was observed in the proximal promoter and far up-stream enhancer regions of CD5, an important cell surface marker that uniquely identifies CLL. Overall, the DNA methylation landscape in CLL patients indicates that CLL B cells possess an active B-cell phenotype; at the same time, U-CLL and M-CLL are faithfully committed to their lineage resembling either naïve or memory B cells. In summary, this comprehensive DNA methylation analysis has identified a large number of novel epigenetic changes in CLL patients. The results from this study will further advance our understanding of the epigenetic contribution to molecular subtypes in CLL. Disclosures: No relevant conflicts of interest to declare.

We applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of ~1 million CpGs in more than 21,408 CGIs and more than 15,946 transcriptional regulatory regions. Of the CpGs analyzed, 77-84% fell on or near capture probe sequences; 69-75% fell within CGIs. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. Differentially methylated regions (DMRs) were identified in the 5'-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X-chromosome among the three breast cancer cell lines analyzed. We chose 46 candidate loci (762 CpGs) for confirmation with PCR-based bisulfite sequencing and demonstrated excellent correlation between two data sets. Targeted bisulfite sequencing of three DNA methyltransferase (DNMT) knockout cell lines and the wild-type HCT116 colon cancer cell line revealed a significant decrease in CpG methylation for the DNMT1 knockout and DNMT1, 3B double knockout cell lines, but not in DNMT3B knockout cell line. We demonstrated the targeted bisulfite sequencing approach to be a powerful method to uncover novel aberrant methylation in the cancer epigenome. Since all targets were captured and sequenced as a pool through a series of single-tube reactions, this method can be easily scaled up to deal with a large number of samples.

Chronic lymphocytic leukemia (CLL) is the most common leukemia of adults in the western world. The clinical course of CLL is highly variable. Some patients are able to live years with no need for treatment; whereas others progress rapidly requiring therapy within a short time after diagnosis. The identification and validation of prognostic molecular markers (including surface markers, cytogenetic abnormalities, and IGHV mutational status) have resulted in refinements in the approach to the management of these patients. Further discovery of biologically relevant factors that influence the heterogeneity and progression of CLL will not only promote our understanding of the disease process, but also allow us to identify rational therapeutic approaches. In this study, we conducted genome-wide DNA methylation analyses in purified CD19+ B-cells from 11 CLL patients with a range of CD38 expression using reduced representation bisulfite sequencing (RRBS). Using one lane of the Illumina sequencing data, we were able to consistently determine the methylation status of approximately 1.8 million CpGs; 45% of these CpGs are located in more than 23,000 CpG islands (CGIs), accounting for more than 80% of all annotated CGIs across the genome. We have identified a large number of CGIs that were differentially methylated between CLL cells and normal CD19+ B-cells. The promoter hypermethylation patterns of many genes previously reported in CLL, such as FOXD3, GRM7, DLEU7 etc, were determined in the 11 CLL samples. In addition, we have observed aberrant DNA methylation changes in all 4 HOX gene clusters in CLL. For instance, HOXD8, HOXD9, and HOXD11 were hypermethylated in 11 out of 11 CLL samples. In addition, we also identified a significant number of DNA methylation alterations in the WNT signaling pathway genes. One-way ANOVA analysis of DNA methylation profiles of 764,984 CpGs shared by all CLL samples identified 570 CpGs that were differentially methylated (p20% CLL cells expressing CD38 as CD38high group). The cluster analysis of the 570 CpGs reveals that it is possible to separate these CLL samples into two distinct groups based on the DNA methylation profiles. The study further confirms our early findings that CLL is affected by CpG island methylation in some genes that segregate with CD38 expression levels, while most others show similar methylation patterns across all levels. The aberrant promoter hypermethylation in certain functional gene groups and pathway-associated genes that are known to be deregulated in CLL provides additional insights into the CLL methylome and epigenetic contribution to cellular dysfunction. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4791. doi:10.1158/1538-7445.AM2011-4791

Recent studies using next-generation sequencing have generated genome-wide, single-base resolution DNA methylation maps. However, it is still very costly to conduct whole genome shotgun bisulfite sequencing. Currently, few methods enable targeted bisulfite sequencing of CpG islands (CGIs) or other specific regions of interest in a highly flexible and efficient manner. Here we present a novel approach that combines solution-phase hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in targeted CGI and promoter regions. We designed 51,466 single strand DNA oligonucleotides (160-mer) which target 23,441 CGIs and the transcription start sites of 19,369 known genes in the human genome. The synthetic long DNA oligonucleotides were converted into biotinylated RNA probes for solution-phase hybridization capture of target DNA. The captured genomic DNA was treated with sodium bisulfite, amplified by PCR and sequenced using Illumina GA IIx sequencer. Using this approach, we conducted bisulfite sequencing on captured DNA from three breast cancer cell lines, MCF10A, MCF7, and MDA-MB-231. 20-30 million single-end 75bp sequencing reads were obtained for each cell line. The raw sequencing reads were mapped to in silico bisulfite-converted human genome. The methylation levels for CpG sites covered with at least 10 sequencing reads were extracted, providing accurate quantification on 900,000-1,000,000 CpGs. 77-84% of CpGs analyzed in these samples fell on or near capture probe sequences; 69-75% lay properly on CGIs. One lane of Illumina sequencing data was sufficient to determine the methylation status of over 22,000 CGIs (75% of all annotated CGIs) in the human genome. More than 85% of capture probes successfully yielded quantitative DNA methylation data of targeted regions. We chose 45 candidate loci (760 CpGs) for confirmation with PCR-based bisulfite sequencing and demonstrated excellent correlation between two data sets. This novel method was further validated by sequencing three DNA methyltransferase (DNMT) knockout cell lines and the parental HCT116 colon cancer cell line. The targeted bisulfite sequencing data shows massive demethylation events in DNMT1 knockout (1KO) and double knockout (DKO) cell lines, but not in DNMT3B knockout (3BKO) and HCT116 cell lines. While the results indicate the critical role of DNMT1 in maintaining global DNA methylation, we have also identified DNMT3B specific demethylation patterns in a small group of genomic loci. In this study, we demonstrated the targeted bisulfite sequencing approach to be a powerful method to uncover novel aberrant methylation in the cancer genome. Since all targets were captured and sequenced as a pool through a series of single-tube reactions, this method can be easily scaled up to deal with a large number of samples. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3003. doi:10.1158/1538-7445.AM2011-3003

MicroRNAs (miRNAs) are a class of small, non-coding RNAs that regulate gene expression by translational repression or mRNA degradation. Although the functions of specific miRNAs in breast cancer development and progression have been extensively investigated, few studies have focused on the systematic identification of miRNAs and their target genes related to breast cancer aggressiveness. In this study, we sought to discover the signatures of miRNA-mRNA target pairs in aggressive breast cancer cell lines through a combination of integrated miRNA and mRNA expression profiling, bioinformatics prediction and functional assays. MiRNA and mRNA expression profiles of 12 breast cancer cell lines including 8 less aggressive lines (MCF10A, MCF12A, BT474, MCF7, MDA-MB-468, SK-BR3, T-47D and ZR-75-1) and 4 aggressive lines (BT549, HS578T, MDA-MB-231 and SUM159) were generated using Affymertrix miRNA Array and U133 Plus 2.0 Array, respectively. The miRNA expression array analysis has shown that 44 out of 847 miRNAs were differentially expressed (p Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4937. doi:10.1158/1538-7445.AM2011-4937

The segregation and pile-up of arsenic atoms at the Si/SiO2 interface in steady state was investigated in detail by a combination of gracing incidence x-ray fluorescence spectroscopy GI-XRF measurements, electrical measurements, etching on the nanometer scale, and measurements of the step heights by interferometry. Using GI-XRF measurements and removal of the highly doped segregation layer by a sensitive etching process it was possible to distinguish clearly between the piled-up atoms and the arsenic atoms in the bulk over a large range of implantation doses, from 31012 to 11016 cm 2. The samples were annealed at different temperatures from 900 C to 1200 C for time periods long enough to make sure that the segregation reflects an equilibrium state. With additional step height measurements at line-space structures, the thickness of the layer with the piled-up arsenic and the shape of the segregation profile was determined. Electrical measurements indicated that the segregated arsenic atoms are deep donors with an electrical activity that increases eventually to full electrical activation for high sheet concentrations of the segregated atoms. The measured data can be modeled as a steady state of neutral arsenic atoms in the segregation layer with positively charged substitutional arsenic atoms and freemore » electrons. For the highest concentration, a saturation of the sheet concentration of segregated arsenic atoms was observed that correlates with the increase in electrical activation. For the use in process simulation programs, a three-phase segregation model was adapted and calibrated.« less