Publications by authors named "Hatice Gulcin Ozer"

34 Publications

Molecular associations, clinical, and prognostic implications of PTPN11 mutations in acute myeloid leukemia (Alliance).

Blood Adv 2021 Nov 30. Epub 2021 Nov 30.

The Ohio State University, United States.

Prognostic factors associated with chemotherapy outcomes in patients with acute myeloid leukemia (AML) are extensively reported, and one gene whose mutation is recognized as conferring resistance to several newer targeted therapies is protein tyrosine phosphatase non-receptor type 11 (PTPN11). The broader clinical implications of PTPN11 mutations in AML are still not well understood. The objective of this study was to determine which cytogenetic abnormalities and gene mutations co-occur with PTPN11 mutations and how PTPN11 mutations impact outcomes of patients treated with intensive chemotherapy. We studied 1,725 newly diagnosed AML patients (excluding acute promyelocytic leukemia) enrolled onto the Cancer and Leukemia Group B/Alliance for Clinical Trials in Oncology trials. In 140 PTPN11-mutated patient samples, PTPN11 most commonly co-occurred with mutations in NPM1, DNMT3A, and TET2. PTPN11 mutations were relatively common in patients with an inv(3)(q21q26)/t(3;3)(q21;q26) and a normal karyotype but were very rare in patients with typical complex karyotype and core-binding factor AML. Mutations in the N-terminal SH2 domain of PTPN11 were associated with a higher early death rate than those in the phosphatase domain. PTPN11 mutations did not affect outcomes of NPM1-mutated patients, but these patients were less likely to have co-occurring kinase mutations (i.e., FLT3-ITD), suggesting activation of overlapping signaling pathways. However, in AML patients with wild-type NPM1, PTPN11 mutations were associated with adverse patient outcomes providing a rationale to study the biology and treatment approaches in this molecular group.
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http://dx.doi.org/10.1182/bloodadvances.2021006242DOI Listing
November 2021

Rare t(X;14)(q28;q32) translocation reveals link between MTCP1 and chronic lymphocytic leukemia.

Nat Commun 2021 11 3;12(1):6338. Epub 2021 Nov 3.

Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.

Rare, recurrent balanced translocations occur in a variety of cancers but are often not functionally interrogated. Balanced translocations with the immunoglobulin heavy chain locus (IGH; 14q32) in chronic lymphocytic leukemia (CLL) are infrequent but have led to the discovery of pathogenic genes including CCND1, BCL2, and BCL3. Following identification of a t(X;14)(q28;q32) translocation that placed the mature T cell proliferation 1 gene (MTCP1) adjacent to the immunoglobulin locus in a CLL patient, we hypothesized that this gene may have previously unrecognized importance. Indeed, here we report overexpression of human MTCP1 restricted to the B cell compartment in mice produces a clonal CD5/CD19 leukemia recapitulating the major characteristics of human CLL and demonstrates favorable response to therapeutic intervention with ibrutinib. We reinforce the importance of genetic interrogation of rare, recurrent balanced translocations to identify cancer driving genes via the story of MTCP1 as a contributor to CLL pathogenesis.
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http://dx.doi.org/10.1038/s41467-021-26400-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8566464PMC
November 2021

Targeting BRD4 in acute myeloid leukemia with partial tandem duplication of the gene.

Haematologica 2021 09 1;106(9):2527-2532. Epub 2021 Sep 1.

The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA; Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH.

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http://dx.doi.org/10.3324/haematol.2020.271627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8409020PMC
September 2021

Aging Phenotypes and Restoring Functional Deficits in Older Adults With Hematologic Malignancy.

J Natl Compr Canc Netw 2021 Mar 26;19(9):1027-1036. Epub 2021 Mar 26.

5Cancer Prevention and Control, The Ohio State University, Columbus, Ohio.

Background: Gauging fitness remains a challenge among older adults with hematologic malignancies, and interventions to restore function are lacking. We pilot a structured exercise intervention and novel biologic correlates of aging using epigenetic clocks and markers of immunosenescence to evaluate changes in function and clinical outcomes.

Methods: Older adults (n=30) with hematologic malignancy actively receiving treatment were screened and enrolled in a 6-month exercise intervention, the Otago Exercise Programme (OEP). The impact of the OEP on geriatric assessment metrics and health-related quality of life were captured. Clinical outcomes of overall survival and hospital utilization (inpatient length of stay and emergency department use) in relationship to geriatric deficits were analyzed.

Results: Older adults (median age, 75.5 years [range, 62-83 years]) actively receiving treatment were enrolled in the OEP. Instrumental activities of daily living and physical health scores (PHS) increased significantly with the OEP intervention (median PHS: visit 1, 55 [range, 0-100]; visit 2, 70 [range, 30-100]; P<.01). Patient-reported Karnofsky performance status increased significantly, and the improvement was sustained (median [range]: visit 1, 80 [40-100]; visit 3, 90 [50-100]; P=.05). Quality of life (Patient-Reported Outcome Measurement Information System [PROMIS]) improved significantly by the end of the 6-month period (median [range]: visit 1, 32.4 [19.9-47.7]; visit 3, 36.2 [19.9-47.7]; P=.01]. Enhanced measures of gait speed and balance, using the Short Physical Performance Battery scores, were associated with a 20% decrease in risk of death (hazard ratio, 0.80; 95% CI, 0.65-0.97; P=.03) and a shorter hospital length of stay (decrease of 1.29 days; 95% CI, -2.46 to -0.13; P=.03). Peripheral blood immunosenescent markers were analyzed in relationship to clinical frailty and reports of mPhenoAge epigenetic analysis are preliminarily reported. Chronologic age had no relationship to overall survival, length of stay, or emergency department utilization.

Conclusions: The OEP was effective in improving quality of life, and geriatric tools predicted survival and hospital utilization among older adults with hematologic malignancies.
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http://dx.doi.org/10.6004/jnccn.2020.7686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8600896PMC
March 2021

A hierarchical and collaborative BRD4/CEBPD partnership governs vascular smooth muscle cell inflammation.

Mol Ther Methods Clin Dev 2021 Jun 27;21:54-66. Epub 2021 Feb 27.

Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.

Bromodomain protein BRD4 reads histone acetylation (H3K27ac), an epigenomic mark of transcription enhancers. CCAAT enhancer binding protein delta (CEBPD) is a transcription factor typically studied in metabolism. While both are potent effectors and potential therapeutic targets, their relationship was previously unknown. Here we investigated their interplay in vascular smooth muscle cell (SMC) inflammation. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) revealed H3K27ac/BRD4 enrichment at in injured rat carotid arteries. While genomic deletion of BRD4-associated enhancer in SMCs decreased transcripts, BRD4 gene silencing also diminished mRNA and protein, indicative of a BRD4 control over CEBPD expression. Bromodomain-1, but not bromodomain-2, accounted for this BRD4 function. Moreover, endogenous BRD4 protein co-immunoprecipitated with CEBPD, and both proteins co-immunoprecipitated the promoter and enhancer DNA fragments. These co-immunoprecipitations (coIPs) were all abolished by the BRD4-bromodomain blocker JQ1, suggesting a BRD4/CEBPD /promoter/enhancer complex. While BRD4 and CEBPD were both upregulated upon tumor necrosis factor alpha (TNF-α) stimulation of SMC inflammation (increased interleukin [IL]-1b, IL-6, and MCP-1), they mediated this stimulation via preferentially elevated expression of platelet-derived growth factor receptor alpha (PDGFRα, versus PDGFRβ), as indicated by loss- and gain-of-function experiments. Taken together, our study unravels a hierarchical yet collaborative BRD4/CEBPD relationship, a previously unrecognized mechanism that prompts SMC inflammation and may underlie other pathophysiological processes as well.
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http://dx.doi.org/10.1016/j.omtm.2021.02.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7966960PMC
June 2021

Gene expression signature predicts relapse in adult patients with cytogenetically normal acute myeloid leukemia.

Blood Adv 2021 03;5(5):1474-1482

The Ohio State University Comprehensive Cancer Center, Columbus OH.

Although ∼80% of adult patients with cytogenetically normal acute myeloid leukemia (CN-AML) achieve a complete remission (CR), more than half of them relapse. Better identification of patients who are likely to relapse can help to inform clinical decisions. We performed RNA sequencing on pretreatment samples from 268 adults with de novo CN-AML who were younger than 60 years of age and achieved a CR after induction treatment with standard "7+3" chemotherapy. After filtering for genes whose expressions were associated with gene mutations known to impact outcome (ie, CEBPA, NPM1, and FLT3-internal tandem duplication [FLT3-ITD]), we identified a 10-gene signature that was strongly predictive of patient relapse (area under the receiver operating characteristics curve [AUC], 0.81). The signature consisted of 7 coding genes (GAS6, PSD3, PLCB4, DEXI, JMY, NRP1, C10orf55) and 3 long noncoding RNAs. In multivariable analysis, the 10-gene signature was strongly associated with relapse (P < .001), after adjustment for the FLT3-ITD, CEBPA, and NPM1 mutational status. Validation of the expression signature in an independent patient set from The Cancer Genome Atlas showed the signature's strong predictive value, with AUC = 0.78. Implementation of the 10-gene signature into clinical prognostic stratification could be useful for identifying patients who are likely to relapse.
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http://dx.doi.org/10.1182/bloodadvances.2020003727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7948288PMC
March 2021

Recurrent XPO1 mutations alter pathogenesis of chronic lymphocytic leukemia.

J Hematol Oncol 2021 01 15;14(1):17. Epub 2021 Jan 15.

Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA.

Background: Exportin 1 (XPO1/CRM1) is a key mediator of nuclear export with relevance to multiple cancers, including chronic lymphocytic leukemia (CLL). Whole exome sequencing has identified hot-spot somatic XPO1 point mutations which we found to disrupt highly conserved biophysical interactions in the NES-binding groove, conferring novel cargo-binding abilities and forcing cellular mis-localization of critical regulators. However, the pathogenic role played by change-in-function XPO1 mutations in CLL is not fully understood.

Methods: We performed a large, multi-center retrospective analysis of CLL cases (N = 1286) to correlate nonsynonymous mutations in XPO1 (predominantly E571K or E571G; n = 72) with genetic and epigenetic features contributing to the overall outcomes in these patients. We then established a mouse model with over-expression of wildtype (wt) or mutant (E571K or E571G) XPO1 restricted to the B cell compartment (Eµ-XPO1). Eµ-XPO1 mice were then crossed with the Eµ-TCL1 CLL mouse model. Lastly, we determined crystal structures of XPO1 (wt or E571K) bound to several selective inhibitors of nuclear export (SINE) molecules (KPT-185, KPT-330/Selinexor, and KPT-8602/Eltanexor).

Results: We report that nonsynonymous mutations in XPO1 associate with high risk genetic and epigenetic features and accelerated CLL progression. Using the newly-generated Eµ-XPO1 mouse model, we found that constitutive B-cell over-expression of wt or mutant XPO1 could affect development of a CLL-like disease in aged mice. Furthermore, concurrent B-cell expression of XPO1 with E571K or E571G mutations and TCL1 accelerated the rate of leukemogenesis relative to that of Eµ-TCL1 mice. Lastly, crystal structures of E571 or E571K-XPO1 bound to SINEs, including Selinexor, are highly similar, suggesting that the activity of this class of compounds will not be affected by XPO1 mutations at E571 in patients with CLL.

Conclusions: These findings indicate that mutations in XPO1 at E571 can drive leukemogenesis by priming the pre-neoplastic lymphocytes for acquisition of additional genetic and epigenetic abnormalities that collectively result in neoplastic transformation.
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http://dx.doi.org/10.1186/s13045-021-01032-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7809770PMC
January 2021

CRISPR/Cas9 Genome Editing of the Human Topoisomerase II Intron 19 5' Splice Site Circumvents Etoposide Resistance in Human Leukemia K562 Cells.

Mol Pharmacol 2021 03 14;99(3):226-241. Epub 2021 Jan 14.

Division of Pharmaceutics and Pharmacology, College of Pharmacy (V.A.H., J.C.-M., J.L.P., J.L., J.C.Y., T.S.E., N.S.) and Department of Biomedical Informatics, College of Medicine (H.G.O), The Ohio State University, Columbus, Ohio

An essential function of DNA topoisomerase II (TOP2; 170 kDa, TOP2/170) is to resolve DNA topologic entanglements during chromosome disjunction by introducing transient DNA double-stranded breaks. TOP2/170 is an important target for DNA damage-stabilizing anticancer drugs, whose clinical efficacy is compromised by drug resistance often associated with decreased TOP2/170 expression. We recently demonstrated that an etoposide-resistant K562 clonal subline, K/VP.5, with reduced levels of TOP2/170, expresses high levels of a novel C-terminal truncated TOP2 isoform (90 kDa, TOP2/90). TOP2/90, the translation product of a TOP2 mRNA that retains a processed intron 19 (I19), heterodimerizes with TOP2/170 and is a resistance determinant through a dominant-negative effect on drug activity. We hypothesized that genome editing to enhance I19 removal would provide a tractable strategy to circumvent acquired TOP2-mediated drug resistance. To enhance I19 removal in K/VP.5 cells, CRISPR/Cas9 was used to make changes (GAG//GTAA →GAG//GTAA ) in the TOP2 gene's suboptimal exon 19/intron 19 5' splice site (E19/I19 5' SS). Gene-edited clones were identified by quantitative polymerase chain reaction and verified by sequencing. Characterization of a clone with all TOP2 alleles edited revealed improved I19 removal, decreased TOP2/90 mRNA/protein, and increased TOP2/170 mRNA/protein. Sensitivity to etoposide-induced DNA damage (H2AX, Comet assays) and growth inhibition was restored to levels comparable to those in parental K562 cells. Together, the results indicate that our gene-editing strategy for optimizing the TOP2 E19/I19 5' SS in K/VP.5 cells circumvents resistance to etoposide and other TOP2-targeted drugs. SIGNIFICANCE STATEMENT: Results presented here indicate that CRISPR/Cas9 gene editing of a suboptimal exon 19/intron 19 5' splice site in the DNA topoisomerase II (TOP2) gene results in circumvention of acquired drug resistance to etoposide and other TOP2-targeted drugs in a clonal K562 cell line by enhancing removal of intron 19 and thereby decreasing formation of a truncated TOP2 90 kDa isoform and increasing expression of full-length TOP2 170 kDa in these resistant cells. Results demonstrate the importance of RNA processing in acquired drug resistance to TOP2-targeted drugs.
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http://dx.doi.org/10.1124/molpharm.120.000173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919865PMC
March 2021

Nullifying epigenetic writer DOT1L attenuates neointimal hyperplasia.

Atherosclerosis 2020 09 2;308:22-31. Epub 2020 Jul 2.

Department of Surgery, College of Medicine and Davis Heart and Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA; Department of Physiology & Cell Biology, College of Medicine and Davis Heart and Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA; Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA; Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA. Electronic address:

Background And Aims: Histone methyltransferases are emerging targets for epigenetic therapy. DOT1L (disruptor of telomeric silencing 1-like) is the only known methylation writer at histone 3 lysine 79 (H3K79). It is little explored for intervention of cardiovascular disease. We investigated the role of DOT1L in neointimal hyperplasia (IH), a basic etiology of occlusive vascular diseases.

Methods And Results: IH was induced via balloon angioplasty in rat carotid arteries. DOT1L and its catalytic products H3K79me2 and H3K79me3 (immunostaining) increased by 4.69 ± 0.34, 2.38 ± 0.052, and 3.07 ± 0.27 fold, respectively, in injured (versus uninjured) carotid arteries at post-injury day 7. Dot1l silencing via shRNA-lentivirus infusion in injured arteries reduced DOT1L, H3K79me2, and IH at day 14 by 54.5%, 37.1%, and 76.5%, respectively. Moreover, perivascular administration of a DOT1L-selective inhibitor (EPZ5676) reduced H3K79me2, H3K79me3, and IH by 56.1%, 58.6%, and 39.9%, respectively. In addition, Dot1l silencing and its inhibition (with EPZ5676) in vivo in injured arteries boosted smooth muscle α-actin immunostaining; pretreatment of smooth muscle cells with EPZ5676 in vitro reduced pro-proliferative marker proteins, including proliferating cell nuclear antigen (PCNA) and cyclin-D1.

Conclusions: While DOT1L is upregulated in angioplasty-injured rat carotid arteries, either its genetic silencing or pharmacological inhibition diminishes injury-induced IH. As such, this study presents a strong rationale for continued mechanistic and translational investigation into DOT1L targeting for treatment of (re)stenotic vascular conditions.
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http://dx.doi.org/10.1016/j.atherosclerosis.2020.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503165PMC
September 2020

Effects of DNA topoisomerase IIα splice variants on acquired drug resistance.

Cancer Drug Resist 2020 27;3(2):161-170. Epub 2020 Feb 27.

Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA.

DNA topoisomerase IIα (170 kDa, TOP2α/170) induces transient DNA double-strand breaks in proliferating cells to resolve DNA topological entanglements during chromosome condensation, replication, and segregation. Therefore, TOP2α/170 is a prominent target for anticancer drugs whose clinical efficacy is often compromised due to chemoresistance. Although many resistance mechanisms have been defined, acquired resistance of human cancer cell lines to TOP2α interfacial inhibitors/poisons is frequently associated with a reduction of Top2α/170 expression levels. Recent studies by our laboratory, in conjunction with earlier findings by other investigators, support the hypothesis that a major mechanism of acquired resistance to TOP2α-targeted drugs is due to alternative RNA processing/splicing. Specifically, several TOP2α mRNA splice variants have been reported which retain introns and are translated into truncated TOP2α isoforms lacking nuclear localization sequences and subsequent dysregulated nuclear-cytoplasmic disposition. In addition, intron retention can lead to truncated isoforms that lack both nuclear localization sequences and the active site tyrosine (Tyr805) necessary for forming enzyme-DNA covalent complexes and inducing DNA damage in the presence of TOP2α-targeted drugs. Ultimately, these truncated TOP2α isoforms result in decreased drug activity against TOP2α in the nucleus and manifest drug resistance. Therefore, the complete characterization of the mechanism(s) regulating the alternative RNA processing of TOP2α pre-mRNA may result in new strategies to circumvent acquired drug resistance. Additionally, novel TOP2α splice variants and truncated TOP2α isoforms may be useful as biomarkers for drug resistance, prognosis, and/or direct future TOP2α-targeted therapies.
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http://dx.doi.org/10.20517/cdr.2019.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304410PMC
February 2020

BISR-RNAseq: an efficient and scalable RNAseq analysis workflow with interactive report generation.

BMC Bioinformatics 2019 Dec 20;20(Suppl 24):670. Epub 2019 Dec 20.

Biomedical Informatics, The Ohio State University, Columbus, OH, USA.

Background: RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high performance computing environment.

Results: Developed as a tool by the Bioinformatics Shared Resource Group (BISR) at the Ohio State University, we have applied the pipeline to a few publicly available RNAseq datasets downloaded from GEO in order to demonstrate the feasibility of this workflow. Source code is available here: workflow: https://code.bmi.osumc.edu/gadepalli.3/BISR-RNAseq-ICIBM2019 and shiny: https://code.bmi.osumc.edu/gadepalli.3/BISR_RNASeq_ICIBM19. Example dataset is demonstrated here: https://dataportal.bmi.osumc.edu/RNA_Seq/.

Conclusion: The workflow allows for the analysis (alignment, QC, gene-wise counts generation) of raw RNAseq data and seamless integration of quality analysis and differential expression results into a configurable R shiny web application.
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http://dx.doi.org/10.1186/s12859-019-3251-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923898PMC
December 2019

hsa-miR-9-3p and hsa-miR-9-5p as Post-Transcriptional Modulators of DNA Topoisomerase II in Human Leukemia K562 Cells with Acquired Resistance to Etoposide.

Mol Pharmacol 2020 03 13;97(3):159-170. Epub 2019 Dec 13.

Division of Pharmaceutics and Pharmacology, College of Pharmacy (E.E.K., J.C.-M., V.A.H., A.E., J.L.P., N.S., J.C.Y., T.S.E.) and Department of Biomedical Informatics, College of Medicine (H.G.O., A.S.Y.), The Ohio State University, Columbus, Ohio

DNA topoisomerase II protein (TOP2) 170 kDa (TOP2/170) is an important target for anticancer agents whose efficacy is often attenuated by chemoresistance. Our laboratory has characterized acquired resistance to etoposide in human leukemia K562 cells. The clonal resistant subline K/VP.5 contains reduced TOP2/170 mRNA and protein levels compared with parental K562 cells. The aim of this study was to determine whether microRNA (miRNA)-mediated mechanisms play a role in drug resistance via decreased expression of TOP2/170. miRNA-sequencing revealed that human miR-9-3p and miR-9-5p were among the top six of those overexpressed in K/VP.5 compared with K562 cells; validation by quantitative polymerase chain reaction demonstrated overexpression of both miRNAs. miRNA recognition elements (MREs) for both miRNAs are present in the 3'-untranslated region (UTR) of TOP2/170. Transfecting K562 cells with a reporter plasmid harboring the TOP2/170 3'-UTR together with either miR-9-3p or miR-9-5p mimics resulted in a statistically significant decrease in luciferase expression. Mutating the miR-9-3p or miR-9-5p MREs prevented this decrease, demonstrating direct interaction between these miRNAs and TOP2/170 mRNA. Transfection of K562 cells with miR-9-3p or miR-9-5p mimics led to decreased TOP2/170 protein levels without a change in TOP2/170 mRNA and resulted in attenuated etoposide-induced DNA damage (gain-of-miRNA-inhibitory function). Conversely, transfection of miR-9-3p or miR-9-5p inhibitors in K/VP.5 cells (overexpressed miR-9 and low TOP2/170) led to increased TOP2/170 protein expression without a change in TOP2/170 mRNA levels and resulted in enhancement of etoposide-induced DNA damage (loss-of-miRNA-inhibitory function). Taken together, these results strongly suggest that these miRNAs play a role in and are potential targets for circumvention of acquired resistance to etoposide. SIGNIFICANCE STATEMENT: Results presented here indicate that miR-9-3p and miR-9-5p decrease DNA topoisomerase II protein 170 kDa expression levels in acquired resistance to etoposide. These findings contribute new information about and potential strategies for circumvention of drug resistance by modulation of microRNA levels. Furthermore, increased expression of miR-9-3p and miR-9-5p in chemoresistant cancer cells may support their validation as biomarkers of responsiveness to DNA topoisomerase II-targeted therapy.
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http://dx.doi.org/10.1124/mol.119.118315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978698PMC
March 2020

Protein arginine methyltransferase 5 represses tumor suppressor miRNAs that down-regulate CYCLIN D1 and c-MYC expression in aggressive B-cell lymphoma.

J Biol Chem 2020 01 10;295(5):1165-1180. Epub 2019 Dec 10.

Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, Ohio 43210

Protein arginine methyltransferase-5 (PRMT5) is overexpressed in aggressive B-cell non-Hodgkin's lymphomas, including mantle cell lymphoma and diffuse large B-cell lymphoma, and supports constitutive expression of CYCLIN D1 and c-MYC. Here, we combined ChIP analysis with next-generation sequencing to identify microRNA (miRNA) genes that are targeted by PRMT5 in aggressive lymphoma cell lines. We identified enrichment of histone 3 dimethylation at Arg-8 (H3(Me2)R8) in the promoter regions of miR33b, miR96, and miR503. PRMT5 knockdown de-repressed transcription of all three miRNAs, accompanied by loss of recruitment of epigenetic repressor complexes containing PRMT5 and either histone deacetylase 2 (HDAC2) or HDAC3, enhanced binding of co-activator complexes containing p300 or CREB-binding protein (CBP), and increased acetylation of specific histones, including H2BK12, H3K9, H3K14, and H4K8 at the miRNA promoters. Re-expression of individual miRNAs in B-cell lymphoma cells down-regulated expression of PRMT5, CYCLIN D1, and c-MYC, which are all predicted targets of these miRNAs, and reduced lymphoma cell survival. Luciferase reporter assays with WT and mutant 3'UTRs of CYCLIN D1 and c-MYC mRNAs revealed that binding sites for miR33b, miR96, and miR503 are critical for translational regulation of the transcripts of these two genes. Our findings link altered PRMT5 expression to transcriptional silencing of tumor-suppressing miRNAs in lymphoma cells and reinforce PRMT5's relevance for promoting lymphoma cell growth and survival.
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http://dx.doi.org/10.1074/jbc.RA119.008742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6996892PMC
January 2020

BRD4 Profiling Identifies Critical Chronic Lymphocytic Leukemia Oncogenic Circuits and Reveals Sensitivity to PLX51107, a Novel Structurally Distinct BET Inhibitor.

Cancer Discov 2018 04 31;8(4):458-477. Epub 2018 Jan 31.

Plexxikon Inc., Berkeley, California.

Bromodomain and extra-terminal (BET) family proteins are key regulators of gene expression in cancer. Herein, we utilize BRD4 profiling to identify critical pathways involved in pathogenesis of chronic lymphocytic leukemia (CLL). BRD4 is overexpressed in CLL and is enriched proximal to genes upregulated or expressed in CLL with known functions in disease pathogenesis and progression. These genes, including key members of the B-cell receptor (BCR) signaling pathway, provide a rationale for this therapeutic approach to identify new targets in alternative types of cancer. Additionally, we describe PLX51107, a structurally distinct BET inhibitor with novel and pharmacologic properties that emulates or exceeds the efficacy of BCR signaling agents in preclinical models of CLL. Herein, the discovery of the involvement of BRD4 in the core CLL transcriptional program provides a compelling rationale for clinical investigation of PLX51107 as epigenetic therapy in CLL and application of BRD4 profiling in other cancers. To date, functional studies of BRD4 in CLL are lacking. Through integrated genomic, functional, and pharmacologic analyses, we uncover the existence of BRD4-regulated core CLL transcriptional programs and present preclinical proof-of-concept studies validating BET inhibition as an epigenetic approach to target BCR signaling in CLL. .
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http://dx.doi.org/10.1158/2159-8290.CD-17-0902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882533PMC
April 2018

Prognostic and biological significance of the proangiogenic factor EGFL7 in acute myeloid leukemia.

Proc Natl Acad Sci U S A 2017 06 22;114(23):E4641-E4647. Epub 2017 May 22.

The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210;

Epithelial growth factor-like 7 (EGFL7) is a protein that is secreted by endothelial cells and plays an important role in angiogenesis. Although EGFL7 is aberrantly overexpressed in solid tumors, its role in leukemia has not been evaluated. Here, we report that levels of both mRNA and EGFL7 protein are increased in blasts of patients with acute myeloid leukemia (AML) compared with normal bone marrow cells. High mRNA expression associates with lower complete remission rates, and shorter event-free and overall survival in older (age ≥60 y) and younger (age <60 y) patients with cytogenetically normal AML. We further show that AML blasts secrete EGFL7 protein and that higher levels of EGFL7 protein are found in the sera from AML patients than in sera from healthy controls. Treatment of patient AML blasts with recombinant EGFL7 in vitro leads to increases in leukemic blast cell growth and levels of phosphorylated AKT. EGFL7 blockade with an anti-EGFL7 antibody reduced the growth potential and viability of AML cells. Our findings demonstrate that increased EGFL7 expression and secretion is an autocrine mechanism supporting growth of leukemic blasts in patients with AML.
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http://dx.doi.org/10.1073/pnas.1703142114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468639PMC
June 2017

Differential mutation frequencies in metastatic cutaneous squamous cell carcinomas versus primary tumors.

Cancer 2017 04 1;123(7):1184-1193. Epub 2016 Dec 1.

Department of Cancer Biology and Genetics, The Ohio State Wexner Medical Center, The Ohio State University, Columbus, Ohio.

Background: Exome and targeted sequencing studies have identified potential driver mutations for a variety of tumor types. Cutaneous squamous cell carcinoma (cSCC) is one of the most highly mutated cancers but typically is associated with low rates of metastasis and high survival rates. Nevertheless, metastatic cSCC is a significant health threat; up to 8800 individuals die each year of this disease.

Methods: Because it is difficult to predict which cSCCs are more likely to metastasize, and because to the best of the authors' knowledge there are no targeted therapies specifically designated for patients with metastatic cSCC, exome and/or targeted sequencing of 18 metastatic and 10 primary cSCCs was performed to identify mutations that were more frequent in metastatic tumors and might be targeted for therapeutic benefit. The authors compared their results with published sequencing results of an additional 223 primary tumors and 68 metastatic cSCCs.

Results: The authors identified genes demonstrating higher mutation frequencies in metastatic cSCC compared with primary tumors, including the chromatin remodeling gene lysine methyltransferase 2D (KMT2D) and the classic skin tumor suppressor tumor protein p53 (TP53), which was found to be mutated in 54% of primary tumors compared with 85% of metastatic tumors (P<.0001).

Conclusions: These studies appear to uncover potential pathways that are important in metastatic cSCC and that broaden understanding of the biology contributing to aggressive tumor behavior. These results may lead to new therapeutic strategies. Cancer 2017;123:1184-1193. © 2016 American Cancer Society.
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http://dx.doi.org/10.1002/cncr.30459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5360561PMC
April 2017

Whole-exome tumor sequencing study in biliary cancer patients with a response to MEK inhibitors.

Oncotarget 2016 Feb;7(5):5306-12

Department of Internal Medicine, Divison of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.

We previously conducted a phase-II study with selumetinib (AZD6244), a small molecule inhibitor of MEK1/2, in advanced biliary tract cancers (BTC), where the primary endpoint was response rate. Several patients experienced objective response. These findings were confirmed with MEK162 in a similar patient population. To assess for tumor-specific genetic variants that mediate sensitivity to MEK inhibition in BTC, we performed whole-exome sequencing in patients with an objective response to selumetinib. Normal and tumor DNA from FFPE tissue from two patients who experienced an objective response underwent whole-exome sequencing. Raw sequence reads were processed with GATK workflow and tumor specific variants were identified using MuTect and VarScan2. Ensemble Variant Effect Predictor was used to determine functional consequences of these variants. Copy number changes and potential gene fusion events were also screened. Findings were compared to assess for any commonality between the two tumor samples, and whether the identified variants were intrinsic to the MAPK pathway. 1169 and 628 tumor-specific variants were identified in the two samples. Further analysis demonstrated 60 and 53 functional and novel variants, respectively. Of the identified tumor-specific variants, fusion events or copy number changes, no commonality was seen. Several variants in genes associated with ERK signaling were present in each tumor sample. Although there were no common tumor-specific variants in the two patients who exhibited an objective response to selumetinib, several genes associated with ERK signaling were identified. Confirmatory studies investigating the role of the identified genes and other potential tumor independent factors need further investigation.
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http://dx.doi.org/10.18632/oncotarget.6632DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868687PMC
February 2016

Characterization of CLL exosomes reveals a distinct microRNA signature and enhanced secretion by activation of BCR signaling.

Blood 2015 May 1;125(21):3297-305. Epub 2015 Apr 1.

Division of Hematology, Department of Internal Medicine, Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH.

Multiple studies show that chronic lymphocytic leukemia (CLL) cells are heavily dependent on their microenvironment for survival. Communication between CLL cells and the microenvironment is mediated through direct cell contact, soluble factors, and extracellular vesicles. Exosomes are small particles enclosed with lipids, proteins, and small RNAs that can convey biological materials to surrounding cells. Our data herein demonstrate that CLL cells release significant amounts of exosomes in plasma that exhibit abundant CD37, CD9, and CD63 expression. Our work also pinpoints the regulation of B-cell receptor (BCR) signaling in the release of CLL exosomes: BCR activation by α-immunoglobulin (Ig)M induces exosome secretion, whereas BCR inactivation via ibrutinib impedes α-IgM-stimulated exosome release. Moreover, analysis of serial plasma samples collected from CLL patients on an ibrutinib clinical trial revealed that exosome plasma concentration was significantly decreased following ibrutinib therapy. Furthermore, microRNA (miR) profiling of plasma-derived exosomes identified a distinct exosome microRNA signature, including miR-29 family, miR-150, miR-155, and miR-223 that have been associated with CLL disease. Interestingly, expression of exosome miR-150 and miR-155 increases with BCR activation. In all, this study successfully characterized CLL exosomes, demonstrated the control of BCR signaling in the release of CLL exosomes, and uncovered a disease-relevant exosome microRNA profile.
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http://dx.doi.org/10.1182/blood-2014-12-618470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440883PMC
May 2015

Mass spectrometry identification of potential mediators of progestin-only contraceptive-induced abnormal uterine bleeding in human endometrial stromal cells.

Contraception 2015 Mar 21;91(3):253-60. Epub 2014 Nov 21.

Department of Obstetrics and Gynecology, The University of South Florida, Tampa, FL 33606, USA.

Objective: Thrombin and hypoxia each target human endometrial stromal cells (HESCs) to mediate long-acting progestin-only contraceptive (LAPC)-induced abnormal uterine bleeding (AUB). Thus, the secretome resulting from treatment of primary cultures of HESCs with thrombin or hypoxia was screened by mass spectrometry (MS) to detect potential protein mediators that lead to AUB.

Study Design: Cultured HESCs were primed with estradiol±medroxyprogesterone acetate (MPA) or etonogestrel (ETO), the respective progestins in MPA-injected and ETO-implanted LAPCs, and then treated by incubation with thrombin or under hypoxia. Collected conditioned medium supernatants were used for protein identification and quantitation of potential AUB mediators by liquid chromatography combined with tandem mass spectrometry analysis. Microarray analysis of parallel cultures and immunostaining of endometrial biopsies of LAPC users vs. nonusers corroborated MS results.

Results: MS identified several proteins displaying changes in expression levels from either thrombin or hypoxia treatments that are integral to angiogenesis or extracellular matrix formation. Several MS-identified proteins were confirmed by mRNA microarray analysis. Overexpressed stanniocalcin-1 (STC-1) was observed in endometrium of LAPC users. Unlike controls, all LAPC users displayed endometrial tubal metaplasia (ETM).

Conclusions: MS analysis identified many proteins that can affect angiogenesis or vessel integrity, thereby contributing to AUB. Confirmation of STC-1 overexpression in LAPC users and microarray data supports the validity of the MS data and suggests STC-1 involvement in AUB. The discovery of ETM in LAPC users indicates that LAPC-related side effects extend beyond AUB. The results presented here demonstrate a complex biological response to LAPC use.

Implications: MS identified several HESC secreted proteins deregulated by thrombin and hypoxia that may mediate LAPC-induced AUB. The revelation of overexpressed STC-1 by combined in vivo and in vitro observations identifies a potential target for future studies to prevent or minimize LAPC-induced AUB.
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http://dx.doi.org/10.1016/j.contraception.2014.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395468PMC
March 2015

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.

Cell Cycle 2014 ;13(18):2847-52

a Department of Pharmacology and Toxicology ; Indiana University School of Medicine ; Indianapolis , IN USA.

Many biologically significant processes, such as cell differentiation and cell cycle progression, gene transcription and DNA replication, chromosome stability and epigenetic silencing etc. depend on the crucial interactions between cellular proteins and DNA. Chromatin immunoprecipitation (ChIP) is an important experimental technique for studying interactions between specific proteins and DNA in the cell and determining their localization on a specific genomic locus. In recent years, the combination of ChIP with second generation DNA-sequencing technology (ChIP-seq) allows precise genomic functional assay. This review addresses the important applications of ChIP-seq with an emphasis on its role in genome-wide mapping of transcription factor binding sites, the revelation of underlying molecular mechanisms of differential gene regulation that are governed by specific transcription factors, and the identification of epigenetic marks. Furthermore, we also describe the ChIP-seq data analysis workflow and a perspective for the exciting potential advancement of ChIP-seq technology in the future.
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http://dx.doi.org/10.4161/15384101.2014.949201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4614920PMC
August 2015

Resistance mechanisms for the Bruton's tyrosine kinase inhibitor ibrutinib.

N Engl J Med 2014 Jun 28;370(24):2286-94. Epub 2014 May 28.

From the Division of Hematology, Department of Internal Medicine (J.A.W., T.-M.L., A.S.R., S.M.J., K.A.B., A.L., A.J.J., J.C. Byrd), the Department of Biomedical Informatics (H.G.O., A.S.Y.), and the Department of Pathology (G.L.), Ohio State University, Columbus; the Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medical College, New York (R.R.F.); the Division of Molecular Genetics, German Cancer Research Center, Heidelberg (M.Z., P.L.), and the Department of Internal Medicine III, University of Ulm, Ulm (S.S.) - both in Germany; Pharmacyclics, Sunnyvale, CA (L.X., D.H.-H.L., S.M.S., D.F.J., J.J.B., B.Y.C.); the Duke Cancer Institute, Duke University, Durham, NC (S.S.D., J.Z.); the Division of Hematology-Oncology, Department of Medicine, Hofstra North Shore-LIJ School of Medicine, New Hyde Park, NY (J.C. Barrientos); and Janssen Research and Development, Beerse, Belgium (M.V.).

Background: Ibrutinib is an irreversible inhibitor of Bruton's tyrosine kinase (BTK) and is effective in chronic lymphocytic leukemia (CLL). Resistance to irreversible kinase inhibitors and resistance associated with BTK inhibition have not been characterized. Although only a small proportion of patients have had a relapse during ibrutinib therapy, an understanding of resistance mechanisms is important. We evaluated patients with relapsed disease to identify mutations that may mediate ibrutinib resistance.

Methods: We performed whole-exome sequencing at baseline and the time of relapse on samples from six patients with acquired resistance to ibrutinib therapy. We then performed functional analysis of identified mutations. In addition, we performed Ion Torrent sequencing for identified resistance mutations on samples from nine patients with prolonged lymphocytosis.

Results: We identified a cysteine-to-serine mutation in BTK at the binding site of ibrutinib in five patients and identified three distinct mutations in PLCγ2 in two patients. Functional analysis showed that the C481S mutation of BTK results in a protein that is only reversibly inhibited by ibrutinib. The R665W and L845F mutations in PLCγ2 are both potentially gain-of-function mutations that lead to autonomous B-cell-receptor activity. These mutations were not found in any of the patients with prolonged lymphocytosis who were taking ibrutinib.

Conclusions: Resistance to the irreversible BTK inhibitor ibrutinib often involves mutation of a cysteine residue where ibrutinib binding occurs. This finding, combined with two additional mutations in PLCγ2 that are immediately downstream of BTK, underscores the importance of the B-cell-receptor pathway in the mechanism of action of ibrutinib in CLL. (Funded by the National Cancer Institute and others.).
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http://dx.doi.org/10.1056/NEJMoa1400029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4144824PMC
June 2014

Identification of medium-sized copy number alterations in whole-genome sequencing.

Cancer Inform 2014 5;13(Suppl 3):105-11. Epub 2015 Mar 5.

Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.

The genome-wide discoveries such as detection of copy number alterations (CNA) from high-throughput whole-genome sequencing data enabled new developments in personalized medicine. The CNAs have been reported to be associated with various diseases and cancers including acute myeloid leukemia. However, there are multiple challenges to the use of current CNA detection tools that lead to high false-positive rates and thus impede widespread use of such tools in cancer research. In this paper, we discuss these issues and propose possible solutions. First, since the entire genome cannot be mapped due to some regions lacking sequence uniqueness, current methods cannot be appropriately adjusted to handle these regions in the analyses. Thus, detection of medium-sized CNAs is also being directly affected by these mappability problems. The requirement for matching control samples is also an important limitation because acquiring matching controls might not be possible or might not be cost efficient. Here we present an approach that addresses these issues and detects medium-sized CNAs in cancer genomes by (1) masking unmappable regions during the initial CNA detection phase, (2) using pool of a few normal samples as control, and (3) employing median filtering to adjust CNA ratios to its surrounding coverage and eliminate false positives.
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http://dx.doi.org/10.4137/CIN.S14023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356486PMC
March 2015

Intensive care unit versus non-intensive care unit postoperative management of head and neck free flaps: comparative effectiveness and cost comparisons.

Head Neck 2014 Apr 18;36(4):536-9. Epub 2013 Jun 18.

Department of Head and Neck Surgery/Plastic and Reconstructive Surgery, Roswell Park Cancer Institute, Buffalo, New York.

Background: Despite its widespread use, there is no consensus on the postoperative management in patients undergoing free flap reconstructions. We report the largest study comparing flap outcomes, morbidity, and cost in patients with head and neck cancer free flaps who recovered in the intensive care unit (ICU) versus a "specialty floor" setting.

Methods: This was a retrospective review of patients undergoing free flap surgery for head and neck defects over a 4-year period. Patients before a certain date went to the ICU for immediate postoperative care and after to a non-ICU setting. Postoperative medical and surgical complications and hospital charges were analyzed.

Results: Patients in the ICU group had a longer length of stay (LOS) and incurred greater hospital costs than the patients in the non-ICU setting. There was no difference in the flap failure rate between the 2 groups.

Conclusion: Consideration should be given to a floor-based postoperative management regimen for this patient population.
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http://dx.doi.org/10.1002/hed.23325DOI Listing
April 2014

DFI: gene feature discovery in RNA-seq experiments from multiple sources.

BMC Genomics 2012 17;13 Suppl 8:S11. Epub 2012 Dec 17.

The Department of Biomedical Informatics and The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.

Background: Differential expression detection for RNA-seq experiments is often biased by normalization algorithms due to their sensitivity to parametric assumptions on the gene count distributions, extreme values of gene expression, gene length and total number of sequence reads.

Results: To overcome limitations of current methodologies, we developed Differential Feature Index (DFI), a non-parametric method for characterizing distinctive gene features across any number of diverse RNA-seq experiments without inter-sample normalization. Validated with qRT-PCR datasets, DFI accurately detected differentially expressed genes regardless of expression levels and consistent with tissue selective expression. Accuracy of DFI was very similar to the currently accepted methods: EdgeR, DESeq and Cuffdiff.

Conclusions: In this study, we demonstrated that DFI can efficiently handle multiple groups of data simultaneously, and identify differential gene features for RNA-Seq experiments from different laboratories, tissue types, and cell origins, and is robust to extreme values of gene expression, size of the datasets and gene length.
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http://dx.doi.org/10.1186/1471-2164-13-S8-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535702PMC
June 2013

JNK3 perpetuates metabolic stress induced by Aβ peptides.

Neuron 2012 Sep;75(5):824-37

Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH 43210, USA.

Although Aβ peptides are causative agents in Alzheimer's disease (AD), the underlying mechanisms are still elusive. We report that Aβ42 induces a translational block by activating AMPK, thereby inhibiting the mTOR pathway. This translational block leads to widespread ER stress, which activates JNK3. JNK3 in turn phosphorylates APP at T668, thereby facilitating its endocytosis and subsequent processing. In support, pharmacologically blocking translation results in a significant increase in Aβ42 in a JNK3-dependent manner. Thus, JNK3 activation, which is increased in human AD cases and a familial AD (FAD) mouse model, is integral to perpetuating Aβ42 production. Concomitantly, deletion of JNK3 from FAD mice results in a dramatic reduction in Aβ42 levels and overall plaque loads and increased neuronal number and improved cognition. This reveals AD as a metabolic disease that is under tight control by JNK3.
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http://dx.doi.org/10.1016/j.neuron.2012.06.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438522PMC
September 2012

Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes.

Nucleic Acids Res 2012 Nov 31;40(20):10172-86. Epub 2012 Aug 31.

The Department of Biomedical Informatics and the Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.

SUMOylation of transcription factors and chromatin proteins is in many cases a negative mark that recruits factors that repress gene expression. In this study, we determined the occupancy of Small Ubiquitin-like MOdifier (SUMO)-1 on chromatin in HeLa cells by use of chromatin affinity purification coupled with next-generation sequencing. We found SUMO-1 localization on chromatin was dynamic throughout the cell cycle. Surprisingly, we observed that from G1 through late S phase, but not during mitosis, SUMO-1 marks the chromatin just upstream of the transcription start site on many of the most active housekeeping genes, including genes encoding translation factors and ribosomal subunit proteins. Moreover, we found that SUMO-1 distribution on promoters was correlated with H3K4me3, another general chromatin activation mark. Depletion of SUMO-1 resulted in downregulation of the genes that were marked by SUMO-1 at their promoters during interphase, supporting the concept that the marking of promoters by SUMO-1 is associated with transcriptional activation of genes involved in ribosome biosynthesis and in the protein translation process.
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http://dx.doi.org/10.1093/nar/gks819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488252PMC
November 2012

From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data.

AMIA Jt Summits Transl Sci Proc 2012 19;2012:1-10. Epub 2012 Mar 19.

Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA;

Next Generation Sequencing is highly resource intensive. NGS Tasks related to data processing, management and analysis require high-end computing servers or even clusters. Additionally, processing NGS experiments requires suitable storage space and significant manual interaction. At The Ohio State University's Biomedical Informatics Shared Resource, we designed and implemented a scalable architecture to address the challenges associated with the resource intensive nature of NGS secondary analysis built around Illumina Genome Analyzer II sequencers and Illumina's Gerald data processing pipeline. The software infrastructure includes a distributed computing platform consisting of a LIMS called QUEST (http://bisr.osumc.edu), an Automation Server, a computer cluster for processing NGS pipelines, and a network attached storage device expandable up to 40TB. The system has been architected to scale to multiple sequencers without requiring additional computing or labor resources. This platform provides demonstrates how to manage and automate NGS experiments in an institutional or core facility setting.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3392054PMC
August 2012

miRNA profiling for biomarker discovery in multiple sclerosis: from microarray to deep sequencing.

J Neuroimmunol 2012 Jul 9;248(1-2):32-9. Epub 2011 Nov 9.

Neurology Department, The Ohio State University Medical Center, 460 W 12th Ave Room 0705, Columbus, OH 43210, USA.

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level. miRNAs are highly expressed in cells of the immune and nervous system, attesting to their importance in Neuroimmunology. Besides their involvement in modulation of physiological and pathological processes, miRNAs hold high promise as disease biomarkers, therapeutic agents and/or drug targets. Several studies have recently explored the involvement of miRNAs in Multiple Sclerosis (MS) using a variety of miRNA profiling techniques. In this review, we discuss basic miRNA biology and nomenclature, the techniques available for miRNA profiling research and recent miRNA profiling studies in Multiple Sclerosis.
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http://dx.doi.org/10.1016/j.jneuroim.2011.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288464PMC
July 2012

Comparing multiple ChIP-sequencing experiments.

J Bioinform Comput Biol 2011 Apr;9(2):269-82

Department of Biomedical Informatics, The Ohio State University , Columbus, OH, 43210, USA.

New high-throughput sequencing technologies can generate millions of short sequences in a single experiment. As the size of the data increases, comparison of multiple experiments on different cell lines under different experimental conditions becomes a big challenge. In this paper, we investigate ways to compare multiple ChIP-sequencing experiments. We specifically studied epigenetic regulation of breast cancer and the effect of estrogen using 50 ChIP-sequencing data from Illumina Genome Analyzer II. First, we evaluate the correlation among different experiments focusing on the total number of reads in transcribed and promoter regions of the genome. Then, we adopt the method that is used to identify the most stable genes in RT-PCR experiments to understand background signal across all of the experiments and to identify the most variable transcribed and promoter regions of the genome. We observed that the most variable genes for transcribed regions and promoter regions are very distinct. Gene ontology and function enrichment analysis on these most variable genes demonstrate the biological relevance of the results. In this study, we present a method that can effectively select differential regions of the genome based on protein-binding profiles over multiple experiments using real data points without any normalization among the samples.
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http://dx.doi.org/10.1142/s0219720011005483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289603PMC
April 2011
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