Repurposing of artesunate, an antimalarial drug, as a potential inhibitor of hepatitis E virus

Hepatitis E virus (HEV) is endemic in several developing countries of Africa and Asia. It mainly causes self-limiting waterborne infections, in either sporadic or outbreak form. Recently, HEV was shown to cause chronic infections in immunosuppressed individuals. Ribavirin and interferon, the current off-label treatment options for hepatitis E, have several side effects. Hence, there is a need for new drugs. We evaluated the antimalarial drug artesunate (ART) against genotype 1 HEV (HEV-1) and HEV-3 using a virus-replicon-based cell culture system. ART exhibited 59% and 43% inhibition of HEV-1 and HEV-3, respectively, at the highest nontoxic concentration. Computational molecular docking analysis showed that ART can bind to the helicase active site (affinity score, -7.4 kcal/mol), indicating its potential to affect ATP hydrolysis activity. An in vitro ATPase activity assay of the helicase indeed showed 24% and 55% inhibition at 19.5 µM (EC50) and 78 µM concentrations of ART, respectively. Since ATP is a substrate of RNA-dependent RNA polymerase (RdRp) as well, we evaluated the effect of ART on the enzymatic activity of the viral polymerase. Interestingly, ART showed 26% and 40% inhibition of the RdRp polymerase activity at 19.5 µM and 78 µM concentrations of ART, respectively. It could be concluded from these findings that ART inhibited replication of both HEV-1 and HEV-3 by directly targeting the activities of the viral enzymes helicase and RdRp. Considering that ART is known to be safe in pregnant women, we think this antimalarial drug deserves further evaluation in animal models.

Modulation of cellular autophagy by genotype 1 hepatitis E virus ORF3 protein

Hepatitis E virus (HEV) egresses from infected hepatocytes as quasienveloped particles containing open reading frame 3 (ORF3) protein. HEV ORF3 (small phosphoprotein) interacts with host proteins to establish a favourable environment for virus replication. It is a functional viroporin that plays an important role during virus release. Our study provides evidence that pORF3 plays a pivotal role in inducing Beclin1-mediated autophagy that helps HEV-1 replication as well as its exit from cells. The ORF3 interacts with host proteins involved in regulation of transcriptional activity, immune response, cellular and molecular processes, and modulation of autophagy, by interacting with proteins, DAPK1, ATG2B, ATG16L2 and also several histone deacetylases (HDACs). For autophagy induction, the ORF3 utilizes non-canonical NF-κB2 pathway and sequesters p52NF-κB and HDAC2 to upregulate DAPK1 expression, leading to enhanced Beclin1 phosphorylation. By sequestering several HDACs, HEV may prevent histone deacetylation to maintain overall cellular transcription intact to promote cell survival. Our findings highlight a novel crosstalk between cell survival pathways participating in ORF3-mediated autophagy.

Cellular Metabolomics Profiles Associated With Drug Chemosensitivity in AML

Background

Acute myeloid leukemia (AML) is a hematological malignancy with a dismal prognosis. For over four decades, AML has primarily been treated by cytarabine combined with an anthracycline. Although a significant proportion of patients achieve remission with this regimen, roughly 40% of children and 70% of adults relapse. Over 90% of patients with resistant or relapsed AML die within 3 years. Thus, relapsed and resistant disease following treatment with standard therapy are the most common clinical failures that occur in treating this disease. In this study, we evaluated the relationship between AML cell line global metabolomes and variation in chemosensitivity.

Methods

We performed global metabolomics on seven AML cell lines with varying chemosensitivity to cytarabine and the anthracycline doxorubicin (MV4.11, KG-1, HL-60, Kasumi-1, AML-193, ME1, THP-1) using ultra-high performance liquid chromatography - mass spectrometry (UHPLC-MS). Univariate and multivariate analyses were performed on the metabolite peak intensity values from UHPLC-MS using MetaboAnalyst to identify cellular metabolites associated with drug chemosensitivity.

Results

A total of 1,624 metabolic features were detected across the leukemic cell lines. Of these, 187 were annotated to known metabolites. With respect to doxorubicin, we observed significantly greater abundance of a carboxylic acid (1-aminocyclopropane-1-carboxylate) and several amino acids in resistant cell lines. Pathway analysis found enrichment of several amino acid biosynthesis and metabolic pathways. For cytarabine resistance, nine annotated metabolites were significantly different in resistance vs. sensitive cell lines, including D-raffinose, guanosine, inosine, guanine, aldopentose, two xenobiotics (allopurinol and 4-hydroxy-L-phenylglycine) and glucosamine/mannosamine. Pathway analysis associated these metabolites with the purine metabolic pathway.

Conclusion

Overall, our results demonstrate that metabolomics differences contribute toward drug resistance. In addition, it could potentially identify predictive biomarkers for chemosensitivity to various anti-leukemic drugs. Our results provide opportunity to further explore these metabolites in patient samples for association with clinical response.

Clinical significance of in vivo cytarabine-induced gene expression signature in AML

Despite initial remission, ∼60-70% of adult and 30% of pediatric patients experience relapse or refractory AML. Studies so far have identified base line gene expression profiles of pathogenic and prognostic significance in AML; however, the extent of change in gene expression post-initiation of treatment has not been investigated. Exposure of leukemic cells to chemotherapeutic agents such as cytarabine, a mainstay of AML chemotherapy, can trigger adaptive response by influencing leukemic cell transcriptome and, hence, development of resistance or refractory disease. It is, however, challenging to perform such a study due to lack of availability of specimens post-drug treatment. The primary objective of this study was to identify in vivo cytarabine-induced changes in leukemia cell transcriptome and to evaluate their impact on clinical outcome. The results highlight genes relevant to cytarabine resistance and support the concept of targeting cytarabine-induced genes as a means of improving response.

Genome-wide association analysis identified splicing single nucleotide polymorphism in CFLAR predictive of triptolide chemo-sensitivity

Background

Triptolide is a therapeutic diterpenoid derived from the Chinese herb Tripterygium wilfordii Hook f. Triptolide has been shown to induce apoptosis by activation of pro-apoptotic proteins, inhibiting NFkB and c-KIT pathways, suppressing the Jak2 transcription, activating MAPK8/JNK signaling and modulating the heat shock responses.

Results

In the present study, we used lymphoblast cell lines (LCLs) derived from 55 unrelated Caucasian subjects to identify genetic markers predictive of cellular sensitivity to triptolide using genome wide association study. Our results identified SNPs on chromosome 2 associated with triptolide IC₅₀ (p < 0.0001). This region included biologically interesting genes as CFLAR, PPIl3, Caspase 8/10, NFkB and STAT6. Identification of a splicing-SNP rs10190751, which regulates CFLAR alternatively spliced isoforms predictive of the triptolide cytotoxicity suggests its role in triptolides action. Our results from functional studies in Panc-1 cell lines further demonstrate potential role of CFLAR in triptolide toxicity. Analysis of gene-expression with cytotoxicity identified JAK1 expression to be a significant predictor of triptolide sensitivity.

Conclusions

Overall out results identified genetic factors associated with triptolide chemo-sensitivity thereby opening up opportunities to better understand its mechanism of action as well as utilize these biomarkers to predict therapeutic response in patients.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1614-1) contains supplementary material, which is available to authorized users.

Abstract 5562: Screening of in vitro cytotoxicity of nucleoside analogs in HapMap cell lines to identify predictive markers of drug sensitivity

Nucleoside analogues (NAs) are synthetic molecules that resemble naturally occurring nucleosides. These analogs are themselves inactive and require activation by multiple phosphorylation steps to their triphosphate forms which depending on the particular agent either inhibits DNA/RNA (cytarabine, clofarabine), or inhibits, ribonucleotide reductases (clofarabine, gemcitabine) or DNA methyl transferases (decitabine). Resistance to nucleoside analogue-based chemotherapy is a major problem in the treatment of cancers. In the current study, we determined the in vitro cytotoxicity of the nucleoside analogs clofarabine, fludarabine and decitabine in 60 unrelated Epstein Barr virus (EBV)-transformed B-lymphoblastoid HapMap cell lines with European ancestry [Centre d'Etude du Polymorphisme Humain (CEU) samples] were obtained from the Coriell Institute for Medical Research. The cell lines were maintained at 37°C in RPMI1640 medium supplemented with 2mM Glutamine. In vitro cytotoxicity was determined by plating LCLs in a 96 well plate at density of 250,000cells/ml. Cell survival was determined using MTT ((3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay 48hr after exposure to varying concentrations of each nucleoside analog. Gen 5 software was used to calculate IC50 values for each cell line and agent. Our results showed wide inter-individual variation in cytotoxicity to nucleoside analogs among HapMap cell lines. Significant correlation was observed between the IC50 values of fludarabine vs. clofarabine (r = 0.732; P = 0.00001). However no significant correlation was observed with the IC50 values of decitabine. The reason for the observed relationship might be the fact that clofarabine is a 2nd generation purine nucleoside and structurally related to fludarabine. Additionally, the mechanism of action of decitabine is different than clofarabine and fludarabine with it being a hypomethylating agent. Since genome-wide genotype and gene expression data on these cell lines is available publicly, currently we are analyzing the data for identification of genomics markers predictive of cell survival and response to these nucleoside analogs. Our preliminary analysis showed that polymorphisms in candidate genes involved in drug metabolism pathway may be involved in cancer drug resistance. For example, a promoter SNP in the gene DCK was associated with both clofarabine IC50 and fludarabine IC50 while another promoter SNP in NT5C2 was associated with fludarabine IC50.

These pharmacogenomic factors may then serve as predictive markers for improvement of cancer chemotherapy.

Citation Format: Taraswi Mitra Ghosh, Tanya J. Feldberg, Neha Bhise, Jatinder K. Lamba. Screening of in vitro cytotoxicity of nucleoside analogs in HapMap cell lines to identify predictive markers of drug sensitivity. [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 5562. doi:10.1158/1538-7445.AM2014-5562

Abstract 2214: Genome-wide association analysis identified genetic markers associated with triptolide cellular sensitivity using HapMap LCLs as model system

Triptolide is a biological diterpenoid derived from the Chinese herb Tripterygium wilfordii Hook f. It has shown to have immunosuppression and anti-inflammation, and antineoplastic effect [Pan et al, Cancer Lett, 20102;3,5]. The anti-tumor effects of triptolide have been shown in wide range of solid tumor and leukemic cell lines in vitro. Present study focused on identifying the genetic markers using EBV transformed (lymphoblast cell lines as model systems). International HapMap Project LCLs derived from subjects with European ancestry (CEU; n=60 unrelated) were obtained from the Coriell Institute for Medical Research. Genotype data and gene expression data on these cell lines is available publically. The cell lines were maintained at 370C in RPMI1640 medium supplemented with 2mM Glutamine. In vitro cytotoxicity was determined by plating LCLs in a 96 well plate at the density of 250,000 cells/mL followed by treatment with six different concentration of triptolide (500, 50, 20, 10, 6.67, and 1.3 nM) 24hr after plating. Cell viability was determined 48 hr post drug treatment by MTT assays. Genome-wide gene expression and genotype data was obtained from publically available source and was evaluated for identification of SNPs and/or gene expression signatures predictive of triptolide cellular sensitivity. Interestingly we observed “clumping” of small p-values in a region on chromosome 2 consisting of SNPs with smallest p-value. SNPs within this region on chromosome 2 spanned across many biologically and functionally important genes such as: genes of importance in apoptosis caspase 8, caspase 10 and CFLR (caspase 8 and FADD like apoptosis regulator). The most significant SNP rs6759004 occurred in the 3’UTR of CFLAR gene and was associated with triptolide cytotoxicity (p=2.5E-07). SNPs in genes involved in DNA replication and repair as ORC2 (origin of replication complex subunit2); in formation of reactive oxygen species as AOX1 and AOX2P (aldehyde oxidase); proteins involved in transcription, RNA processing and splicing as protein kinase CLK1 (CDC-kine linase-1), NIF3L1 etc were also significantly associated with triptolide chemosensitivity. The two most interesting candidate markers identified by association of genome-wide expression with triptolide cytotoxicity includes JAK1, (Janus kinase 1) which is involved in JAK/STAT signaling and plays significant role in cell differentiation, growth, transformation, apoptosis, proliferation etc. and DTX1, which plays role in NOTCH1 signaling.

Overall our results identified biomarkers of biological and clinical significance that predict response to triptolide and would be of clinical relevance to patients being treated by triptolide

Citation Format: Jatinder K. lamba, Tanya Feldberg, Taraswi Mitra Ghosh, Neha Bhise, Brooke Fridley. Genome-wide association analysis identified genetic markers associated with triptolide cellular sensitivity using HapMap LCLs as model system. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2214. doi:10.1158/1538-7445.AM2013-2214

Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies

The main objective of this study was to investigate the feasibility of using PharmGKB, a pharmacogenomic database, as a source of training data in combination with text of MEDLINE abstracts for a text mining approach to identification of potential gene targets for pathway-driven pharmacogenomics research. We used the manually curated relations between drugs and genes in PharmGKB database to train a support vector machine predictive model and applied this model prospectively to MEDLINE abstracts. The gene targets suggested by this approach were subsequently manually reviewed. Our quantitative analysis showed that a support vector machine classifiers trained on MEDLINE abstracts with single words (unigrams) used as features and PharmGKB relations used for supervision, achieve an overall sensitivity of 85% and specificity of 69%. The subsequent qualitative analysis showed that gene targets "suggested" by the automatic classifier were not anticipated by expert reviewers but were subsequently found to be relevant to the three drugs that were investigated: carbamazepine, lamivudine and zidovudine. Our results show that this approach is not only feasible but may also find new gene targets not identifiable by other methods thus making it a valuable tool for pathway-driven pharmacogenomics research.