Browsing by Author "Skaar, Todd"

Now showing 1 - 6 of 6
  • Thumbnail Image
    Item
    Cytochrome P450 Oxidoreductase (POR) Associated with Severe Paclitaxel-Induced Peripheral Neuropathy in Patients of European Ancestry from ECOG-ACRIN E5103
    (American Association for Cancer Research, 2023) Shen, Fei; Jiang, Guanglong; Philips, Santosh; Gardner, Laura; Xue, Gloria; Cantor, Erica; Ly, Reynold C.; Osei, Wilberforce; Wu, Xi; Dang, Chau; Northfelt, Donald; Skaar, Todd; Miller, Kathy D.; Sledge, George W.; Schneider, Bryan P.; Medicine, School of Medicine
    Purpose: Paclitaxel is a widely used anticancer therapeutic. Peripheral neuropathy is the dose-limiting toxicity and negatively impacts quality of life. Rare germline gene markers were evaluated for predicting severe taxane-induced peripheral neuropathy (TIPN) in the patients of European ancestry. In addition, the impact of Cytochrome P450 (CYP) 2C8, CYP3A4, and CYP3A5 metabolizer status on likelihood of severe TIPN was also assessed. Experimental design: Whole-exome sequencing analyses were performed in 340 patients of European ancestry who received a standard dose and schedule of paclitaxel in the adjuvant, randomized phase III breast cancer trial, E5103. Patients who experienced grade 3-4 (n = 168) TIPN were compared to controls (n = 172) who did not experience TIPN. For the analyses, rare variants with a minor allele frequency ≤ 3% and predicted to be deleterious by protein prediction programs were retained. A gene-based, case-control analysis using SKAT was performed to identify genes that harbored an imbalance of deleterious variants associated with increased risk of severe TIPN. CYP star alleles for CYP2C8, CYP3A4, and CYP3A5 were called. An additive logistic regression model was performed to test the association of CYP2C8, CYP3A4, and CYP3A5 metabolizer status with severe TIPN. Results: Cytochrome P450 oxidoreductase (POR) was significantly associated with severe TIPN (P value = 1.8 ×10-6). Six variants were predicted to be deleterious in POR. There were no associations between CYP2C8, CYP3A4, or CYP3A5 metabolizer status with severe TIPN. Conclusions: Rare variants in POR predict an increased risk of severe TIPN in patients of European ancestry who receive paclitaxel.
  • Thumbnail Image
    Item
    DACS-DB: An Annotation and Dissemination Model for Disease Associated Cytokine SNPs
    (2011-10-19) Bhushan, Sushant; Perumal, Narayanan B.; Mahoui, Malika; Skaar, Todd
    Cytokines mediate crucial functions in innate and adaptive immunity. They play valuable roles in immune cell growth and lineage specification, and are associated with various disease pathologies. A large number of low, medium and high throughput studies have implicated association of single nucleotide polymorphisms (SNPs) in cytokine genes with diseases. A preponderance of such experiments have not shown any causality of an identified SNP to the associated disease. Instead, they have identified statistically significant SNP-disease associations; hence, it is likely that some of these cytokine gene variants may directly or indirectly cause the disease phenotype(s). To fill this knowledge gap and derive study parameters for cytokine SNP-disease causality relationships, we have designed and developed the Disease Associated Cytokine SNP Database (DACS-DB). DACS-DB has data on 456 cytokine genes, approximately 61,000 SNPs, and 891 SNP-associated diseases. In DACS-DB, among other attributes, we present functional annotation, and heterozygosity allele frequency for the SNPs, and literature-validated SNP association for diseases. Users of the DB can run queries such as the ones to find disease-associated SNPs in a cytokine gene, and all the SNPs involved in a disease. We have developed a web front end (available at http://www.iupui.edu/~cytosnp) to disseminate this information for immunologists, biomedical researchers, and other interested biological researchers. Since there is no such comprehensive collection of disease associated cytokine SNPs, this DB will be vital to understanding the role of cytokine SNPs as markers in disease, and, more importantly, in causality to disease thus helping to identify drug targets for common inflammatory diseases. Due to the presence of rich annotations, the DACS-DB can be a good source for building a tool for the prediction of the "disease association potential (DAP)" of a given SNP. In a preliminary effort to devise such a methodology for DAP prediction, we have applied a support vector machine (SVM) to classify SNPs. Employing the SNP attributes of function class, heterozygosity value, and heterozygosity standard error, 864 SNPs were classified into two classes, "disease" and "non-disease". The SVM returned a classification of these SNPs into the disease and non-disease classes with an accuracy of 74%. By modifying various SNP and disease attributes in the training data sets, such a predictive algorithm can be extrapolated to identify potential disease associated SNPs among newly sequenced cytokine variations. In the long run, this approach can provide a means for future gene variation based therapeutic regimens.
  • Thumbnail Image
    Item
    Estrogenic Activity of the Polybrominated Diphenyl Ether Flame Retardant Mixture DE-71
    (2008-03-05T20:08:04Z) Mercado-Feliciano, Minerva; Bigsby, Robert M.; Klaunig, James E.; Jeng, Meei-Huey; Kamendulis, Lisa; Skaar, Todd; Sullivan, William J., Jr.
    Polybrominated diphenyl ethers (PBDEs) are widely used flame retardants suspected to act as endocrine disruptors. We tested the commercial PBDE mixture DE-71 and its in vivo metabolites for estrogenic activity. MCF-7 breast cancer cells culture, ERE-luciferase gene expression, 3H-β-estradiol displacement from recombinant ERα, and ovariectomized (OVX) mice served as bioassays. Although DE-71 did not bind ERα, it was able to increase MCF-7 cell proliferation and this was prevented by the antiestrogen fulvestrant. DE-71 co-treatment reduced the effect of estradiol in MCF-7 cells. In the OVX mouse (BALB/c) 3-day assay, DE-71 administered alone had no effect on uterine or vaginal tissues but when administered subcutaneously potentiated estradiol’s effect on uterine weight in a dose-dependent manner. DE-71 administered SQ to BALB/c mice for 34 days slightly increased uterine epithelial height (UEH), vaginal epithelial thickness (VET) and mammary ductal lumen area, and attenuated the estradiol-induced increase in UEH; these effects were not seen in C57BL/6 mice. DE-71 increased liver weight in BALB/c, C57BL/6 and estrogen receptor-alpha knockout (ERαKO) mice. Liver cytochrome P450 1A (CYP1A) and CYP2B activities increased 2.5-fold and 7-fold respectively when DE-71 was administered PO, but only CYP2B increased (5-fold) after SQ treatment. Six OH-PBDE metabolites were found in mice after 34-day DE-71 treatment and all were able to bind recombinant ERα. Para-hydroxylated metabolites displayed a 10- to 30-fold higher affinity for ERα compared to ortho-hydroxylated PBDEs. Para-OH-PBDEs induced ERE-luciferase and produced an additive effect when coadministered with β-estradiol. DE-71 was also additive with β-estradiol. At high concentrations (≥ 5x10-5 M), ortho-OH-PBDEs were antiestrogenic in the ERE-luciferase assay. In conclusion, DE-71 behaves as a weak estrogen in both MCF-7 breast cancer cells and ovariectomized adult mice. Mice strain, treatment route and duration determined if DE-71 was estrogenic. BALB/c mice are more susceptible to DE-71 effects in estrogen target tissues than C57BL/6 mice. DE-71 increased liver weight, 5%-51% depending on mouse strain and treatment regime, independently of ERα. The observations that the DE-71 mixture does not displace 3H-β-estradiol from ERα while the hydroxylated metabolites do, suggest that the cellular and tissue effects were due to a metabolic activation of individual congeners.
  • No Thumbnail Available
    Item
    Genomic Medicine: Translating Genetic Discoveries into Clinical Care
    (Center for Translating Research Into Practice, IU Indianapolis, 2022-10-06) Skaar, Todd
    The 2022 Bantz-Petronio Translating Research Into Practice Faculty Award recipient is Todd Skaar, PhD. Dr. Skaar, an internationally recognized leader in the field of pharmacogenomics, received this award in recognition of his groundbreaking research and his dedication to mentoring the next generation of translational scholars. Dr. Skaar and his research team study ways to improve the success of cancer treatment drug therapies. His work focuses on the impact of genomic variability in how these drugs interact with each other and in the body. Better understanding these drug interactions can improve outcomes and reduce hospitalizations.
  • Thumbnail Image
    Item
    The Impact of SBF2 on Taxane-Induced Peripheral Neuropathy
    (2021-05) Cunningham, Geneva Mari; Schneider, Bryan P.; Radovich, Milan; Liu, Yunlong; Skaar, Todd; Meyer, Jason; Ivan, Mircea
    The main focus of this study is to determine the impact of Set-Binding Factor 2 (SBF2) on human-derived neurons in the context of taxane-induced peripheral neuropathy. Taxane-induced peripheral neuropathy (TIPN) is a devastating survivorship issue for many cancer patients; SBF2 has been previously identified as a potential germline predictor that has been found to be significantly associated with severe TIPN in African American (AA) patients. The work described here provides ex vivo support for the use of SBF2 as a genotypic biomarker to identify a priori which patients are at a higher risk of manifesting severe TIPN. This study demonstrates that diminished expression of SBF2 exacerbated the effect of paclitaxel on viability and morphology and altered the functional response of a neuronal model exposed to paclitaxel treatment. Furthermore, transcriptomic work showed that reduced expression of SBF2 in a neuronal model treated with paclitaxel impacted the expression of genes that modulate stress-induced cell death and pain threshold. Altogether, these findings suggest that SBF2 plays a role in the development of TIPN. This work sheds light on the pathways potentially involving SBF2 that can be studied to further evaluate the function of this gene in neurons and its contribution to severe TIPN. Further functional approaches investigating these pathways will be pivotal in elucidating the underlying biological mechanism for this toxicity and identifying novel targeted therapeutic strategies to prevent or treat TIPN.
  • Thumbnail Image
    Item
    Targeting Protein Arginine Methyltransferase 5 as a Novel Therapeutic Approach in Pancreatic & Colorectal Cancer
    (2018-12) Prabhu, Lakshmi Milind; Lu, Tao; Safa, Ahmad; Pollok, Karen; Skaar, Todd; Zhang, Jian-Ting
    Pancreatic ductal adenocarcinoma (PDAC) and colorectal cancer (CRC) are among the most commonly diagnosed forms of cancer in the United States. Due to their widespread prevalence and high mortality rate, it is vital to develop effective therapeutic drugs to combat these deadly diseases. In both PDAC and CRC, the multifunctional factor nuclear factor kappa B (NF-kB), a central coordinator of cellular immune responses, is activated abnormally, leading to tumorigenesis and cancer progression. Therefore, controlling NF-kB activity is critical in the treatment of these cancers. In a previous study, we identified a new mechanism by which NF-kB activity is regulated by an epigenetic enzyme known as protein arginine methyltransferase 5 (PRMT5). We showed that overexpression of PRMT5 not only activated NF-kB, but also significantly promoted several characteristics associated with cancer, including increased cell proliferation, migration, and anchorage-independent growth in both PDAC and CRC cells. Moreover, in order to examine the therapeutic potential of PRMT5 in these cancers, we adapted the state-of-the-art AlphaLISA technique into a high throughput screen (HTS) platform to screen for PRMT5 inhibitors. As a result, we successfully identified the small molecule PR5-LL-CM01 as our lead hit. Further validation experiments confirmed that PR5-LL-CM01 is a potent and specific PRMT5 inhibitor that exhibits significant anti-tumor efficacy in both in vitro and in vivo models of PDAC and CRC. Additionally, in a second screen, we discovered two natural compounds, P1608K04 and P1618J22, that can also function as the PRMT5 inhibitors. These findings further highlight the robustness of the PRMT5- specific AlphaLISA HTS technique. To conclude, we describe here for the first time a novel role of PRMT5 as a tumor-promoting factor in PDAC and CRC through NF-kB activation. By successfully developing and applying an innovative AlphaLISA HTS technique, we discovered PR5-LL-CM01, P1608K04, and P1618J22 as novel PRMT5 inhibitors, with PR5-LL-CM01 showing the strongest potency in both PDAC and CRC models. Therefore, we demonstrated that PRMT5 is a promising therapeutic target in PDAC and CRC, and the novel PRMT5 inhibitor PR5-LL-CM01 could serve as a promising basis for new drug development in PDAC and CRC.