Browsing by Author "Fishel, Melissa"

Now showing 1 - 8 of 8
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    A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data
    (Cold Spring Harbor Laboratory, 2021) Alghamdi, Norah; Chang, Wennan; Dang, Pengtao; Lu, Xiaoyu; Wan, Changlin; Gampala, Silpa; Huang, Zhi; Wang, Jiashi; Ma, Qin; Zang, Yong; Fishel, Melissa; Cao, Sha; Zhang, Chi; Medical and Molecular Genetics, School of Medicine
    The metabolic heterogeneity and metabolic interplay between cells are known as significant contributors to disease treatment resistance. However, with the lack of a mature high-throughput single-cell metabolomics technology, we are yet to establish systematic understanding of the intra-tissue metabolic heterogeneity and cooperative mechanisms. To mitigate this knowledge gap, we developed a novel computational method, namely, single-cell flux estimation analysis (scFEA), to infer the cell-wise fluxome from single-cell RNA-sequencing (scRNA-seq) data. scFEA is empowered by a systematically reconstructed human metabolic map as a factor graph, a novel probabilistic model to leverage the flux balance constraints on scRNA-seq data, and a novel graph neural network-based optimization solver. The intricate information cascade from transcriptome to metabolome was captured using multilayer neural networks to capitulate the nonlinear dependency between enzymatic gene expressions and reaction rates. We experimentally validated scFEA by generating an scRNA-seq data set with matched metabolomics data on cells of perturbed oxygen and genetic conditions. Application of scFEA on this data set showed the consistency between predicted flux and the observed variation of metabolite abundance in the matched metabolomics data. We also applied scFEA on five publicly available scRNA-seq and spatial transcriptomics data sets and identified context- and cell group-specific metabolic variations. The cell-wise fluxome predicted by scFEA empowers a series of downstream analyses including identification of metabolic modules or cell groups that share common metabolic variations, sensitivity evaluation of enzymes with regards to their impact on the whole metabolic flux, and inference of cell-tissue and cell-cell metabolic communications.
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    Adapting AlphaLISA high throughput screen to discover a novel small-molecule inhibitor targeting protein arginine methyltransferase 5 in pancreatic and colorectal cancers
    (Impact Journals, 2017-05-23) Prabhu, Lakshmi; Wei, Han; Chen, Lan; Demir, Özlem; Sandusky, George; Sun, Emily; Wang, John; Mo, Jessica; Zeng, Lifan; Fishel, Melissa; Safa, Ahmad; Amaro, Rommie; Korc, Murray; Zhang, Zhong-Yin; Lu, Tao; Pharmacology and Toxicology, School of Medicine
    Pancreatic ductal adenocarcinoma (PDAC) and colorectal cancer (CRC) are notoriously challenging for treatment. Hyperactive nuclear factor κB (NF-κB) is a common culprit in both cancers. Previously, we discovered that protein arginine methyltransferase 5 (PRMT5) methylated and activated NF-κB. Here, we show that PRMT5 is highly expressed in PDAC and CRC. Overexpression of PRMT5 promoted cancer progression, while shRNA knockdown showed an opposite effect. Using an innovative AlphaLISA high throughput screen, we discovered a lead compound, PR5-LL-CM01, which exhibited robust tumor inhibition effects in both cancers. An in silico structure prediction suggested that PR5-LL-CM01 inhibits PRMT5 by binding with its active pocket. Importantly, PR5-LL-CM01 showed higher anti-tumor efficacy than the commercial PRMT5 inhibitor, EPZ015666, in both PDAC and CRC. This study clearly highlights the significant potential of PRMT5 as a therapeutic target in PDAC and CRC, and establishes PR5-LL-CM01 as a promising basis for new drug development in the future.
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    APE1/REF-1 redox signaling regulates HIF1A-mediated CA9 expression in hypoxic pancreatic cancer cells : combination treatment in patient-derived pancreatic tumor model
    (2017-12-14) Logsdon, Derek Paul; Kelly, Mark; Fishel, Melissa; Jerde, Travis; Vasko, Michael; Fehrenbacher, Jill
    Pancreatic ductal adenocarcinoma (PDAC) is an extremely deadly disease characterized by aggressive metastasis and therapeutic resistance. Reactive stroma in pancreatic tumors contributes to tumor signaling, fibrosis, inflammation, and hypoxia. Hypoxia signaling creates a more aggressive phenotype with increased potential for metastasis and decreased therapeutic efficacy. Carbonic anhydrase IX (CA9) functions as part of the cellular response to hypoxia by regulating intracellular pH to promote cell survival. Apurinic/Apyrimidinic Endonuclease-1-Reduction/oxidation Effector Factor 1 (APE1/Ref-1) is a multi-functional protein with two major activities: endonuclease activity in DNA base excision repair and a redox signaling activity that reduces oxidized transcription factors, enabling them to bind target sequences in DNA. APE1/Ref-1 is a central node in redox signaling, contributing to the activation of transcription factors involved in tumor survival, growth, and hypoxia signaling. This work evaluates the mechanisms underlying PDAC cell responses to hypoxia and APE1/Ref-1 redox signaling control of hypoxia inducible factor 1 alpha (HIF1a), a critical factor in hypoxia-induced CA9 transcription. We hypothesized that obstructing the HIF-CA9 axis at two points via APE1/Ref-1 inhibition and CA9 inhibition results in enhanced PDAC cell killing under hypoxic conditions. We found that HIF1a-mediated induction of CA9 is significantly attenuated following APE1/Ref-1 knock-down or redox signaling inhibition in patient-derived PDAC cells and pancreatic cancer-associated fibroblast cells. Additionally, dual-targeting of APE1/Ref-1 redox signaling activity and CA9 activity results in enhanced acidification and cytotoxicity of PDAC cells under hypoxic conditions as well as decreased tumor growth in an ex-vivo 3-dimensional tumor co-culture model. Further experiments characterized novel analogs of clinically relevant drugs targeting the key enzymes in this pathway, resulting in improved potency. These results underscore the notion that combination therapy is essential and demonstrate the potential clinical utility of blocking APE1/Ref-1 and CA9 function for novel PDAC therapeutic treatment.
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    Investigating the Mechanisms of Resistance to Dual PI3K/MTOR Inhibitor in PIK3CA Mutant Basal Like Bladder Cancer
    (2019-03) Elbanna, May F.M.; Pili, Roberto; Jerde, Travis; Zhang, Jian-Ting; Lu, Tao; Fishel, Melissa
    Muscle invasive bladder cancer (MIBC) carries a poor prognosis where the overall 5 year survival ranges from 48% to 66%. To date, targeted therapies, except for immune checkpoint inhibitors have not been shown to be effective in the management of this disease, where conventional chemotherapy (i.e. cisplatin) continues to be the standard of care. Therefore, the challenge lies in identifying key molecular events that can predict response to targeted therapies and thereby provide patients with maximal clinical benefit. Using two MIBC patient derived xenograft models (PDX) that carry alterations in PI3K signaling, one of the most dysregulated signaling pathways in bladder cancer, we studied determinants of response to PI3K targeted inhibition and mechanisms of resistance. We found that PIK3CA mutation status as well as tumor subtype (luminal-like or basal-like) play cooperative role in driving treatment response, where PIK3CA E542K mutation in basal-like tumors is associated with resistance to PI3K inhibition. Resistance is driven by feedback activation of alternative feedback signaling such as RAS-MAPK pathway. Based on the mechanistic changes induced upon resistance, we tested different drug combinations that can overcome resistance to PI3K targeted inhibition. Interestingly, we observed bromodomain inhibition by JQ1 to be the most effective strategy to re-sensitize resistant cells to PI3K targeted therapy. Overall, this project provides a predictive paradigm of response to PI3K targeted inhibition in PIK3CA mutant MIBC and sets the stage for future rational clinical trial design.
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    Lansoprazole and its Metabolites in the Treatment of TNBC and the Contribution of ABCG2 to CC-115 Resistance
    (2019-08) Beebe, Jennifer Diane; Zhang, Jian-Ting; Jerde, Travis; Safa, Ahmad; Xie, Jingwu; Fishel, Melissa
    Triple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer with a dismal prognosis. Targeted therapies for breast cancer with expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) are currently available; however, due to the lack of ER, PR, and HER2 in TNBC, targeted therapies are limited. While surgery and traditional chemotherapy remain the standard of care, development of a new treatment strategy for TNBC is needed to improve clinical outcomes. Fatty acid synthase (FASN) has been implicated as a metabolic oncogene and has given cancer cells a survival advantage by increasing NHEJ repair. Recently, it has been shown that FDA-approved proton pump inhibitors, used for the treatment of acid related digestive diseases, have antitumor effects. Here, I show that a metabolite of lansoprazole, 5-hydroxy lansoprazole sulfide, has increased potency over parent compound lansoprazole. 5-hydroxy lansoprazole sulfide inhibits FASN, leading to a decrease in PARP and NHEJ DNA repair activity in TNBC. Ultimately, this leads to an increase in DNA damage and cell death via apoptosis. These findings suggest that 5-hydroxy lansoprazole sulfide, as a metabolite of lansoprazole, may have better activity in suppressing TNBC cells and that 5-hydroxy lansoprazole sulfide may be developed as a therapeutic for TNBC treatment. Furthermore, due to the role of FASN in increasing NHEJ repair, we hypothesized that FASN played a role in resistance to CC-115, a dual mTOR/DNA-PK inhibitor currently in clinical trials, by increasing DNA-PK activity. However, it was found that ABCG2, an ATP-binding cassette transporter, and not FASN, has a role in CC-115 resistance. ABCG2 effluxes CC-115 from cancer cells, increasing resistance to treatment. Inhibition of ABCG2 by FTC or PZ39C8 led to accumulation of CC-115 within cells and sensitization to treatment. Therefore, ABCG2 status should be assessed to stratify patients into treatment groups, increasing the efficacy of CC-115 treatment.
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    Quantitative Immunohistochemistry Evaluating APE1 Expression in a Mouse Pancreatic Adenocarcinoma Model
    (Office of the Vice Chancellor for Research, 2015-04-17) McElyea, Kyle; Fishel, Melissa; Kelley, Mark R.; Sandusky, George
    High levels of APE1 expression have been reported in numerous malignant tumors (brain, ovarian, pancreatic, and prostate). APE1 is an emerging target for a variety of novel anticancer drugs. Human apurinic endonuclease/redox factor 1 (APE1/Ref-1) mediates the repair of baseless sites in DNA caused by alkylation and oxidative DNA damage. Compound E3330 targets the redox signaling function of APE1. A pancreatic cancer mouse model was used to evaluate the drug effects of E3330 and Gemcitabine. The following doses were used across eight mice groups: E3330 at 12.5mg/kg, 25mg/kg, and 50mg/kg), Gemcitabine (35mg/kg), a combination of E3330 and Gemcitabine at 12.5mg/kg, 25mg/kg, and 50mg/kg), and an untreated vehicle control group. Mice were dosed i.p. 3 times weekly (MWF) and the study was completed at day 39. At termination, tumors were harvested and cross-sections were processed into a Paraffin block. Tissue sections were prepared and stained for H&E and an immunostain for CD31 (angiogenesis marker). Slides were imaged via Aperio whole slide digital system. The immunostains were evaluated to predict the effectiveness of treatment for pancreatic adenocarcinoma. IHC slides were quantitated using an Aperio positive pixel algorithm to determine the percent of angiogenesis in the various drug treatment groups. A biologically significant correlation was seen amongst the low and middle dose E3330 drug groups in comparison to the vehicle control. The (12.5 & 25) E3330 groups had an anti-angiogenic effect (shown by decreased CD31 positivity). These were slightly lower than the combinations of E3330 and Gemcitabine at the same dose treatment groups (possibly due to blunting of E3330). These results support previous studies demonstrating the antiangiogenic activity of E3330.
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    QUANTITATIVE IMMUNOHISTOCHEMISTRY USING THE APERIO WHOLE SLIDE IMAGING SYSTEM EVALUATING ANGIOGENESIS AND HYPOXIA MARKERS IN PANCREATIC CARCINOMA MOUSE MODEL TREATED WITH VEHICLE CONTROL, E3330, AND A STAT 3 INHIBITOR
    (Office of the Vice Chancellor for Research, 2012-04-13) Spencer, Cleandrea; Sandusky, George; Fishel, Melissa; Kelley, Mark R.
    Investigation of the signaling pathways and molecular mechanisms that are major contributors to pancreatic tumor progression and its resistance to traditional therapies is lacking. Human apurinic endonuclease/redox factor 1 (APE/Ref-1) mediates repair of radiation-induced DNA lesions and regulates transcription via redox-based activation. Transcriptional factors HIF-1α, NFκB, and AP-1 are regulated by Ref-1 and are implicated in pancreatic tu-mor growth and the response to hypoxia. CD31 and CA IX (carbonic anhy-drase) were biomarkers used in an in vivo study to evaluate the effective-ness of E3330, an APE 1 inhibitor, in a pancreatic mouse model. Immunostained slides were scanned using the Aperio automated whole slide scanning system (Scanscope CS) and were viewed using ImageScopeTM. Single fields of view from each WSDI measuring ∼10,000,000 μm2 and rep-resenting the whole area of the tumor were selected for analysis using the Aperio positive pixel algorithm. The preclinical xenograft model evaluated human pancreatic carcinoma cell lines grown in NOD/SCID mice treated with the E3330 compound, a STAT 3 inhibitor, and an untreated vehicle control group. Immunohisto-chemistry (IHC) was used to predict effectiveness of treatment for pancreat-ic carcinoma based on CD31 and CA IX biomarker expression. IHC slides were quantified using both a traditional pathology hand count and the Aperio Imaging Analysis System. The positive pixel algorithm data closely mirrored the hand count for two biomarkers (CD31 and CA IX). In the E3330 treated group, the data showed CD31 (angiogenesis) was significantly knocked down with increased CA IX expression compared to the vehicle control. Hypoxia of the tumor cells was up in both treated groups. In summary, the Aperio im-aging analysis system matched the hand count pathology data. The drug ef-fects with E3330 exhibited both anti-angiogenesis and tumor hypoxia activi-ty in the tumors. This project was supported by the Center for Research and Learning’s Diversity Scholars Re-search Program.
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    Tissue Transglutaminase Activates Cancer-Associated Fibroblasts and Contributes to Gemcitabine Resistance in Pancreatic Cancer
    (Elsevier, 2016-11) Lee, Jiyoon; Yakubov, Bakhtiyor; Ivan, Cristina; Jones, David R.; Caperell-Grant, Andrea; Fishel, Melissa; Cardenas, Horacio; Matei, Daniela; Department of Otolaryngology--Head & Neck Surgery, School of Medicine
    Resistance to chemotherapy is a hallmark of pancreatic ductal adenocarcinoma (PDA) and has been partly attributed to the dense desmoplastic stroma, which forms a protective niche for cancer cells. Tissue transglutaminase (TG2), a Ca(2+)-dependent enzyme, is secreted by PDA cells and cross-links proteins in the tumor microenvironment (TME) through acyl-transfer between glutamine and lysine residues, promoting PDA growth. The objective of the current study was to determine whether secreted TG2 by PDA cells alters the response of pancreatic tumors to gemcitabine. Orthotopic pancreatic xenografts and co-culture of PDA and stromal cells were employed to determine the mechanisms by which TG2 alters tumor-stroma interactions and response to gemcitabine. Analysis of the pancreatic The Cancer Genome Atlas (TCGA) database demonstrated that increased TG2 expression levels correlate with worse overall survival (hazard ratio=1.37). Stable TG2 knockdown in PDA cells led to decreased size of pancreatic xenografts and increased sensitivity to gemcitabine in vivo. However, TG2 downregulation did not increase cytotoxicity of gemcitabine in vitro. Additionally, multivessel density and gemcitabine uptake in pancreatic tumor tissue, as measured by mass spectrometry (MS-HPLC), were not significantly different in tumors expressing TG2 versus tumors in which TG2 was knocked down. Fibroblasts, stimulated by TG2 secreted by PDA cells, secrete laminin A1, which protects cancer cells from gemcitabine-induced cytotoxicity. In all, our results demonstrate that TG2 secreted in the pancreatic TME orchestrates the cross talk between cancer cells and stroma, impacting tumor growth and response to chemotherapy. Our study supports TG2 inhibition to increase the antitumor effects of gemcitabine in PDA.