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Item Cracd Marks the First Wave of Meiosis during Spermatogenesis and Is Mis-Expressed in Azoospermia Mice(MDPI, 2020-09-18) Snider, Paige L.; Simmons, Olga; Conway, Simon J.; Pediatrics, School of MedicineTesticular development starts in utero and maturation continues postnatally, requiring a cascade of gene activation and differentiation into different cell types, with each cell type having its own specific function. As we had previously reported that the Capping protein inhibiting regulator of actin (Cracd) gene was expressed in the adult mouse testis, herein we examine when and where the β-catenin associated Cracd is initially expressed during postnatal testis development. Significantly, Cracd mRNA is present in both the immature postnatal and adult testis in round spermatid cells, with highest level of expression occurring during the first wave of meiosis and spermatogenesis. In the juvenile testes, Cracd is initially expressed within the innermost region but as maturation occurs, Cracd mRNA switches to a more peripheral location. Thereafter, Cracd is downregulated to maintenance levels in the haploid male germ cell lineage. As Cracd mRNA was expressed within developing round spermatids, we tested its effectiveness as a biomarker of non-obstructive azoospermia using transgenic knockout mice models. Meaningfully, Cracd expression was absent in Deleted in azoospermia like (Dazl) null testis, which exhibit a dramatic germ cell loss. Moreover, Cracd was abnormally regulated and ectopically mis-expressed in Polypyrimidine tract binding protein-2 (Ptbp2) conditional germ cell restricted knockout testis, which exhibit a block during spermatid differentiation and a reduction in the number of late stage spermatocytes coincident with reduced β-catenin expression. Combined, these data suggest that Cracd is a useful first wave of spermatogenesis biomarker of azoospermia phenotypes, even prior to an overt phenotype being evident.Item Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing(Elsevier, 2019-04) Ganem, Nabeel S.; Ben-Asher, Noa; Manning, Aidan C.; Deffit, Sarah N.; Washburn, Michael C.; Wheeler, Emily C.; Yeo, Gene W.; Ben-Naim Zgayer, Orna; Mantsur, Einav; Hundley, Heather A.; Lamm, Ayelet T.A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes on the RNA editing process. We performed comprehensive phenotypic, transcriptomics, proteomics, and RNA binding screens on worms mutated in a single ADAR gene. We found that ADR-1 mutants exhibit more-severe phenotypes than ADR-2, and some of them are a result of non-editing functions of ADR-1. We also show that ADR-1 significantly binds edited genes and regulates mRNA expression, whereas the effect on protein levels is minor. In addition, ADR-1 primarily promotes editing by ADR-2 at the L4 stage of development. Our results suggest that ADR-1 has a significant role in the RNA editing process and in altering editing levels that affect RNA expression; loss of ADR-1 results in severe phenotypes.Item Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach(2010-07) Janga, Sarath Chandra; Contreras-Moreira, BrunoIn prokaryotes, regulation of gene expression is predominantly controlled at the level of transcription. Transcription in turn is mediated by a set of DNA-binding factors called transcription factors (TFs). In this study, we map the complete repertoire of ∼300 TFs of the bacterial model, Escherichia coli, onto gene expression data for a number of nonredundant experimental conditions and show that TFs are generally expressed at a lower level than other gene classes. We also demonstrate that different conditions harbor varying number of active TFs, with an average of about 15% of the total repertoire, with certain stress and drug-induced conditions exhibiting as high as one-third of the collection of TFs. Our results also show that activators are more frequently expressed than repressors, indicating that activation of promoters might be a more common phenomenon than repression in bacteria. Finally, to understand the association of TFs with different conditions and to elucidate their dynamic interplay with other TFs, we develop a network-based framework to identify TFs which act as markers, defined as those which are responsible for condition-specific transcriptional rewiring. This approach allowed us to pinpoint several marker TFs as being central in various specialized conditions such as drug induction or growth condition variations, which we discuss in light of previously reported experimental findings. Further analysis showed that a majority of identified markers effectively control the expression of their regulons and, in general, transcriptional programs of most conditions can be effectively rewired by a very small number of TFs. It was also found that closeness is a key centrality measure which can aid in the successful identification of marker TFs in regulatory networks. Our results suggest the utility of the network-based approaches developed in this study to be applicable for understanding other interactomic data sets.Item Epigenetic Regulation of Viral Biological Processes(MDPI, 2017-11-17) Balakrishnan, Lata; Milavetz, Barry; Biology, School of ScienceIt is increasingly clear that DNA viruses exploit cellular epigenetic processes to control their life cycles during infection. This review will address epigenetic regulation in members of the polyomaviruses, adenoviruses, human papillomaviruses, hepatitis B, and herpes viruses. For each type of virus, what is known about the roles of DNA methylation, histone modifications, nucleosome positioning, and regulatory RNA in epigenetic regulation of the virus infection will be discussed. The mechanisms used by certain viruses to dysregulate the host cell through manipulation of epigenetic processes and the role of cellular cofactors such as BRD4 that are known to be involved in epigenetic regulation of host cell pathways will also be covered. Specifically, this review will focus on the role of epigenetic regulation in maintaining viral episomes through the generation of chromatin, temporally controlling transcription from viral genes during the course of an infection, regulating latency and the switch to a lytic infection, and global dysregulation of cellular function.Item Essentiality and Transcriptome-Enriched Pathway Scores Predict Drug-Combination Synergy(MDPI, 2020-09-07) Li, Jin; Huo, Yang; Wu, Xue; Liu, Enze; Zeng, Zhi; Tian, Zhen; Fan, Kunjie; Stover, Daniel; Cheng, Lijun; Li, Lang; Medicine, School of MedicineIn the prediction of the synergy of drug combinations, systems pharmacology models expand the scope of experiment screening and overcome the limitations of current computational models posed by their lack of mechanical interpretation and integration of gene essentiality. We therefore investigated the synergy of drug combinations for cancer therapies utilizing records in NCI ALMANAC, and we employed logistic regression to test the statistical significance of gene and pathway features in that interaction. We trained our predictive models using 43 NCI-60 cell lines, 165 KEGG pathways, and 114 drug pairs. Scores of drug-combination synergies showed a stronger correlation with pathway than gene features in overall trend analysis and a significant association with both genes and pathways in genome-wide association analyses. However, we observed little overlap of significant gene expressions and essentialities and no significant evidence that associated target and non-target genes and their pathways. We were able to validate four drug-combination pathways between two drug combinations, Nelarabine-Exemestane and Docetaxel-Vermurafenib, and two signaling pathways, PI3K-AKT and AMPK, in 16 cell lines. In conclusion, pathways significantly outperformed genes in predicting drug-combination synergy, and because they have very different mechanisms, gene expression and essentiality should be considered in combination rather than individually to improve this prediction.Item Ethanol Activates Immune Response In Lymphoblastoid Cells(Elsevier, 2019) McClintick, Jeanette N.; Tischfield, Jay A.; Deng, Li; Kapoor, Manav; Xuei, Xiaoling; Edenberg, Howard J.; Biochemistry and Molecular Biology, School of MedicineThe short term effects of alcohol on gene expression in brain tissue cannot directly be studied in humans. Because neuroimmune signaling is altered by alcohol, immune cells are a logical, accessible choice to study and might provide biomarkers. RNAseq was used to study the effects of 48 h exposure to ethanol on lymphoblastoid cell lines (LCLs) from 21 alcoholics and 21 controls. Ethanol exposure resulted in differential expression of 4,577 of the 12,526 genes detectably expressed in the LCLs (FDR ≤ 0.05); 55% of these showed increased expression. Cells from alcoholics and controls responded similarly. The genes whose expression changed fell into many pathways. NFκB, neuroinflammation, IL-6, and dendritic cell maturation pathways were activated, consistent with increased signaling by NFκB, TNF, TGFβ, IL1, IL4, IL18, TLR4, and LPS. Signaling by Interferons A and B decreased, which may be responsible for a slightly blunted immune response compared to 24 h ethanol treatment. EIF2, phospholipase C and VEGF signaling were decreased. Baseline gene expression patterns were similar in LCLs from alcoholics and controls. At relaxed stringency (p<0.05), 1164 genes differed, 340 of which were also affected by ethanol. There was a suggestion of compensation, with 77% showing opposing fold changes. Aldosterone signaling and phospholipase C signaling differed. The pattern of expression was consistent with increased signaling by several cytokines and TLR2 in alcoholics. The cholesterol biosynthesis pathway was lower in alcoholics, including a decrease in the rate-limiting enzyme HMGCR. LCLs show many effects of ethanol exposure, some of which might provide biomarkers for AUD and aid in interpreting the effects of genes identified by GWAS.Item Interactions between folate intake and genetic predictors of gene expression levels associated with colorectal cancer risk(Springer, 2022-11-07) Haas, Cameron B.; Su, Yu-Ru; Petersen, Paneen; Wang, Xiaoliang; Bien, Stephanie A.; Lin, Yi; Albanes, Demetrius; Weinstein, Stephanie J.; Jenkins, Mark A.; Figueiredo, Jane C.; Newcomb, Polly A.; Casey, Graham; Marchand, Loic Le; Campbell, Peter T.; Moreno, Victor; Potter, John D.; Sakoda, Lori C.; Slattery, Martha L.; Chan, Andrew T.; Li, Li; Giles, Graham G.; Milne, Roger L.; Gruber, Stephen B.; Rennert, Gad; Woods, Michael O.; Gallinger, Steven J.; Berndt, Sonja; Hayes, Richard B.; Huang, Wen-Yi; Wolk, Alicja; White, Emily; Nan, Hongmei; Nassir, Rami; Lindor, Noralane M.; Lewinger, Juan P.; Kim, Andre E.; Conti, David; Gauderman, W. James; Buchanan, Daniel D.; Peters, Ulrike; Hsu , Li; Epidemiology, Richard M. Fairbanks School of Public HealthObservational studies have shown higher folate consumption to be associated with lower risk of colorectal cancer (CRC). Understanding whether and how genetic risk factors interact with folate could further elucidate the underlying mechanism. Aggregating functionally relevant genetic variants in set-based variant testing has higher power to detect gene-environment (G × E) interactions and may provide information on the underlying biological pathway. We investigated interactions between folate consumption and predicted gene expression on colorectal cancer risk across the genome. We used variant weights from the PrediXcan models of colon tissue-specific gene expression as a priori variant information for a set-based G × E approach. We harmonized total folate intake (mcg/day) based on dietary intake and supplemental use across cohort and case-control studies and calculated sex and study specific quantiles. Analyses were performed using a mixed effects score tests for interactions between folate and genetically predicted expression of 4839 genes with available genetically predicted expression. We pooled results across 23 studies for a total of 13,498 cases with colorectal tumors and 13,918 controls of European ancestry. We used a false discovery rate of 0.2 to identify genes with suggestive evidence of an interaction. We found suggestive evidence of interaction with folate intake on CRC risk for genes including glutathione S-Transferase Alpha 1 (GSTA1; p = 4.3E-4), Tonsuko Like, DNA Repair Protein (TONSL; p = 4.3E-4), and Aspartylglucosaminidase (AGA: p = 4.5E-4). We identified three genes involved in preventing or repairing DNA damage that may interact with folate consumption to alter CRC risk. Glutathione is an antioxidant, preventing cellular damage and is a downstream metabolite of homocysteine and metabolized by GSTA1. TONSL is part of a complex that functions in the recovery of double strand breaks and AGA plays a role in lysosomal breakdown of glycoprotein.Item MLO-Y4 osteocytic cell clones express distinct gene expression patterns characteristic of different stages of osteocyte differentiation(2017-09) Atkinson, Emily G.; Marcial, Alejandro; Sánchez, Zuleima; Porter, Christian; Plotkin, Lilian I.; Anatomy and Cell Biology, School of MedicineOsteocytes are the most abundant bone cell and are formed when osteoblasts become embedded in the bone matrix. Through changes in gene expression and paracrine effects, osteocytes regulate the number of osteoblasts, bone forming cells, and osteoclasts, bone resorbing cells, which are needed to maintain bone mass. MLO-Y4 is the better characterized osteocytic cell line; however, lacks expression of sclerostin, the product of the SOST gene, which is fundamental for osteocyte function and blocks bone formation. With the objective to isolate MLO-Y4 clones with different gene expression profiles, we performed cultures at very low density of MLO-Y4 cells stably transfected with nuclear green fluorescent protein (MLO-nGFP). Cell morphology was visualized under a fluorescence microscope. Once the cells reached 80% confluency, RNA was extracted and quantitative real time PCR was performed. Clones exhibit different sizes and morphology, with some cells showing a spindle-like shape and others with abundant projections and a star-like shape. Gene expression also differed among clones. However, none of the clones examined expressed SOST. We conclude that the MLO-nGFP clones constitute a useful tool to study osteocyte differentiation and the role of osteocytes in the control of bone formation and resorption in vitro.Item Molecular targets of alcohol action: translational research for pharmacotherapy development and screening.(Elsevier, 2011) Gorini, Giorgio; Bell, Richard L.; Mayfield, R. Dayne; Department of Psychology, School of ScienceAlcohol abuse and dependence are multifaceted disorders with neurobiological, psychological, and environmental components. Research on other complex neuropsychiatric diseases suggests that genetically influenced intermediate characteristics affect the risk for heavy alcohol consumption and its consequences. Diverse therapeutic interventions can be developed through identification of reliable biomarkers for this disorder and new pharmacological targets for its treatment. Advances in the fields of genomics and proteomics offer a number of possible targets for the development of new therapeutic approaches. This brain-focused review highlights studies identifying neurobiological systems associated with these targets and possible pharmacotherapies, summarizing evidence from clinically relevant animal and human studies, as well as sketching improvements and challenges facing the fields of proteomics and genomics. Concluding thoughts on using results from these profiling technologies for medication development are also presented.Item Rapid Development of Clinical Trial Candidates Using Cancer Systems Pharmacology: a Lymphoma Case Study(Office of the Vice Chancellor for Research, 2015-04-17) Arkenberg, Matthew; Johnson, Kylee; Kaur, Palakpreet; Moors, Kelly; Weisman, MichaelDue to intrinsic complex molecular interactions, the “one disease – one target – one drug” strategy for disease treatment is no longer the best option to treat complex diseases such as cancers. To assess drug pharmacological effects, we assume that “ideal” drugs for patients can treat or prevent the disease by modulating its gene expression profile to a similar level of those in healthy people. A drug that may not have been approved to treat a cancer yet, based on its gene expression target profile is the most successfully at modulating the gene expression to being of similar level to a healthy person is known as drug repurposing. The goal of this study was to develop an in silico framework which would determine which drug(s) could be repurposed to treat more complex disease of interest such as cancers. Using three subcategories of Non-Hodgkin’s Lymphoma (Burkitt’s, Mantle, Diffuse Large B-Cell) as case studies, manual curation was done to collect data on drug-protein interaction, drug similarity analysis based on structure and protein target, and curation; disease-protein interactions, and protein-protein interactions. A network will be created from the curated data known as a Pharmacology Effect Network (PEN). The Pharmacological Effect on Target (PET) algorithm will then be used to rank the curated drugs. This ranking will help determine which of the investigated drugs not currently used to treat one of the three subsets of Non-Hodgkin’s lymphoma could possibly be recommended to treat them. Although this project was primarily done using manual curation, the framework of each curated relationship used by each curator has been incorporated into a web interface. This webpage will allow for more automation of the curation process with little help from the curator and should improve the speed and accuracy of the curation process. Mentors: Jake Chen7, Xiaogang Wu7, Walter Jessen8 7IU Center for Systems Biology and Personalized Medicine, IUPUI; 8Informatics, Covance, Greenfield