Browsing by Subject "mRNA"

Now showing 1 - 10 of 10
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    AluY-mediated germline deletion, duplication and somatic stem cell reversion in UBE2T defines a new subtype of Fanconi anemia
    (Oxford University Press, 2015-09-15) Virts, Elizabeth L.; Jankowska, Anna; Mackay, Craig; Glaas, Marcel F.; Wiek, Constanze; Kelich, Stephanie L.; Lottmann, Nadine; Kennedy, Felicia M.; Marchal, Christophe; Lehnert, Erik; Scharf, Rüdiger E.; Dufour, Carlo; Lanciotti, Marina; Farruggia, Piero; Santoro, Alessandra; Savasan, Süreyya; Scheckenbach, Kathrin; Schipper, Jörg; Wagenmann, Martin; Lewis, Todd; Leffak, Michael; Farlow, Janice L.; Foroud, Tatiana M.; Honisch, Ellen; Niederacher, Dieter; Chakraborty, Sujata C.; Vance, Gail H.; Pruss, Dmitry; Timms, Kirsten M.; Lanchbury, Jerry S.; Alpi, Arno F.; Hanenberg, Helmut; Department of Pediatrics, IU School of Medicine
    Fanconi anemia (FA) is a rare inherited disorder clinically characterized by congenital malformations, progressive bone marrow failure and cancer susceptibility. At the cellular level, FA is associated with hypersensitivity to DNA-crosslinking genotoxins. Eight of 17 known FA genes assemble the FA E3 ligase complex, which catalyzes monoubiquitination of FANCD2 and is essential for replicative DNA crosslink repair. Here, we identify the first FA patient with biallelic germline mutations in the ubiquitin E2 conjugase UBE2T. Both mutations were aluY-mediated: a paternal deletion and maternal duplication of exons 2–6. These loss-of-function mutations in UBE2T induced a cellular phenotype similar to biallelic defects in early FA genes with the absence of FANCD2 monoubiquitination. The maternal duplication produced a mutant mRNA that could encode a functional protein but was degraded by nonsense-mediated mRNA decay. In the patient's hematopoietic stem cells, the maternal allele with the duplication of exons 2–6 spontaneously reverted to a wild-type allele by monoallelic recombination at the duplicated aluY repeat, thereby preventing bone marrow failure. Analysis of germline DNA of 814 normal individuals and 850 breast cancer patients for deletion or duplication of UBE2T exons 2–6 identified the deletion in only two controls, suggesting aluY-mediated recombinations within the UBE2T locus are rare and not associated with an increased breast cancer risk. Finally, a loss-of-function germline mutation in UBE2T was detected in a high-risk breast cancer patient with wild-type BRCA1/2. Cumulatively, we identified UBE2T as a bona fide FA gene (FANCT) that also may be a rare cancer susceptibility gene.
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    A Case of Autoimmune Hemolytic Anemia after the First Dose of COVID-19 mRNA-1273 Vaccine with Undetected Pernicious Anemia
    (Hindawi, 2022-01-29) Jaydev, Fnu; Kumar, Vinod; Khatri, Jaikumar; Shahani, Shobha; Beganovic, Sead; Medicine, School of Medicine
    By this time, multiple vaccines have been approved to limit the spread of SARS-CoV-2 worldwide. These include new-generation vaccines that contain mRNA of the target organism. Some common side effects were identified and reported during phase 3 clinical trials of vaccination, but more rare adverse events were reported in the literature. One such concern is autoimmune conditions that SARS-CoV-2 viral antigens could have possibly incited. We are presenting here a case of a young female with no known autoimmune diseases, diagnosed with autoimmune hemolytic anemia about a week after receiving her first dose of the COVID-19 mRNA vaccine. We discuss the possible culprit for precipitation of autoimmune hemolytic anemia after the SARS-CoV-2 mRNA vaccine, which encodes virus spike protein. This case highlights the importance of being vigilant for identifying rare adverse events that could appear during mass vaccination.
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    Effectiveness of a Third Dose of mRNA Vaccines Against COVID-19–Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant Predominance — VISION Network, 10 States, August 2021–January 2022
    (U.S. Department of Health & Human Services, 2022-01-28) Thompson, Mark G.; Natarajan, Karthik; Irving, Stephanie A.; Rowley, Elizabeth A.; Griggs, Eric P.; Gaglani, Manjusha; Klein, Nicola P.; Grannis, Shaun J.; DeSilva, Malini B.; Stenehjem, Edward; Reese, Sarah E.; Dickerson, Monica; Naleway, Allison L.; Han, Jungmi; Konatham, Deepika; McEvoy, Charlene; Rao, Suchitra; Dixon, Brian E.; Dascomb, Kristin; Lewis, Ned; Levy, Matthew E.; Patel, Palak; Liao, I-Chia; Kharbanda, Anupam B.; Barron, Michelle A.; Fadel, William F.; Grisel, Nancy; Goddard, Kristin; Yang, Duck-Hye; Wondimu, Mehiret H.; Murthy, Kempapura; Valvi, Nimish R.; Arndorfer, Julie; Fireman, Bruce; Dunne, Margaret M.; Embi, Peter; Azziz-Baumgartner, Eduardo; Zerbo, Ousseny; Bozio, Catherine H.; Reynolds, Sue; Ferdinands, Jill; Williams, Jeremiah; Link-Gelles, Ruth; Schrag, Stephanie J.; Verani, Jennifer R.; Ball, Sarah; Ong, Toan C.; Family Medicine, School of Medicine
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    Hepatitis B Virus X Protein Crosses Out Smc5/6 Complex to Maintain cccDNA Transcription
    (Wiley, 2016-12) Mitra, Bidisha; Guo, Haitao; Microbiology and Immunology, School of Medicine
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    Mapping the miRNA‐mRNA Interactome in Human Hepatocytes and Identification of Functional mirSNPs in Pharmacogenes
    (American Society for Clinical Pharmacology & Therapeutics, 2021-10) Powell, Nicholas R.; Zhao, Harrison; Ipe, Joseph; Liu, Yunlong; Skaar, Todd C.; Medicine, School of Medicine
    MiRNAs regulate the expression of hepatic genes involved in pharmacokinetics and pharmacodynamics. Genetic variants affecting miRNA binding (mirSNPs) have been associated with altered drug response, but previously used methods to identify miRNA binding sites and functional mirSNPs in pharmacogenes are indirect and limited by low throughput. We utilized the high-throughput chimeric-eCLIP assay to directly map thousands of miRNA-mRNA interactions and define the miRNA binding sites in primary hepatocytes. We then used the high-throughput PASSPORT-seq assay to functionally test 262 potential mirSNPs with coordinates overlapping the identified miRNA binding sites. Using chimeric-eCLIP, we identified a network of 448 miRNAs that collectively target 11,263 unique genes in primary hepatocytes pooled from 100 donors. Our data provide an extensive map of miRNA binding of each gene, including pharmacogenes, expressed in primary hepatocytes. For example, we identified the hsa-mir-27b-DPYD interaction at a previously validated binding site. A second example is our identification of 19 unique miRNAs that bind to CYP2B6 across 20 putative binding sites on the transcript. Using PASSPORT-seq, we then identified 24 mirSNPs that functionally impacted reporter mRNA levels. To our knowledge, this is the most comprehensive identification of miRNA binding sites in pharmacogenes. Combining chimeric-eCLIP with PASSPORT-seq successfully identified functional mirSNPs in pharmacogenes that may affect transcript levels through altered miRNA binding. These results provide additional insights into potential mechanisms contributing to interindividual variability in drug response.
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    New Twists in Detecting mRNA Modification Dynamics
    (Elsevier, 2020-07-01) Anreiter, Ina; Mir, Quoseena; Simpson, Jared T.; Janga, Sarath C.; Soller, Matthias; BioHealth Informatics, School of Informatics and Computing
    Modified nucleotides in mRNA are an essential addition to the standard genetic code of four nucleotides in animals, plants, and their viruses. The emerging field of epitranscriptomics examines nucleotide modifications in mRNA and their impact on gene expression. The low abundance of nucleotide modifications and technical limitations, however, have hampered systematic analysis of their occurrence and functions. Selective chemical and immunological identification of modified nucleotides has revealed global candidate topology maps for many modifications in mRNA, but further technical advances to increase confidence will be necessary. Single-molecule sequencing introduced by Oxford Nanopore now promises to overcome such limitations, and we summarize current progress with a particular focus on the bioinformatic challenges of this novel sequencing technology.
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    Ossabaw Pig Demonstrates Detrusor Fibrosis and Detrusor Underactivity Associated with Oxidative Stress in Metabolic Syndrome
    (American Association for Laboratory Animal Science, 2020-10) Powell, Charles R.; Kim, Albert; Roth, Joshua; Byrd, James P.; Mohammad, Khalid; Khalid, Mouhamad; Alloosh, Mouhamad; Vittal, Ragini; Sturek, Michael; Urology, School of Medicine
    Metabolic Syndrome (MetS) has detrimental effects on the bladder, including detrusor underactivity. The progression and mechanism of disease are poorly understood. A swine model for diabetic bladder dysfunction (DBD) was established because of the pig's human-sized bladder and its ability to develop MetS by dietary modification alone. The hypothesis of this study is that this swine model will demonstrate oxidative stress associated with MetS, which contributes to both bladder fibrosis and detrusor underactivity (DU). Ossabaw pigs underwent dietary modification consisting of a hypercaloric, atherogenic diet for 10 mo to induce MetS, and were compared with a group of control (lean) pigs. Urodynamic studies were performed in both groups to confirm DU. Thiobarbituric acid reactive substances (TBARS) detected in the urine were used to measure oxidative stress activity in the urinary tract, and urinary IL17a was used to detect profibrotic activity. MetS was confirmed by assessing body weight, blood pressure, glucose tolerance, total cholesterol, and triglycerides. The MetS group exhibited an increase in the relative levels of urinary TBARS and IL17a. Bladder pressures at capacity were lower in the MetS group, suggesting DU. Histologic analysis of a cohort of control (lean) and MetS pigs revealed that as compared with the control pigs, the MetS pigs had significantly more collagen in the muscularis layer, but not in the submucosa or mucosa layer. In conclusion, the Ossabaw pig model for diet-induced MetS is associated with oxidative stress and profibrotic activity in the bladder, which results in DU. This has previously been shown in mice and rats, but never in pigs. This novel model will better represent human MetS and DBD because the mechanism and size of the pig bladder more closely resemble that of a human, resulting in a more valid model and facilitating further study into the signaling mechanisms responsible for this impairment.
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    PROGgene: gene expression based survival analysis web application for multiple cancers
    (Springer, 2013-10-28) Goswami, Chirayu Pankaj; Nakshatri, Harikrishna
    Background Identification of prognostic mRNA biomarkers has been done for various cancer types. The data that are published from such studies are archived in public repositories. There are hundreds of such datasets available for multiple cancer types in public repositories. Wealth of such data can be utilized to study prognostic implications of mRNA in different cancers as well as in different populations or subtypes of same cancer. Description We have created a web application that can be used for studying prognostic implications of mRNA biomarkers in a variety of cancers. We have compiled data from public repositories such as GEO, EBI Array Express and The Cancer Genome Atlas for creating this tool. With 64 patient series from 18 cancer types in our database, this tool provides the most comprehensive resource available for survival analysis to date. The tool is called PROGgene and it is available at http://www.compbio.iupui.edu/proggene. Conclusions We present this tool as a hypothesis generation tool for researchers to identify potential prognostic mRNA biomarkers to follow up with further research. For this reason, we have kept the web application very simple and straightforward. We believe this tool will be useful in accelerating biomarker discovery in cancer and quickly providing results that may indicate disease-specific prognostic value of specific biomarkers.
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    Renal Tubular Cell-Derived Extracellular Vesicles Accelerate the Recovery of Established Renal Ischemia Reperfusion Injury
    (American Society of Nephrology, 2017-12) Dominguez, Jesus H.; Liu, Yunlong; Gao, Hongyu; Dominguez, James M., II; Xie, Danhui; Kelly, Katherine J.; Medicine, School of Medicine
    Ischemic renal injury is a complex syndrome; multiple cellular abnormalities cause accelerating cycles of inflammation, cellular damage, and sustained local ischemia. There is no single therapy that effectively resolves the renal damage after ischemia. However, infusions of normal adult rat renal cells have been a successful therapy in several rat renal failure models. The sustained broad renal benefit achieved by relatively few donor cells led to the hypothesis that extracellular vesicles (EV, largely exosomes) derived from these cells are the therapeutic effector in situ We now show that EV from adult rat renal tubular cells significantly improved renal function when administered intravenously 24 and 48 hours after renal ischemia in rats. Additionally, EV treatment significantly improved renal tubular damage, 4-hydroxynanoneal adduct formation, neutrophil infiltration, fibrosis, and microvascular pruning. EV therapy also markedly reduced the large renal transcriptome drift observed after ischemia. These data show the potential utility of EV to limit severe renal ischemic injury after the occurrence.
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    Small-Molecule Binding Sites to Explore New Targets in the Cancer Proteome
    (2016-10-20) Xu, David; Jalal, Shadia I.; Sledge, George W.; Meroueh, Samy O.; Biochemistry and Molecular Biology, School of Medicine
    The Cancer Genome Atlas (TCGA) offers an unprecedented opportunity to identify small-molecule binding sites on proteins with overexpressed mRNA levels that correlate with poor survival. Here, we analyze RNA-seq and clinical data for 10 tumor types to identify genes that are both overexpressed and correlate with patient survival. Protein products of these genes were scanned for binding sites that possess shape and physicochemical properties that can accommodate small-molecule probes or therapeutic agents (druggable). These binding sites were classified as enzyme active sites (ENZ), protein-protein interaction sites (PPI), or other sites whose function is unknown (OTH). Interestingly, the overwhelming majority of binding sites were classified as OTH. We find that ENZ, PPI, and OTH binding sites often occurred on the same structure suggesting that many of these OTH cavities can be used for allosteric modulation of enzyme activity or protein-protein interactions with small molecules. We discovered several ENZ (PYCR1, QPRT, and HSPA6) and PPI (CASC5, ZBTB32, and CSAD) binding sites on proteins that have been seldom explored in cancer. We also found proteins that have been extensively studied in cancer that have not been previously explored with small molecules that harbor ENZ (PKMYT1, STEAP3, and NNMT) and PPI (HNF4A, MEF2B, and CBX2) binding sites. All binding sites were classified by the signaling pathways to which the protein that harbors them belongs using KEGG. In addition, binding sites were mapped onto structural protein-protein interaction networks to identify promising sites for drug discovery. Finally, we identify pockets that harbor missense mutations previously identified from analysis of the TCGA data. The occurrence of mutations in these binding sites provides new opportunities to develop small-molecule probes to explore their function in cancer.,