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Plassmeyer SP, Florian CP, Kasper MJ, Chase R, Mueller S, Liu Y, White KM, Jungers CF, Djuranovic SP, Djuranovic S, Dougherty JD. A Massively Parallel Screen of 5'UTR Mutations Identifies Variants Impacting Translation and Protein Production in Neurodevelopmental Disorder Genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.02.23297961. [PMID: 37961498 PMCID: PMC10635273 DOI: 10.1101/2023.11.02.23297961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
De novo mutations cause a variety of neurodevelopmental disorders including autism. Recent whole genome sequencing from individuals with autism has shown that many de novo mutations also occur in untranslated regions (UTRs) of genes, but it is difficult to predict from sequence alone which mutations are functional, let alone causal. Therefore, we developed a high throughput assay to screen the transcriptional and translational effects of 997 variants from 5'UTR patient mutations. This assay successfully enriched for elements that alter reporter translation, identifying over 100 potentially functional mutations from probands. Studies in patient-derived cell lines further confirmed that these mutations can alter protein production in individuals with autism, and some variants fall in genes known to cause syndromic forms of autism, suggesting a diagnosis for these individual patients. Since UTR function varies by cell type, we further optimized this high throughput assay to enable assessment of mutations in neurons in vivo. First, comparing in cellulo to in vivo results, we demonstrate neurons have different principles of regulation by 5'UTRs, consistent with a more robust mechanism for reducing the impact of RNA secondary structure. Finally, we discovered patient mutations specifically altering the translational activity of additional known syndromic genes LRRC4 and ZNF644 in neurons of the brain. Overall our results highlight a new approach for assessing the impact of 5'UTR mutations across cell types and suggest that some cases of neurodevelopmental disorder may be caused by such variants.
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Affiliation(s)
- Stephen P. Plassmeyer
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Colin P. Florian
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J. Kasper
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rebecca Chase
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shayna Mueller
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kelli McFarland White
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Courtney F. Jungers
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Sergej Djuranovic
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D. Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University, St. Louis, MO 63130, USA
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Mukherjee D, Chakraborty S, Bercz L, D’Alesio L, Wedig J, Torok MA, Pfau T, Lathrop H, Jasani S, Guenther A, McGue J, Adu-Ampratwum D, Fuchs JR, Frankel TL, Pietrzak M, Culp S, Strohecker AM, Skardal A, Mace TA. Tomatidine targets ATF4-dependent signaling and induces ferroptosis to limit pancreatic cancer progression. iScience 2023; 26:107408. [PMID: 37554459 PMCID: PMC10405072 DOI: 10.1016/j.isci.2023.107408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/19/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with high metastasis and therapeutic resistance. Activating transcription factor 4 (ATF4), a master regulator of cellular stress, is exploited by cancer cells to survive. Prior research and data reported provide evidence that high ATF4 expression correlates with worse overall survival in PDAC. Tomatidine, a natural steroidal alkaloid, is associated with inhibition of ATF4 signaling in multiple diseases. Here, we discovered that in vitro and in vivo tomatidine treatment of PDAC cells inhibits tumor growth. Tomatidine inhibited nuclear translocation of ATF4 and reduced the transcriptional binding of ATF4 with downstream promoters. Tomatidine enhanced gemcitabine chemosensitivity in 3D ECM-hydrogels and in vivo. Tomatidine treatment was associated with induction of ferroptosis signaling validated by increased lipid peroxidation, mitochondrial biogenesis, and decreased GPX4 expression in PDAC cells. This study highlights a possible therapeutic approach utilizing a plant-derived metabolite, tomatidine, to target ATF4 activity in PDAC.
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Affiliation(s)
- Debasmita Mukherjee
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Srija Chakraborty
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Lena Bercz
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Liliana D’Alesio
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jessica Wedig
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Molly A. Torok
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Timothy Pfau
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Hannah Lathrop
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shrina Jasani
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Abigail Guenther
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jake McGue
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Adu-Ampratwum
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH 43210, USA
| | - James R. Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, The Ohio State University, Columbus, OH 43210, USA
| | | | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Stacey Culp
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Anne M. Strohecker
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Cancer Biology & Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Aleksander Skardal
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Thomas A. Mace
- The James Comprehensive Cancer Center, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Internal Medicine, Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University, Columbus, OH 43210, USA
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Sadee W, Wang D, Hartmann K, Toland AE. Pharmacogenomics: Driving Personalized Medicine. Pharmacol Rev 2023; 75:789-814. [PMID: 36927888 PMCID: PMC10289244 DOI: 10.1124/pharmrev.122.000810] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Personalized medicine tailors therapies, disease prevention, and health maintenance to the individual, with pharmacogenomics serving as a key tool to improve outcomes and prevent adverse effects. Advances in genomics have transformed pharmacogenetics, traditionally focused on single gene-drug pairs, into pharmacogenomics, encompassing all "-omics" fields (e.g., proteomics, transcriptomics, metabolomics, and metagenomics). This review summarizes basic genomics principles relevant to translation into therapies, assessing pharmacogenomics' central role in converging diverse elements of personalized medicine. We discuss genetic variations in pharmacogenes (drug-metabolizing enzymes, drug transporters, and receptors), their clinical relevance as biomarkers, and the legacy of decades of research in pharmacogenetics. All types of therapies, including proteins, nucleic acids, viruses, cells, genes, and irradiation, can benefit from genomics, expanding the role of pharmacogenomics across medicine. Food and Drug Administration approvals of personalized therapeutics involving biomarkers increase rapidly, demonstrating the growing impact of pharmacogenomics. A beacon for all therapeutic approaches, molecularly targeted cancer therapies highlight trends in drug discovery and clinical applications. To account for human complexity, multicomponent biomarker panels encompassing genetic, personal, and environmental factors can guide diagnosis and therapies, increasingly involving artificial intelligence to cope with extreme data complexities. However, clinical application encounters substantial hurdles, such as unknown validity across ethnic groups, underlying bias in health care, and real-world validation. This review address the underlying science and technologies germane to pharmacogenomics and personalized medicine, integrated with economic, ethical, and regulatory issues, providing insights into the current status and future direction of health care. SIGNIFICANCE STATEMENT: Personalized medicine aims to optimize health care for the individual patients with use of predictive biomarkers to improve outcomes and prevent adverse effects. Pharmacogenomics drives biomarker discovery and guides the development of targeted therapeutics. This review addresses basic principles and current trends in pharmacogenomics, with large-scale data repositories accelerating medical advances. The impact of pharmacogenomics is discussed, along with hurdles impeding broad clinical implementation, in the context of clinical care, ethics, economics, and regulatory affairs.
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Affiliation(s)
- Wolfgang Sadee
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Danxin Wang
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Katherine Hartmann
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
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Hartmann K, Seweryn M, Sadee W. Interpreting coronary artery disease GWAS results: A functional genomics approach assessing biological significance. PLoS One 2022; 17:e0244904. [PMID: 35192625 PMCID: PMC8863290 DOI: 10.1371/journal.pone.0244904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/01/2022] [Indexed: 01/09/2023] Open
Abstract
Genome-wide association studies (GWAS) have implicated 58 loci in coronary artery disease (CAD). However, the biological basis for these associations, the relevant genes, and causative variants often remain uncertain. Since the vast majority of GWAS loci reside outside coding regions, most exert regulatory functions. Here we explore the complexity of each of these loci, using tissue specific RNA sequencing data from GTEx to identify genes that exhibit altered expression patterns in the context of GWAS-significant loci, expanding the list of candidate genes from the 75 currently annotated by GWAS to 245, with almost half of these transcripts being non-coding. Tissue specific allelic expression imbalance data, also from GTEx, allows us to uncover GWAS variants that mark functional variation in a locus, e.g., rs7528419 residing in the SORT1 locus, in liver specifically, and rs72689147 in the GUYC1A1 locus, across a variety of tissues. We consider the GWAS variant rs1412444 in the LIPA locus in more detail as an example, probing tissue and transcript specific effects of genetic variation in the region. By evaluating linkage disequilibrium (LD) between tissue specific eQTLs, we reveal evidence for multiple functional variants within loci. We identify 3 variants (rs1412444, rs1051338, rs2250781) that when considered together, each improve the ability to account for LIPA gene expression, suggesting multiple interacting factors. These results refine the assignment of 58 GWAS loci to likely causative variants in a handful of cases and for the remainder help to re-prioritize associated genes and RNA isoforms, suggesting that ncRNAs maybe a relevant transcript in almost half of CAD GWAS results. Our findings support a multi-factorial system where a single variant can influence multiple genes and each genes is regulated by multiple variants.
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Affiliation(s)
- Katherine Hartmann
- Department of Cancer Biology and Genetics, Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, United States of America
- * E-mail:
| | - Michał Seweryn
- Biobank Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Wolfgang Sadee
- Department of Cancer Biology and Genetics, Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, United States of America
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Xu J, Wu PJ, Lai TH, Sharma P, Canella A, Welker AM, Beattie C, Timmers CD, Lang FF, Jacob NK, Elder JB, Lonser R, Easley M, Pietrzak M, Sampath D, Puduvalli VK. Disruption of DNA Repair and Survival Pathways through Heat Shock Protein inhibition by Onalespib to Sensitize Malignant Gliomas to Chemoradiation therapy. Clin Cancer Res 2022; 28:1979-1990. [PMID: 35140124 PMCID: PMC9064967 DOI: 10.1158/1078-0432.ccr-20-0468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/10/2021] [Accepted: 02/04/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Proficient DNA repair by homologous recombination (HR) facilitates resistance to chemo-radiation in glioma stem cells (GSCs). We evaluated whether compromising HR by targeting HSP90, a molecular chaperone required for the function of key HR proteins, using onalespib, a long-acting, brain-penetrant HSP90 inhibitor, would sensitize high-grade gliomas to chemo-radiation in vitro and in vivo Experimental Design: The ability of onalespib to deplete HR client proteins, impair HR repair capacity, and sensitize GBM to chemo-radiation was evaluated in vitro in GSCs, and in vivo using zebrafish and mouse intracranial glioma xenograft models. The effects of HSP90 inhibition on the transcriptome and cytoplasmic proteins was assessed in GSCs and in ex vivo organotypic human glioma slice cultures. RESULTS Treatment with onalespib depleted CHK1 and RAD51, two key proteins of the HR pathway, and attenuated HR repair, sensitizing GSCs to the combination of radiation and temozolomide (TMZ). HSP90 inhibition reprogrammed the transcriptome of GSCs and broadly altered expression of cytoplasmic proteins including known and novel client proteins relevant to GSCs. The combination of onalespib with radiation and TMZ extended survival in a zebra fish and a mouse xenograft model of GBM compared to the standard of care (radiation and TMZ) or onalespib with radiation. CONCLUSIONS The results of this study demonstrate that targeting HR by HSP90 inhibition sensitizes GSCs to radiation and chemotherapy and extends survival in zebrafish and mouse intracranial models of GBM. These results provide a preclinical rationale for assessment of HSP90 inhibitors in combination with chemoradiation in GBM patients.
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Affiliation(s)
- Jihong Xu
- Neuro-Oncology, The University of Texas MD Anderson Cancer Center
| | - Pei-Jung Wu
- Division of Neuro-oncology, The Ohio State University
| | - Tzung-Huei Lai
- Division of Hematology, Department of Medicine, The Ohio State University
| | - Pratibha Sharma
- Department of Neuro-oncology, The University of Texas MD Anderson Cancer Center
| | | | | | | | | | - Frederick F Lang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center
| | - Naduparambil K Jacob
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center
| | - J Bradley Elder
- Dardinger Neuro-Oncology Center, Department of Neurosurgery, The Ohio State University
| | - Russell Lonser
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke
| | | | | | - Deepa Sampath
- Hematopoeitic Biology and Malignancy, The University of Texas MD Anderson Cancer Center
| | - Vinay K Puduvalli
- Department of Neuro-oncology, The University of Texas MD Anderson Cancer Center
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Nanotherapeutics approaches to overcome P-glycoprotein-mediated multi-drug resistance in cancer. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 40:102494. [PMID: 34775061 DOI: 10.1016/j.nano.2021.102494] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/08/2021] [Accepted: 10/27/2021] [Indexed: 12/19/2022]
Abstract
Multidrug resistance (MDR) in cancer chemotherapy is a growing concern for medical practitioners. P-glycoprotein (P-gp) overexpression is one of the major reasons for multidrug resistance in cancer chemotherapy. The P-gp overexpression in cancer cells depends on several factors like adenosine triphosphate (ATP) hydrolysis, hypoxia-inducible factor 1 alpha (HIF-1α), and drug physicochemical properties such as lipophilicity, molecular weight, and molecular size. Further multiple exposures of anticancer drugs to the P-gp efflux protein cause acquired P-gp overexpression. Unique structural and functional characteristics of nanotechnology-based drug delivery systems provide opportunities to circumvent P-gp mediated MDR. The primary mechanism behind the nanocarrier systems in P-gp inhibition includes: bypassing or inhibiting the P-gp efflux pump to combat MDR. In this review, we discuss the role of P-gp in MDR and highlight the recent progress in different nanocarriers to overcome P-gp mediated MDR in terms of their limitations and potentials.
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Functional expression of human arylamine N-acetyltransferase NAT1*10 and NAT1*11 alleles: a mini review. Pharmacogenet Genomics 2019; 28:238-244. [PMID: 30222709 DOI: 10.1097/fpc.0000000000000350] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The arylamine N-acetyltransferase (NAT) nomenclature committee assigns functional phenotypes for human arylamine N-acetyltransferase 1 (NAT1) alleles in those instances in which the committee determined a consensus has been achieved in the scientific literature. In the most recent nomenclature update, the committee announced that functional phenotypes for NAT1*10 and NAT1*11 alleles were not provided owing to a lack of consensus. Phenotypic inconsistencies observed among various studies for NAT1*10 and NAT1*11 may be owing to variable allelic expression among different tissues, the limitations of the genotyping assays (which mostly relied on techniques not involving direct DNA sequencing), the differences in recombinant protein expression systems used (bacteria, yeast, and mammalian cell lines) and/or the known inherent instability of human NAT1 protein, which requires very careful handling of native and recombinant cell lysates. Three recent studies provide consistent evidence of the mechanistic basis underlying the functional phenotype of NAT1*10 and NAT1*11 as 'increased-activity' alleles. Some NAT1 variants (e.g. NAT1*14, NAT1*17, and NAT1*22) may be designated as 'decreased-activity' alleles and other NAT1 variants (e.g. NAT1*15 and NAT1*19) may be designated as 'no-activity' alleles compared with the NAT1*4 reference allele. We propose that phenotypic designations as 'rapid' and 'slow' acetylator should be discontinued for NAT1 alleles, although these designations remain very appropriate for NAT2 alleles.
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Dhaini HR, El Hafi B, Khamis AM. NAT1 genotypic and phenotypic contribution to urinary bladder cancer risk: a systematic review and meta-analysis. Drug Metab Rev 2017; 50:208-219. [PMID: 29258340 DOI: 10.1080/03602532.2017.1415928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
N-acetyltransferase 1 (NAT1), a polymorphic Phase II enzyme, plays an essential role in metabolizing heterocyclic and aromatic amines, which are implicated in urinary bladder cancer (BCa). This systematic review investigates a possible association between the different NAT1 genetic polymorphisms and BCa risk. Medline, PubMed, EMBASE, Scopus, Web of Science, OpenGrey, and BASE databases were searched to identify eligible studies. The random-effect model was used to calculate pooled effects estimates. Statistical heterogeneity was tested with Chi-square and I2. Twenty case-control studies, including 5606 cases and 6620 controls, met the inclusion criteria. Pooled odds ratios (OR) analyses showed a statistically significant difference in NAT1*10 versus non-NAT1*10 acetylators in the total sample (OR: 0.87; 95% CI: 0.79-0.96) but was borderline among Caucasians (OR: 0.88 with 95% CI: 0.77-1.01). No statistically significant differences in BCa risk were found for: NAT1*10 versus NAT1*4 wild type (OR: 0.97; 95% CI: 0.78-1.19), NAT1 'Fast' versus 'Normal' acetylators (OR: 1.03; 95% CI: 0.84-1.27), and NAT1 'Slow' versus 'Fast' (OR: 2.32; 95% CI: 0.93-5.84) or 'Slow' versus 'Normal' acetylators (OR: 1.84; 95% CI: 0.92-3.68). When stratifying by smoking status, no statistically significant differences in BCa risk were found for NAT1*10 versus non-NAT1*10 acetylators among the different subgroups. Our study suggests a modest protective role for NAT1*10 and a possible risk contributory role for slow acetylation genotypes in BCa risk. Further research is recommended to confirm these associations.
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Affiliation(s)
- Hassan R Dhaini
- a Department of Environmental Health, Faculty of Health Sciences , American University of Beirut , Beirut , Lebanon
| | - Bassam El Hafi
- b Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine , American University of Beirut , Beirut , Lebanon
| | - Assem M Khamis
- c Faculty of Medicine , Clinical Research Institute, American University of Beirut , Beirut , Lebanon
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Sá ACC, Sadee W, Johnson JA. Whole Transcriptome Profiling: An RNA-Seq Primer and Implications for Pharmacogenomics Research. Clin Transl Sci 2017; 11:153-161. [PMID: 28945944 PMCID: PMC5866981 DOI: 10.1111/cts.12511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/03/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Ana Caroline C Sá
- Center for Pharmacogenomics & Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Genetics & Genomic Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics, Department of Cancer Biology and Genetic, College of Medicine, Ohio State University, Columbus, Ohio, USA
| | - Julie A Johnson
- Center for Pharmacogenomics & Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Genetics & Genomic Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida, USA.,Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, Florida, USA
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10
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Protein-Coding Genes' Retrocopies and Their Functions. Viruses 2017; 9:v9040080. [PMID: 28406439 PMCID: PMC5408686 DOI: 10.3390/v9040080] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of “relaxed” selection and remain “dormant” because they are lacking regulatory regions; however, many become functional. In the course of evolution, they may undergo subfunctionalization, neofunctionalization, or replace their progenitors. Functional retrocopies (retrogenes) can encode proteins, novel or similar to those encoded by their progenitors, can be used as alternative exons or create chimeric transcripts, and can also be involved in transcriptional interference and participate in the epigenetic regulation of parental gene expression. They can also act in trans as natural antisense transcripts, microRNA (miRNA) sponges, or a source of various small RNAs. Moreover, many retrocopies of protein-coding genes are linked to human diseases, especially various types of cancer.
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Abstract
This paper is the thirty-eighth consecutive installment of the annual review of research concerning the endogenous opioid system. It summarizes papers published during 2015 that studied the behavioral effects of molecular, pharmacological and genetic manipulation of opioid peptides, opioid receptors, opioid agonists and opioid antagonists. The particular topics that continue to be covered include the molecular-biochemical effects and neurochemical localization studies of endogenous opioids and their receptors related to behavior, and the roles of these opioid peptides and receptors in pain and analgesia, stress and social status, tolerance and dependence, learning and memory, eating and drinking, drug abuse and alcohol, sexual activity and hormones, pregnancy, development and endocrinology, mental illness and mood, seizures and neurologic disorders, electrical-related activity and neurophysiology, general activity and locomotion, gastrointestinal, renal and hepatic functions, cardiovascular responses, respiration and thermoregulation, and immunological responses.
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Affiliation(s)
- Richard J Bodnar
- Department of Psychology and Neuropsychology Doctoral Sub-Program, Queens College, City University of New York, Flushing, NY 11367, United States.
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12
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Pietrzak M, Papp A, Curtis A, Handelman SK, Kataki M, Scharre DW, Rempala G, Sadee W. Gene expression profiling of brain samples from patients with Lewy body dementia. Biochem Biophys Res Commun 2016; 479:875-880. [PMID: 27666482 DOI: 10.1016/j.bbrc.2016.09.114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/22/2016] [Indexed: 11/28/2022]
Abstract
Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative disorder in the elderly. The development and progression of DLB remain unclear. In this study we used next generation sequencing to assess RNA expression profiles and cellular processes associated with DLB in the anterior cingulate cortex, a brain region affected by DLB pathology. The expression measurements were made in autopsy brain tissues from 8 DLB subjects and 10 age-matched controls using AmpliSeq technology with ion torrent sequencing. The analysis of RNA expression profiles revealed 490 differentially expressed genes, among which 367 genes were down-regulated and 123 were up-regulated. Functional enrichment analysis of genes differentially expressed in DLB indicated downregulation of genes associated with myelination, neurogenesis, and regulation of nervous system development. miRNA binding sites enriched in these mRNAs yielded a list of candidate miRNAs participating in DLB pathophysiology. Our study provides a comprehensive picture of gene expression landscape in DLB, identifying key cellular processes associated with DLB pathology.
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Affiliation(s)
- Maciej Pietrzak
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA; Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, USA
| | - Audrey Papp
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Amanda Curtis
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Samuel K Handelman
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Maria Kataki
- Department of Neurology, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Douglas W Scharre
- Department of Neurology, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Grzegorz Rempala
- Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, USA; Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA.
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Nam JW, Choi SW, You BH. Incredible RNA: Dual Functions of Coding and Noncoding. Mol Cells 2016; 39:367-74. [PMID: 27137091 PMCID: PMC4870183 DOI: 10.14348/molcells.2016.0039] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/20/2016] [Accepted: 03/29/2016] [Indexed: 11/27/2022] Open
Abstract
Since the RNA world hypothesis was proposed, a large number of regulatory noncoding RNAs (ncRNAs) have been identified in many species, ranging from microorganisms to mammals. During the characterization of these newly discovered RNAs, RNAs having both coding and noncoding functions were discovered, and these were considered bifunctional RNAs. The recent use of computational and high-throughput experimental approaches has revealed increasing evidence of various sources of bifunctional RNAs, such as protein-coding mRNAs with a noncoding isoform and long ncRNAs bearing a small open reading frame. Therefore, the genomic diversity of Janus-faced RNA molecules that have dual characteristics of coding and noncoding indicates that the functional roles of RNAs have to be revisited in cells on a genome-wide scale. Such studies would allow us to further understand the complex gene-regulatory network in cells. In this review, we discuss three major genomic sources of bifunctional RNAs and present a handful of examples of bifunctional RNA along with their functional roles.
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Affiliation(s)
- Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763,
Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763,
Korea
| | - Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763,
Korea
| | - Bo-Hyun You
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763,
Korea
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