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Demin DE, Murashko MM, Uvarova AN, Stasevich EM, Shyrokova EY, Gorlachev GE, Zaretsky AR, Korneev KV, Ustiugova AS, Tkachenko EA, Kostenko VV, Tatosyan KA, Sheetikov SA, Spirin PV, Kuprash DV, Schwartz AM. Adversary of DNA integrity: A long non-coding RNA stimulates driver oncogenic chromosomal rearrangement in human thyroid cells. Int J Cancer 2023; 152:1452-1462. [PMID: 36510744 DOI: 10.1002/ijc.34396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/01/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
The flurry of publications devoted to the functions of long non-coding RNAs (lncRNAs) published in the last decade leaves no doubt about the exceptional importance of lncRNAs in various areas including tumor biology. However, contribution of lncRNAs to the early stages of oncogenesis remains poorly understood. In this study we explored a new role for lncRNAs: stimulation of specific chromosomal rearrangements upon DNA damage. We demonstrated that lncRNA CASTL1 (ENSG00000269945) stimulates the formation of the CCDC6-RET inversion (RET/PTC1) in human thyroid cells subjected to radiation or chemical DNA damage. Facilitation of chromosomal rearrangement requires lncRNA to contain regions complementary to the introns of both CCDC6 and RET genes as deletion of these regions deprives CASTL1 of the ability to stimulate the gene fusion. We found that CASTL1 expression is elevated in tumors with CCDC6-RET fusion which is the most frequent rearrangement in papillary thyroid carcinoma. Our results open a new venue for the studies of early oncogenesis in various tumor types, especially those associated with physical or chemical DNA damage.
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Affiliation(s)
- Denis Eriksonovich Demin
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Matvey Mikhailovich Murashko
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Aksinya Nicolaevna Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Mikhailovna Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena Yurievna Shyrokova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia.,Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrew Rostislavovich Zaretsky
- Department of Molecular Technologies, Research Institute of Translational Medicine, N. I. Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation
| | - Kirill Viktorovich Korneev
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,National Research Center for Hematology, Moscow, Russia
| | - Alina Sergeevna Ustiugova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena Andreevna Tkachenko
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Valentina Vitalevna Kostenko
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Karina Aleksandrovna Tatosyan
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Saveliy Andreevich Sheetikov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,National Research Center for Hematology, Moscow, Russia
| | - Pavel Vladimirovich Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Vladimirovich Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anton Markovich Schwartz
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Zhang R, Ge F, Li H, Chen Y, Zhao Y, Gao Y, Liu Z, Yang L. PCIR: a database of Plant Chloroplast Inverted Repeats. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5611292. [PMID: 31696928 PMCID: PMC6835207 DOI: 10.1093/database/baz127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/26/2019] [Accepted: 10/07/2019] [Indexed: 01/06/2023]
Abstract
Inverted repeats (IRs) serve as potential biomarkers for genomic instability, DNA replication and other genetic processes. However, little information can be found in databases to help researchers recognize potential IR nucleotides, explore junction sites and annotate related functional genes. Plant Chloroplast Inverted Repeats (PCIR) is an interactive, web-based platform containing various sequenced chloroplast genomes that enables detection, searching and visualization of large-scale detailed information on IRs. PCIR contains many datasets, including 21 433 IRs, 113 plants chloroplast genomes, 16 948 functional genes and 21 659 visual maps. This database offers an online prediction tool for detecting IRs based on DNA sequences. PCIR can also analyze phylogenetic relationships using IR information among different species and provide users with high-quality marker maps. This database will be a valuable resource for IR distribution patterns, related genes and architectural features.
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Affiliation(s)
- Rui Zhang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Fangfang Ge
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Huayang Li
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Yudong Chen
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Ying Zhao
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Ying Gao
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Zhiguo Liu
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Long Yang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
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Nikitin D, Penzar D, Garazha A, Sorokin M, Tkachev V, Borisov N, Poltorak A, Prassolov V, Buzdin AA. Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins. Front Immunol 2018; 9:30. [PMID: 29441061 PMCID: PMC5797644 DOI: 10.3389/fimmu.2018.00030] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022] Open
Abstract
Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS). Most of REs hosting TFBS were highly diverged repeats, and for the evolutionary young (0–8% diverged) elements we identified only ~7% of all RE-linked TFBS. The gene-specific distributions of RE-linked TFBS generally correlated with the distributions for all TFBS. However, several groups of molecular processes were highly enriched in the RE-linked TFBS regulation. They were strongly connected with the immunity and response to pathogens, with the negative regulation of gene transcription, ubiquitination, and protein degradation, extracellular matrix organization, regulation of STAT signaling, fatty acids metabolism, regulation of GTPase activity, protein targeting to Golgi, regulation of cell division and differentiation, development and functioning of perception organs and reproductive system. By contrast, the processes most weakly affected by the REs were linked with the conservative aspects of embryo development. We also identified differences in the regulation features by the younger and older fractions of the REs. The regulation by the older fraction of the REs was linked mainly with the immunity, cell adhesion, cAMP, IGF1R, Notch, Wnt, and integrin signaling, neuronal development, chondroitin sulfate and heparin metabolism, and endocytosis. The younger REs regulate other aspects of immunity, cell cycle progression and apoptosis, PDGF, TGF beta, EGFR, and p38 signaling, transcriptional repression, structure of nuclear lumen, catabolism of phospholipids, and heterocyclic molecules, insulin and AMPK signaling, retrograde Golgi-ER transport, and estrogen signaling. The immunity-linked pathways were highly represented in both categories, but their functional roles were different and did not overlap. Our results point to the most quickly evolving molecular pathways in the recent and ancient evolution of human genome.
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Affiliation(s)
- Daniil Nikitin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitry Penzar
- The Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Andrew Garazha
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,OmicsWay Corp., Walnut, CA, United States
| | - Maxim Sorokin
- OmicsWay Corp., Walnut, CA, United States.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Nicolas Borisov
- OmicsWay Corp., Walnut, CA, United States.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
| | - Alexander Poltorak
- Program in Immunology, Sackler Graduate School, Tufts University, Boston, MA, United States
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anton A Buzdin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,OmicsWay Corp., Walnut, CA, United States.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
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Buzdin AA, Prassolov V, Garazha AV. Friends-Enemies: Endogenous Retroviruses Are Major Transcriptional Regulators of Human DNA. Front Chem 2017. [PMID: 28642863 PMCID: PMC5462908 DOI: 10.3389/fchem.2017.00035] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Endogenous retroviruses are mobile genetic elements hardly distinguishable from infectious, or “exogenous,” retroviruses at the time of insertion in the host DNA. Human endogenous retroviruses (HERVs) are not rare. They gave rise to multiple families of closely related mobile elements that occupy ~8% of the human genome. Together, they shape genomic regulatory landscape by providing at least ~320,000 human transcription factor binding sites (TFBS) located on ~110,000 individual HERV elements. The HERVs host as many as 155,000 mapped DNaseI hypersensitivity sites, which denote loci active in the regulation of gene expression or chromatin structure. The contemporary view of the HERVs evolutionary dynamics suggests that at the early stages after insertion, the HERV is treated by the host cells as a foreign genetic element, and is likely to be suppressed by the targeted methylation and mutations. However, at the later stages, when significant number of mutations has been already accumulated and when the retroviral genes are broken, the regulatory potential of a HERV may be released and recruited to modify the genomic balance of transcription factor binding sites. This process goes together with further accumulation and selection of mutations, which reshape the regulatory landscape of the human DNA. However, developmental reprogramming, stress or pathological conditions like cancer, inflammation and infectious diseases, can remove the blocks limiting expression and HERV-mediated host gene regulation. This, in turn, can dramatically alter the gene expression equilibrium and shift it to a newer state, thus further amplifying instability and exacerbating the stressful situation.
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Affiliation(s)
- Anton A Buzdin
- Department of Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia.,Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute,"Moscow, Russia
| | - Vladimir Prassolov
- Department of Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Andrew V Garazha
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscow, Russia.,Department of Biomedicine, Moscow Institute of Physics and TechnologyMoscow, Russia
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5
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Garazha A, Ivanova A, Suntsova M, Malakhova G, Roumiantsev S, Zhavoronkov A, Buzdin A. New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome. Cell Cycle 2016; 14:1476-84. [PMID: 25853282 PMCID: PMC4612461 DOI: 10.1080/15384101.2015.1022696] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ∼8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ∼110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of “domestication” of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci.
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Affiliation(s)
- Andrew Garazha
- a Group for Genomic Regulation of Cell Signaling Systems ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry ; Moscow , Russia
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Suntsova M, Garazha A, Ivanova A, Kaminsky D, Zhavoronkov A, Buzdin A. Molecular functions of human endogenous retroviruses in health and disease. Cell Mol Life Sci 2015; 72:3653-75. [PMID: 26082181 PMCID: PMC11113533 DOI: 10.1007/s00018-015-1947-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/29/2015] [Accepted: 06/03/2015] [Indexed: 12/13/2022]
Abstract
Human endogenous retroviruses (HERVs) and related genetic elements form 504 distinct families and occupy ~8% of human genome. Recent success of high-throughput experimental technologies facilitated understanding functional impact of HERVs for molecular machinery of human cells. HERVs encode active retroviral proteins, which may exert important physiological functions in the body, but also may be involved in the progression of cancer and numerous human autoimmune, neurological and infectious diseases. The spectrum of related malignancies includes, but not limits to, multiple sclerosis, psoriasis, lupus, schizophrenia, multiple cancer types and HIV. In addition, HERVs regulate expression of the neighboring host genes and modify genomic regulatory landscape, e.g., by providing regulatory modules like transcription factor binding sites (TFBS). Indeed, recent bioinformatic profiling identified ~110,000 regulatory active HERV elements, which formed at least ~320,000 human TFBS. These and other peculiarities of HERVs might have played an important role in human evolution and speciation. In this paper, we focus on the current progress in understanding of normal and pathological molecular niches of HERVs, on their implications in human evolution, normal physiology and disease. We also review the available databases dealing with various aspects of HERV genetics.
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Affiliation(s)
- Maria Suntsova
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia.
| | - Andrew Garazha
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia.
| | - Alena Ivanova
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
| | - Dmitry Kaminsky
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
| | - Alex Zhavoronkov
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
- Department of Translational and Regenerative Medicine, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow, 141700, Russia.
| | - Anton Buzdin
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, 1, Akademika Kurchatova sq., Moscow, 123182, Russia.
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Lu S, Wang G, Bacolla A, Zhao J, Spitser S, Vasquez KM. Short Inverted Repeats Are Hotspots for Genetic Instability: Relevance to Cancer Genomes. Cell Rep 2015; 10:1674-1680. [PMID: 25772355 DOI: 10.1016/j.celrep.2015.02.039] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 01/26/2015] [Accepted: 02/16/2015] [Indexed: 12/25/2022] Open
Abstract
Analyses of chromosomal aberrations in human genetic disorders have revealed that inverted repeat sequences (IRs) often co-localize with endogenous chromosomal instability and breakage hotspots. Approximately 80% of all IRs in the human genome are short (<100 bp), yet the mutagenic potential of such short cruciform-forming sequences has not been characterized. Here, we find that short IRs are enriched at translocation breakpoints in human cancer and stimulate the formation of DNA double-strand breaks (DSBs) and deletions in mammalian and yeast cells. We provide evidence for replication-related mechanisms of IR-induced genetic instability and a novel XPF cleavage-based mechanism independent of DNA replication. These discoveries implicate short IRs as endogenous sources of DNA breakage involved in disease etiology and suggest that these repeats represent a feature of genome plasticity that may contribute to the evolution of the human genome by providing a means for diversity within the population.
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Affiliation(s)
- Steve Lu
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Albino Bacolla
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Junhua Zhao
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Scott Spitser
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA.
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