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Lee SY, Jeong YW, Choe YH, Oh SJ, Miah R, Lee WJ, Lee SL, Bok EY, Yoo DS, Son YB. Identification of Reference Gene for Quantitative Gene Expression in Early-Term and Late-Term Cultured Canine Fibroblasts Derived from Ear Skin. Animals (Basel) 2024; 14:2722. [PMID: 39335311 PMCID: PMC11429031 DOI: 10.3390/ani14182722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 09/06/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Fibroblasts are cells that reside within the fibrous or loose connective tissues of most mammalian organs. For research purposes, fibroblasts are often subjected to long-term culture under defined conditions, during which their properties can significantly change. It is essential to understand and document these changes to obtain reliable outcomes. For the quantification of specific gene expressions, the most reliable and widely used technique is quantitative real-time polymerase chain reaction (qRT-PCR). Here, we assessed the impact of a reference gene's stability on a qRT-PCR analysis of long-term cultured canine skin fibroblasts. After successfully isolating the fibroblasts from canine skin tissues, they were cultured and evaluated for proliferation and β-galactosidase activity at different passage numbers. With extended culture, the fibroblasts showed a long doubling time and elevated β-galactosidase activity. Using three widely used algorithms, geNorm, Normfinder, and Bestkeeper, we identified HPRT1, YWHAZ, and GUSB as the most stable reference genes for both early- and late-passage fibroblasts. Conventional reference genes such as GAPDH were found to be less stable than those genes. The normalization of Vimentin by the stable genes showed statistical differences, whereas normalization by an unstable gene did not. Collectively, this study indicates that using stable reference genes is essential for accurately and reliably measuring gene expression in both early- and late-passage fibroblasts. These findings provide valuable insights into internal controls for gene expression studies and are expected to be utilized for analyzing gene expression patterns in molecular biology research.
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Affiliation(s)
- Sang-Yun Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 52628, Republic of Korea
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Yeon-Woo Jeong
- Department of Companion Animal and Animal Resources Science, Joongbu University, Geumsan 32713, Republic of Korea
| | - Yong-Ho Choe
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 52628, Republic of Korea
| | - Seong-Ju Oh
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 52628, Republic of Korea
| | - Rubel Miah
- Department of Obstetrics, College of Veterinary Medicine, Chonnam National University, 300 Yonbongdong, Buk-gu, Gwangju 61186, Republic of Korea
| | - Won-Jae Lee
- Department of Obstetrics, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sung-Lim Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 52628, Republic of Korea
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Eun-Yeong Bok
- Division of Animal Diseases & Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Dae-Sung Yoo
- Departement of Veterinary Epidemiology, College of Veterinary Medicine, Chonnam National University, 300 Yonbongdong, Buk-gu, Gwangju 61186, Republic of Korea
| | - Young-Bum Son
- Department of Obstetrics, College of Veterinary Medicine, Chonnam National University, 300 Yonbongdong, Buk-gu, Gwangju 61186, Republic of Korea
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2
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Hu S, Habib A, Xiong W, Chen L, Bi L, Wen L. Mass Spectrometry Imaging Techniques: Non-Ambient and Ambient Ionization Approaches. Crit Rev Anal Chem 2024:1-54. [PMID: 38889072 DOI: 10.1080/10408347.2024.2362703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Molecular information can be acquired from sample surfaces in real time using a revolutionary molecular imaging technique called mass spectrometry imaging (MSI). The technique can concurrently provide high spatial resolution information on the spatial distribution and relative proportion of many different compounds. Thus, many scientists have been drawn to the innovative capabilities of the MSI approach, leading to significant focus in various fields during the past few decades. This review describes the sampling protocol, working principle and applications of a few non-ambient and ambient ionization mass spectrometry imaging techniques. The non-ambient techniques include secondary ionization mass spectrometry and matrix-assisted laser desorption ionization, while the ambient techniques include desorption electrospray ionization, laser ablation electrospray ionization, probe electro-spray ionization, desorption atmospheric pressure photo-ionization and femtosecond laser desorption ionization. The review additionally addresses the advantages and disadvantages of ambient and non-ambient MSI techniques in relation to their suitability, particularly for biological samples used in tissue diagnostics. Last but not least, suggestions and conclusions are made regarding the challenges and future prospects of MSI.
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Affiliation(s)
- Shundi Hu
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Ahsan Habib
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- Department of Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Wei Xiong
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - La Chen
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Lei Bi
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Luhong Wen
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
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3
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Callisto A, Strutz J, Leeper K, Kalhor R, Church G, Tyo KE, Bhan N. Post-translation digital data encoding into the genomes of mammalian cell populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.591851. [PMID: 38765976 PMCID: PMC11100781 DOI: 10.1101/2024.05.12.591851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
High resolution cellular signal encoding is critical for better understanding of complex biological phenomena. DNA-based biosignal encoders alter genomic or plasmid DNA in a signal dependent manner. Current approaches involve the signal of interest affecting a DNA edit by interacting with a signal specific promoter which then results in expression of the effector molecule (DNA altering enzyme). Here, we present the proof of concept of a biosignal encoding system where the enzyme terminal deoxynucleotidyl transferase (TdT) acts as the effector molecule upon directly interacting with the signal of interest. A template independent DNA polymerase (DNAp), TdT incorporates nucleotides at the 3' OH ends of DNA substrate in a signal dependent manner. By employing CRISPR-Cas9 to create double stranded breaks in genomic DNA, we make 3'OH ends available to act as substrate for TdT. We show that this system can successfully resolve and encode different concentrations of various biosignals into the genomic DNA of HEK-293T cells. Finally, we develop a simple encoding scheme associated with the tested biosignals and encode the message "HELLO WORLD" into the genomic DNA of HEK-293T cells at a population level with 91% accuracy. This work demonstrates a simple and engineerable system that can reliably store local biosignal information into the genomes of mammalian cell populations.
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Affiliation(s)
- Alec Callisto
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Jonathan Strutz
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Kathleen Leeper
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Reza Kalhor
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Keith E.J. Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Namita Bhan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Biomedical Research at Novartis, Cambridge, MA, USA
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4
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Tian Q, Chung H, Wen D. The role of lipids in genome integrity and pluripotency. Biochem Soc Trans 2024; 52:639-650. [PMID: 38506536 PMCID: PMC11088914 DOI: 10.1042/bst20230479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
Pluripotent stem cells (PSCs), comprising embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), offer immense potential for regenerative medicine due to their ability to differentiate into all cell types of the adult body. A critical aspect of harnessing this potential is understanding their metabolic requirements during derivation, maintenance, and differentiation in vitro. Traditional culture methods using fetal bovine serum often lead to issues such as heterogeneous cell populations and diminished pluripotency. Although the chemically-defined 2i/LIF medium has provided solutions to some of these challenges, prolonged culturing of these cells, especially female ESCs, raises concerns related to genome integrity. This review discusses the pivotal role of lipids in genome stability and pluripotency of stem cells. Notably, the introduction of lipid-rich albumin, AlbuMAX, into the 2i/LIF culture medium offers a promising avenue for enhancing the genomic stability and pluripotency of cultured ESCs. We further explore the unique characteristics of lipid-induced pluripotent stem cells (LIP-ESCs), emphasizing their potential in regenerative medicine and pluripotency research.
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Affiliation(s)
- Qiyu Tian
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Hoyoung Chung
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
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5
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Yan J, Wu J, Xu M, Wang M, Guo W. Disrupted de novo pyrimidine biosynthesis impairs adult hippocampal neurogenesis and cognition in pyridoxine-dependent epilepsy. SCIENCE ADVANCES 2024; 10:eadl2764. [PMID: 38579001 PMCID: PMC10997211 DOI: 10.1126/sciadv.adl2764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Despite seizure control by early high-dose pyridoxine (vitamin B6) treatment, at least 75% of pyridoxine-dependent epilepsy (PDE) patients with ALDH7A1 mutation still suffer from intellectual disability. It points to a need for additional therapeutic interventions for PDE beyond pyridoxine treatment, which provokes us to investigate the mechanisms underlying the impairment of brain hemostasis by ALDH7A1 deficiency. In this study, we show that ALDH7A1-deficient mice with seizure control exhibit altered adult hippocampal neurogenesis and impaired cognitive functions. Mechanistically, ALDH7A1 deficiency leads to the accumulation of toxic lysine catabolism intermediates, α-aminoadipic-δ-semialdehyde and its cyclic form, δ-1-piperideine-6-carboxylate, which in turn impair de novo pyrimidine biosynthesis and inhibit NSC proliferation and differentiation. Notably, supplementation of pyrimidines rescues abnormal neurogenesis and cognitive impairment in ALDH7A1-deficient adult mice. Therefore, our findings not only define the important role of ALDH7A1 in the regulation of adult hippocampal neurogenesis but also provide a potential therapeutic intervention to ameliorate the defective mental capacities in PDE patients with seizure control.
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Affiliation(s)
- Jianfei Yan
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100093, China
| | - Junjie Wu
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100093, China
| | - Mingyue Xu
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100093, China
| | - Min Wang
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weixiang Guo
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100093, China
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6
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Wolf-Johnston A, Ikeda Y, Zabbarova I, Kanai AJ, Bastacky S, Moldwin R, Stern JN, Jackson EK, Birder LA. Purine nucleoside phosphorylase inhibition is an effective approach for the treatment of chemical hemorrhagic cystitis. JCI Insight 2024; 9:e176103. [PMID: 38271096 PMCID: PMC10972598 DOI: 10.1172/jci.insight.176103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/22/2024] [Indexed: 01/27/2024] Open
Abstract
Hemorrhagic cystitis may be induced by infection, radiation therapy, or medications or may be idiopathic. Along with hemorrhagic features, symptoms include urinary urgency and frequency, dysuria (painful urination), and visceral pain. Cystitis-induced visceral pain is one of the most challenging types of pain to treat, and an effective treatment would address a major unmet medical need. We assessed the efficacy of a purine nucleoside phosphorylase inhibitor, 8-aminoguanine (8-AG), for the treatment of hemorrhagic/ulcerative cystitis. Lower urinary tract (LUT) function and structure were assessed in adult Sprague-Dawley rats, treated chronically with cyclophosphamide (CYP; sacrificed day 8) and randomized to daily oral treatment with 8-AG (begun 14 days prior to CYP induction) or its vehicle. CYP-treated rats exhibited multiple abnormalities, including increased urinary frequency and neural mechanosensitivity, reduced bladder levels of inosine, urothelial inflammation/damage, and activation of spinal cord microglia, which is associated with pain hypersensitivity. 8-AG treatment of CYP-treated rats normalized all observed histological, structural, biochemical, and physiological abnormalities. In cystitis 8-AG improved function and reduced both pain and inflammation likely by increasing inosine, a tissue-protective purine metabolite. These findings demonstrate that 8-AG has translational potential for reducing pain and preventing bladder damage in cystitis-associated LUT dysfunctions.
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Affiliation(s)
| | - Youko Ikeda
- Renal-Electrolyte Division, Department of Medicine
| | | | - Anthony J Kanai
- Renal-Electrolyte Division, Department of Medicine
- Department of Pharmacology and Chemical Biology; and
| | - Sheldon Bastacky
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert Moldwin
- Arthur Smith Institute for Urology, Northwell Health, Zucker School of Medicine at Hofstra/Northwell, Lake Success, New York, USA
| | - Joel Nh Stern
- Arthur Smith Institute for Urology, Northwell Health, Zucker School of Medicine at Hofstra/Northwell, Lake Success, New York, USA
| | | | - Lori A Birder
- Renal-Electrolyte Division, Department of Medicine
- Department of Pharmacology and Chemical Biology; and
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7
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Marghany F, Ayobahan SU, Salinas G, Schäfers C, Hollert H, Eilebrecht S. Transcriptomic and proteomic fingerprints induced by the fungicides difenoconazole and metalaxyl in zebrafish embryos. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 105:104348. [PMID: 38135202 DOI: 10.1016/j.etap.2023.104348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
In this study, we applied OMICs analysis to identify substance-specific biomarker candidates, which may act as early indicators for specific ecotoxic modes of actions (MoA). Zebrafish embryos were exposed to two sublethal concentrations of difenoconazole and metalaxyl according to a modified protocol of the OECD test guideline No. 236. At the end of exposure, total RNA and protein were extracted, followed by transcriptomics and proteomics analysis. The analysis of significantly differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) revealed a positive exposure-response correlation in all test concentrations for both fungicides. Similarly, also a positive correlation between the obtained transcriptome and proteome data was observed, highlighting the robustness of our approach. From the detected DEGs, candidate biomarkers specific for difenoconazole (apoa1b, gatm, mylpfb and acta1b) and metalaxyl (lgals2b, abat, fabp1b.1 and myh9a) were selected, and their biological functions were discussed to assess the predictive potential.
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Affiliation(s)
- Fatma Marghany
- Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany; Department Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany; Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
| | - Steve U Ayobahan
- Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | - Gabriela Salinas
- NGS-Services for Integrative Genomics, University of Göttingen, Göttingen, Germany
| | - Christoph Schäfers
- Department Ecotoxicology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | - Henner Hollert
- Department Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany; Department Environmental Media Related Ecotoxicology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | - Sebastian Eilebrecht
- Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany.
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8
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Zhong L, Gordillo M, Wang X, Qin Y, Huang Y, Soshnev A, Kumar R, Nanjangud G, James D, David Allis C, Evans T, Carey B, Wen D. Dual role of lipids for genome stability and pluripotency facilitates full potency of mouse embryonic stem cells. Protein Cell 2023; 14:591-602. [PMID: 37029701 PMCID: PMC10392030 DOI: 10.1093/procel/pwad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/09/2023] [Indexed: 02/18/2023] Open
Abstract
While Mek1/2 and Gsk3β inhibition ("2i") supports the maintenance of murine embryonic stem cells (ESCs) in a homogenous naïve state, prolonged culture in 2i results in aneuploidy and DNA hypomethylation that impairs developmental potential. Additionally, 2i fails to support derivation and culture of fully potent female ESCs. Here we find that mouse ESCs cultured in 2i/LIF supplemented with lipid-rich albumin (AlbuMAX) undergo pluripotency transition yet maintain genomic stability and full potency over long-term culture. Mechanistically, lipids in AlbuMAX impact intracellular metabolism including nucleotide biosynthesis, lipid biogenesis, and TCA cycle intermediates, with enhanced expression of DNMT3s that prevent DNA hypomethylation. Lipids induce a formative-like pluripotent state through direct stimulation of Erk2 phosphorylation, which also alleviates X chromosome loss in female ESCs. Importantly, both male and female "all-ESC" mice can be generated from de novo derived ESCs using AlbuMAX-based media. Our findings underscore the importance of lipids to pluripotency and link nutrient cues to genome integrity in early development.
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Affiliation(s)
- Liangwen Zhong
- Department of Reproductive Medicine, Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Miriam Gordillo
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Xingyi Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yiren Qin
- Department of Reproductive Medicine, Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yuanyuan Huang
- Department of Reproductive Medicine, Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alexey Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
| | - Ritu Kumar
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
- Gladstone Institutes, 1650 Owens St, San Francisco, CA 94158, USA
| | - Gouri Nanjangud
- Molecular Cytogenetics Core. Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daylon James
- Department of Reproductive Medicine, Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Bryce Carey
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Duancheng Wen
- Department of Reproductive Medicine, Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, USA
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9
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Lancaster MS, Graham BH. Succinyl-CoA Synthetase Dysfunction as a Mechanism of Mitochondrial Encephalomyopathy: More than Just an Oxidative Energy Deficit. Int J Mol Sci 2023; 24:10725. [PMID: 37445899 PMCID: PMC10342173 DOI: 10.3390/ijms241310725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Biallelic pathogenic variants in subunits of succinyl-CoA synthetase (SCS), a tricarboxylic acid (TCA) cycle enzyme, are associated with mitochondrial encephalomyopathy in humans. SCS catalyzes the interconversion of succinyl-CoA to succinate, coupled to substrate-level phosphorylation of either ADP or GDP, within the TCA cycle. SCS-deficient encephalomyopathy typically presents in infancy and early childhood, with many patients succumbing to the disease during childhood. Common symptoms include abnormal brain MRI, basal ganglia lesions and cerebral atrophy, severe hypotonia, dystonia, progressive psychomotor regression, and growth deficits. Although subunits of SCS were first identified as causal genes for progressive metabolic encephalomyopathy in the early 2000s, recent investigations are now beginning to unravel the pathomechanisms underlying this metabolic disorder. This article reviews the current understanding of SCS function within and outside the TCA cycle as it relates to the complex and multifactorial mechanisms underlying SCS-related mitochondrial encephalomyopathy.
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Affiliation(s)
| | - Brett H. Graham
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, 975 W. Walnut St., Room IB257, Indianapolis, IN 46202, USA;
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10
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Persaud AK, Bernier MC, Massey MA, Agrawal S, Kaur T, Nayak D, Xie Z, Weadick B, Raj R, Hill K, Abbott N, Joshi A, Anabtawi N, Bryant C, Somogyi A, Cruz-Monserrate Z, Amari F, Coppola V, Sparreboom A, Baker SD, Unadkat JD, Phelps MA, Govindarajan R. Increased renal elimination of endogenous and synthetic pyrimidine nucleosides in concentrative nucleoside transporter 1 deficient mice. Nat Commun 2023; 14:3175. [PMID: 37264059 PMCID: PMC10235067 DOI: 10.1038/s41467-023-38789-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Concentrative nucleoside transporters (CNTs) are active nucleoside influx systems, but their in vivo roles are poorly defined. By generating CNT1 knockout (KO) mice, here we identify a role of CNT1 in the renal reabsorption of nucleosides. Deletion of CNT1 in mice increases the urinary excretion of endogenous pyrimidine nucleosides with compensatory alterations in purine nucleoside metabolism. In addition, CNT1 KO mice exhibits high urinary excretion of the nucleoside analog gemcitabine (dFdC), which results in poor tumor growth control in CNT1 KO mice harboring syngeneic pancreatic tumors. Interestingly, increasing the dFdC dose to attain an area under the concentration-time curve level equivalent to that achieved by wild-type (WT) mice rescues antitumor efficacy. The findings provide new insights into how CNT1 regulates reabsorption of endogenous and synthetic nucleosides in murine kidneys and suggest that the functional status of CNTs may account for the optimal action of pyrimidine nucleoside analog therapeutics in humans.
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Affiliation(s)
- Avinash K Persaud
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew C Bernier
- Campus Chemical Instrument Center Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael A Massey
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- The Center for Life Sciences Education, College of Arts and Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Shipra Agrawal
- Division of Nephrology & Hypertension, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Tejinder Kaur
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Debasis Nayak
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhiliang Xie
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Brenna Weadick
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Ruchika Raj
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Kasey Hill
- Pharmacoanalytic Shared Resource (PhASR), The Ohio State University, Columbus, OH, 43205, USA
| | - Nicole Abbott
- Pharmacoanalytic Shared Resource (PhASR), The Ohio State University, Columbus, OH, 43205, USA
| | - Arnav Joshi
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Nadeen Anabtawi
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Claire Bryant
- Center for Clinical & Translational Research, Nationwide Children's Hospital, Columbus, OH, 43210, USA
| | - Arpad Somogyi
- Campus Chemical Instrument Center Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH, 43210, USA
| | - Zobeida Cruz-Monserrate
- Division of Gastroenterology, Hepatology, and Nutrition, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Foued Amari
- Genetically Engineered Mouse Modeling Core, Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Vincenzo Coppola
- Genetically Engineered Mouse Modeling Core, Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Alex Sparreboom
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Sharyn D Baker
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Jashvant D Unadkat
- Department of Pharmaceutics, College of Pharmacy, University of Washington, Seattle, WA, 98195, USA
- Translational Therapeutics, Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH, 43210, USA
| | - Mitch A Phelps
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- Pharmacoanalytic Shared Resource (PhASR), The Ohio State University, Columbus, OH, 43205, USA
| | - Rajgopal Govindarajan
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA.
- Translational Therapeutics, Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH, 43210, USA.
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11
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Costello SM, Cheney AM, Waldum A, Tripet B, Cotrina-Vidal M, Kaufmann H, Norcliffe-Kaufmann L, Lefcort F, Copié V. A Comprehensive NMR Analysis of Serum and Fecal Metabolites in Familial Dysautonomia Patients Reveals Significant Metabolic Perturbations. Metabolites 2023; 13:metabo13030433. [PMID: 36984872 PMCID: PMC10057143 DOI: 10.3390/metabo13030433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Central metabolism has a profound impact on the clinical phenotypes and penetrance of neurological diseases such as Alzheimer’s (AD) and Parkinson’s (PD) diseases, Amyotrophic Lateral Sclerosis (ALS) and Autism Spectrum Disorder (ASD). In contrast to the multifactorial origin of these neurological diseases, neurodevelopmental impairment and neurodegeneration in Familial Dysautonomia (FD) results from a single point mutation in the ELP1 gene. FD patients represent a well-defined population who can help us better understand the cellular networks underlying neurodegeneration, and how disease traits are affected by metabolic dysfunction, which in turn may contribute to dysregulation of the gut–brain axis of FD. Here, 1H NMR spectroscopy was employed to characterize the serum and fecal metabolomes of FD patients, and to assess similarities and differences in the polar metabolite profiles between FD patients and healthy relative controls. Findings from this work revealed noteworthy metabolic alterations reflected in energy (ATP) production, mitochondrial function, amino acid and nucleotide catabolism, neurosignaling molecules, and gut-microbial metabolism. These results provide further evidence for a close interconnection between metabolism, neurodegeneration, and gut microbiome dysbiosis in FD, and create an opportunity to explore whether metabolic interventions targeting the gut–brain–metabolism axis of FD could be used to redress or slow down the progressive neurodegeneration observed in FD patients.
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Affiliation(s)
- Stephanann M. Costello
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Alexandra M. Cheney
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Annie Waldum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Brian Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Maria Cotrina-Vidal
- Department of Neurology, New York University School of Medicine, New York, NY 10017, USA
| | - Horacio Kaufmann
- Department of Neurology, New York University School of Medicine, New York, NY 10017, USA
| | | | - Frances Lefcort
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
- Correspondence: ; Tel.: +1-406-994-7244
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12
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Liu J, Qi M, Yuan Z, Wong TY, Song X, Lam H. Nontargeted metabolomics reveals differences in the metabolite profiling among methicillin-resistant and methicillin-susceptible Staphylococcus aureus in response to antibiotics. Mol Omics 2022; 18:948-956. [PMID: 36218091 DOI: 10.1039/d2mo00229a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Staphylococcus aureus (S. aureus) causes infections and can be fatal. In the long-term struggle against antibiotics, S. aureus has acquired resistance toward antibiotics and become more difficult to kill. Metabolomics could directly reflect the responses of S. aureus toward antibiotics, which is effective for studying the resistance mechanism of S. aureus. In this study, based on a nontargeted metabolic figure printing technique, the metabolome of a pair of isogenic methicillin-susceptible and resistant S. aureus strains ATCC25923 (MSSA) and ATCC43300 (MRSA) treated with or without oxacillin was characterized. 7 and 29 significantly changed metabolites in MRSA and MSSA were identified by combined accurate mass and mass fragmentation analysis. Pathway enrichment analysis suggested that DNA repair and flavin biosynthesis are the universal pathways of both MSSA and MRSA under antibiotic stress. MRSA systematically and effectively fights against oxacillin through precise control of energy production, PBP2a substrate biosynthesis and antioxidant function. In contrast, MSSA lacks effective defense pathways against oxacillin. The different metabolome responses of MSSA and MRSA toward antibiotics provide us with new insights into how S. aureus develops antibiotic resistance.
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Affiliation(s)
- Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China. .,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Mingyang Qi
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
| | - Zichen Yuan
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Tin Yan Wong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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13
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Borowik AK, Davidyan A, Peelor FF, Voloviceva E, Doidge SM, Bubak MP, Mobley CB, McCarthy JJ, Dupont-Versteegden EE, Miller BF. Skeletal Muscle Nuclei in Mice are not Post-mitotic. FUNCTION 2022; 4:zqac059. [PMID: 36569816 PMCID: PMC9772608 DOI: 10.1093/function/zqac059] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
The skeletal muscle research field generally accepts that nuclei in skeletal muscle fibers (ie, myonuclei) are post-mitotic and unable to proliferate. Because our deuterium oxide (D2O) labeling studies showed DNA synthesis in skeletal muscle tissue, we hypothesized that resident myonuclei can replicate in vivo. To test this hypothesis, we used a mouse model that temporally labeled myonuclei with GFP followed by D2O labeling during normal cage activity, functional overload, and with satellite cell ablation. During normal cage activity, we observed deuterium enrichment into myonuclear DNA in 7 out of 7 plantaris (PLA), 6 out of 6 tibialis anterior (TA), 5 out of 7 gastrocnemius (GAST), and 7 out of 7 quadriceps (QUAD). The average fractional synthesis rates (FSR) of DNA in myonuclei were: 0.0202 ± 0.0093 in PLA, 0.0239 ± 0.0040 in TA, 0.0076 ± 0. 0058 in GAST, and 0.0138 ± 0.0039 in QUAD, while there was no replication in myonuclei from EDL. These FSR values were largely reproduced in the overload and satellite cell ablation conditions, although there were higher synthesis rates in the overloaded PLA muscle. We further provided evidence that myonuclear replication is through endoreplication, which results in polyploidy. These novel findings contradict the dogma that skeletal muscle nuclei are post-mitotic and open potential avenues to harness the intrinsic replicative ability of myonuclei for muscle maintenance and growth.
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Affiliation(s)
- Agnieszka K Borowik
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | - Arik Davidyan
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
- Department of Biological Sciences, California State University Sacramento, 6000 J Street, Sacramento, CA, 95819, USA
| | - Frederick F Peelor
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | - Evelina Voloviceva
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | - Stephen M Doidge
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | - Matthew P Bubak
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
| | | | - John J McCarthy
- Center for Muscle Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
| | - Esther E Dupont-Versteegden
- Center for Muscle Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, 900 S Limestone, Lexington, KY 40536, USA
| | - Benjamin F Miller
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 NE 13th St, Oklahoma City, OK 73104, USA
- Oklahoma City VA Medical Center, 921 NE 13th St, Oklahoma City, OK 73104, USA
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14
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MYCN and Metabolic Reprogramming in Neuroblastoma. Cancers (Basel) 2022; 14:cancers14174113. [PMID: 36077650 PMCID: PMC9455056 DOI: 10.3390/cancers14174113] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Neuroblastoma is a pediatric cancer responsible for approximately 15% of all childhood cancer deaths. Aberrant MYCN activation, as a result of genomic MYCN amplification, is a major driver of high-risk neuroblastoma, which has an overall survival rate of less than 50%, despite the best treatments currently available. Metabolic reprogramming is an integral part of the growth-promoting program driven by MYCN, which fuels cell growth and proliferation by increasing the uptake and catabolism of nutrients, biosynthesis of macromolecules, and production of energy. This reprogramming process also generates metabolic vulnerabilities that can be exploited for therapy. In this review, we present our current understanding of metabolic reprogramming in neuroblastoma, focusing on transcriptional regulation as a key mechanism in driving the reprogramming process. We also highlight some important areas that need to be explored for the successful development of metabolism-based therapy against high-risk neuroblastoma.
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15
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Chen WJ, Lin IH, Lee CW, Yoshioka K, Ono Y, Yan YT, Yen Y, Chen YF. Ribonucleotide reductase M2B in the myofibers modulates stem cell fate in skeletal muscle. NPJ Regen Med 2022; 7:37. [PMID: 35906243 PMCID: PMC9338274 DOI: 10.1038/s41536-022-00231-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 07/06/2022] [Indexed: 11/17/2022] Open
Abstract
The balance among quiescence, differentiation, and self-renewal of skeletal muscle stem cells (MuSCs) is tightly regulated by their intrinsic and extrinsic properties from the niche. How the niche controls MuSC fate remains unclear. Ribonucleotide reductase M2B (Rrm2b) modulates MuSC quiescence/differentiation in muscle in response to injury. Rrm2b knockout in myofibers, but not in MuSCs, led to weakness of muscles, such as a loss of muscle mass and strength. After muscle injury, damaged myofibers were more efficiently repaired in the Rrm2b myofiber-specific knockout mice than the control mice, but these myofibers were thinner and showed weak functioning. Rrm2b-deleted myofibers released several myokines, which trigger MuSCs to differentiate but not re-enter the quiescent stage to replenish the stem cell pool. Overall, Rrm2b in the myofibers plays a critical role in modulating the MuSC fate by modifying the microenvironment, and it may lead to a possible strategy to treat muscle disorders.
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Affiliation(s)
- Wan-Jing Chen
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, 11529, Taiwan
| | - I-Hsuan Lin
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, 11031, Taipei, Taiwan
| | - Chien-Wei Lee
- Center for Translational Genomics Research, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Kiyoshi Yoshioka
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Yusuke Ono
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Yu-Ting Yan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun Yen
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, 11031, Taipei, Taiwan. .,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, 11031, Taipei, Taiwan. .,Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, 11031, Taipei, Taiwan. .,Cancer Center, Taipei Municipal WanFang Hospital, 116081, Taipei, Taiwan. .,Center for Cancer Translational Research, Tzu Chi University, Hualien, Taiwan.
| | - Yi-Fan Chen
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, 11529, Taiwan. .,Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, 11031, Taipei, Taiwan. .,International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, 11031, Taipei, Taiwan. .,Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan.
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16
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Ugbogu EA, Schweizer LM, Schweizer M. Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. Cells 2022; 11:1909. [PMID: 35741038 PMCID: PMC9221600 DOI: 10.3390/cells11121909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphoribosyl pyrophosphate synthetase (PRS EC 2.7.6.1) is a rate-limiting enzyme that irreversibly catalyzes the formation of phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate and adenosine triphosphate (ATP). This key metabolite is required for the synthesis of purine and pyrimidine nucleotides, the two aromatic amino acids histidine and tryptophan, the cofactors nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), all of which are essential for various life processes. Despite its ubiquity and essential nature across the plant and animal kingdoms, PRPP synthetase displays species-specific characteristics regarding the number of gene copies and architecture permitting interaction with other areas of cellular metabolism. The impact of mutated PRS genes in the model eukaryote Saccharomyces cerevisiae on cell signalling and metabolism may be relevant to the human neuropathies associated with PRPS mutations. Human PRPS1 and PRPS2 gene products are implicated in drug resistance associated with recurrent acute lymphoblastic leukaemia and progression of colorectal cancer and hepatocellular carcinoma. The investigation of PRPP metabolism in accepted model organisms, e.g., yeast and zebrafish, has the potential to reveal novel drug targets for treating at least some of the diseases, often characterized by overlapping symptoms, such as Arts syndrome and respiratory infections, and uncover the significance and relevance of human PRPS in disease diagnosis, management, and treatment.
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Affiliation(s)
- Eziuche A. Ugbogu
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Lilian M. Schweizer
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK; (E.A.U.); (L.M.S.)
| | - Michael Schweizer
- Institute of Biological Chemistry, Biophysics & Engineering (IB3), School of Engineering &Physical Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK
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17
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Li L, Qiao X, Liu F, Wang J, Shen H, Fu H, Mao JH. Description of the Molecular and Phenotypic Spectrum of Lesch-Nyhan Disease in Eight Chinese Patients. Front Genet 2022; 13:868942. [PMID: 35559039 PMCID: PMC9086273 DOI: 10.3389/fgene.2022.868942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Lesch-Nyhan disease (LND) is a rare disorder involving pathogenic variants in the HPRT1 gene encoding the enzyme hypoxanthine-guanine phosphoribosyltransferase (HGPRT) that result in hyperuricemia, intellectual disability, dystonic movement disorder, and compulsive self-mutilation. The purpose of the present study was to characterize the genetic basis of LND and describe its phenotypic heterogeneity by identifying the variation in the HPRT1 gene in a cohort of Chinese LND patients. Results: The median age at diagnosis was 31 mo (interquartile range (IQR): 7-76 mo), and the initial manifestations were mainly head control weakness and motor development delay. The median age of self-mutilation behavior onset was 19 mo (IQR: 17-24 mo), and all patients were required to travel in a wheelchair and fall into the predicament of compulsive self-harm behavior. There were two patients whose blood uric acid levels were normal for their high urinary acid excretion fraction without taking uric acid-lowering drugs. Seven different pathogenic variants of the HPRT1 gene were identified among eight independent pedigrees, including four novel mutations [c.299 (exon 3) T > A; loss (exon: 6) 84 bp; c.277_281delATTGC; c.468_470delGAT]. The pathogenic variant sites were mainly concentrated in exon 3, and truncating mutations (including frameshift mutations and nonsense mutations) were the most common genetic variant types (5/7, 71.4%). Conclusion: The present study described the phenotypic and molecular spectrum of LND in eight Chinese families, including four novel mutations, which expands our understanding of LND.
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Affiliation(s)
- Lu Li
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaohui Qiao
- Department of Nephrology, Ningbo Women and Children's Hospital, Ningbo, China
| | - Fei Liu
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingjing Wang
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang University School of Medicine, Hangzhou, China
| | - Huijun Shen
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang University School of Medicine, Hangzhou, China
| | - Haidong Fu
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian-Hua Mao
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Zhejiang University School of Medicine, Hangzhou, China
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18
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Milosavljevic S, Glinton KE, Li X, Medeiros C, Gillespie P, Seavitt JR, Graham BH, Elsea SH. Untargeted Metabolomics of Slc13a5 Deficiency Reveal Critical Liver-Brain Axis for Lipid Homeostasis. Metabolites 2022; 12:metabo12040351. [PMID: 35448538 PMCID: PMC9032242 DOI: 10.3390/metabo12040351] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 01/17/2023] Open
Abstract
Though biallelic variants in SLC13A5 are known to cause severe encephalopathy, the mechanism of this disease is poorly understood. SLC13A5 protein deficiency reduces citrate transport into the cell. Downstream abnormalities in fatty acid synthesis and energy generation have been described, though biochemical signs of these perturbations are inconsistent across SLC13A5 deficiency patients. To investigate SLC13A5-related disorders, we performed untargeted metabolic analyses on the liver, brain, and serum from a Slc13a5-deficient mouse model. Metabolomic data were analyzed using the connect-the-dots (CTD) methodology and were compared to plasma and CSF metabolomics from SLC13A5-deficient patients. Mice homozygous for the Slc13a5tm1b/tm1b null allele had perturbations in fatty acids, bile acids, and energy metabolites in all tissues examined. Further analyses demonstrated that for several of these molecules, the ratio of their relative tissue concentrations differed widely in the knockout mouse, suggesting that deficiency of Slc13a5 impacts the biosynthesis and flux of metabolites between tissues. Similar findings were observed in patient biofluids, indicating altered transport and/or flux of molecules involved in energy, fatty acid, nucleotide, and bile acid metabolism. Deficiency of SLC13A5 likely causes a broader state of metabolic dysregulation than previously recognized, particularly regarding lipid synthesis, storage, and metabolism, supporting SLC13A5 deficiency as a lipid disorder.
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Affiliation(s)
- Sofia Milosavljevic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (S.M.); (K.E.G.); (X.L.); (J.R.S.)
- Harvard Medical School, Boston, MA 02215, USA
| | - Kevin E. Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (S.M.); (K.E.G.); (X.L.); (J.R.S.)
| | - Xiqi Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (S.M.); (K.E.G.); (X.L.); (J.R.S.)
| | - Cláudia Medeiros
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (C.M.); (P.G.); (B.H.G.)
| | - Patrick Gillespie
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (C.M.); (P.G.); (B.H.G.)
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (S.M.); (K.E.G.); (X.L.); (J.R.S.)
| | - Brett H. Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (C.M.); (P.G.); (B.H.G.)
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (S.M.); (K.E.G.); (X.L.); (J.R.S.)
- Correspondence: ; Tel.: +1-713-798-5484
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19
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Lazado CC, Breiland MW, Furtado F, Burgerhout E, Strand D. The circulating plasma metabolome of Neoparamoeba perurans-infected Atlantic salmon (Salmo salar). Microb Pathog 2022; 166:105553. [DOI: 10.1016/j.micpath.2022.105553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
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20
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Yao H, Xu H, Qiu S, Chen J, Lin Z, Zhu J, Sun X, Gao Q, Chen X, Xi C, Huang D, Zhang F, Gao S, Wang Z, Zhang J, Liu X, Ren G, Tao X, Li M, Chen W. Choline deficiency-related multi-omics characteristics are susceptible factors for chemotherapy-induced thrombocytopenia. Pharmacol Res 2022; 178:106155. [DOI: 10.1016/j.phrs.2022.106155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 02/06/2023]
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21
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Manini A, Meneri M, Rodolico C, Corti S, Toscano A, Comi GP, Musumeci O, Ronchi D. Case Report: Thymidine Kinase 2 (TK2) Deficiency: A Novel Mutation Associated With Childhood-Onset Mitochondrial Myopathy and Atypical Progression. Front Neurol 2022; 13:857279. [PMID: 35280287 PMCID: PMC8914305 DOI: 10.3389/fneur.2022.857279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 01/31/2022] [Indexed: 11/30/2022] Open
Abstract
The nuclear gene TK2 encodes the mitochondrial thymidine kinase, an enzyme involved in the phosphorylation of deoxycytidine and deoxythymidine nucleosides. Biallelic TK2 mutations are associated with a spectrum of clinical presentations mainly affecting skeletal muscle and featuring muscle mitochondrial DNA (mtDNA) instability. Current classification includes infantile- ( ≤ 1 year), childhood- (1–12 years), and late-onset (≥12 years) forms. In addition to age at onset, these forms differ for progression, life expectancy, and signs of mtDNA instability (mtDNA depletion vs. accumulation of multiple mtDNA deletions). Childhood-onset TK2 deficiency typically causes a rapidly progressive proximal myopathy, which leads to wheelchair-bound status within 10 years of disease onset, and severe respiratory impairment. Muscle biopsy usually reveals a combination of mitochondrial myopathy and dystrophic features with reduced mtDNA content. Here we report the case of an Italian patient presenting childhood-onset, slowly progressive mitochondrial myopathy, ptosis, hypoacusis, dysphonia, and dysphagia, harboring the TK2 variants c.278A>G and c.543del, the latter unreported so far. Compared to other childhood-onset TK2-patients, our case displays atypical features, including slowly progressive muscle weakness and absence of respiratory failure, which are usually observed in late-onset forms. This report extends the genetic background of TK2-related myopathy, highlighting the clinical overlap among different forms.
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Affiliation(s)
- Arianna Manini
- Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Megi Meneri
- Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Carmelo Rodolico
- Unit of Neurology and Neuromuscular Disorders, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Stefania Corti
- Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Toscano
- Unit of Neurology and Neuromuscular Disorders, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giacomo Pietro Comi
- Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Olimpia Musumeci
- Unit of Neurology and Neuromuscular Disorders, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
- Olimpia Musumeci
| | - Dario Ronchi
- Dino Ferrari Center, Neuroscience Section, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- *Correspondence: Dario Ronchi
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Zhang H, Li Y, Li Z, Lam CWK, Zhu P, Wang C, Zhou H, Zhang W. MTBSTFA derivatization-LC-MS/MS approach for the quantitative analysis of endogenous nucleotides in human colorectal carcinoma cells. J Pharm Anal 2022; 12:77-86. [PMID: 35573880 PMCID: PMC9073140 DOI: 10.1016/j.jpha.2021.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/28/2020] [Accepted: 01/14/2021] [Indexed: 11/28/2022] Open
Abstract
Endogenous ribonucleotides (RNs) and deoxyribonucleotides (dRNs) are important metabolites related to the pathogenesis of many diseases. In light of their physiological and pathological significances, a novel and sensitive pre-column derivatization method with N-(t-butyldimethylsilyl)-N-methyltrifluoroacetamide (MTBSTFA) was developed to determine RNs and dRNs in human cells using high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). A one-step extraction of cells with 85% methanol followed by a simple derivatization reaction within 5 min at room temperature contributed to shortened analysis time. The derivatives of 22 nucleoside mono-, di- and triphosphates were retained on the typical C18 column and eluted by ammonium acetate and acetonitrile in 9 min. Under these optimal conditions, good linearity was achieved in the tested calibration ranges. The lower limit of quantitation (LLOQ) was determined to be 0.1-0.4 μM for the tested RNs and 0.001-0.1 μM for dRNs. In addition, the precision (CV) was <15% and the RSD of stability was lower than 10.4%. Furthermore, this method was applied to quantify the endogenous nucleotides in human colorectal carcinoma cell lines HCT 116 exposed to 10-hydroxycamptothecin. In conclusion, our method has proven to be simple, rapid, sensitive, and reliable. It may be used for specific expanded studies on intracellular pharmacology in vitro.
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Affiliation(s)
| | | | - Zheng Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Christopher Wai-Kei Lam
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Peng Zhu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Caiyun Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
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23
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Birder LA, Jackson EK. Dysregulated Purine Metabolism Contributes to Age-Associated Lower Urinary Tract Dysfunctions. ADVANCES IN GERIATRIC MEDICINE AND RESEARCH 2021; 3:e210018. [PMID: 34676378 PMCID: PMC8527459 DOI: 10.20900/agmr20210018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lower urinary tract (LUT) dysfunction is common in the older adult. Aging is associated with a number of both storage and voiding problems which are classified into syndromes with overlapping symptoms. Despite the prevalence and consequences of these syndromes, LUT disorders continue to be undertreated as few therapeutic options exist. Here, we propose that dysregulated metabolism of purine nucleotides results in an accumulation of uro-damaging hypoxanthine (a source of reactive oxygen species or ROS), which provides a mechanism for defects in sensory signaling and contractility, culminating in abnormal urodynamic behavior.
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Affiliation(s)
- Lori A. Birder
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh PA 15261, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261, USA
| | - Edwin K. Jackson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261, USA
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24
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Nucleotide Pool Imbalance and Antibody Gene Diversification. Vaccines (Basel) 2021; 9:vaccines9101050. [PMID: 34696158 PMCID: PMC8538681 DOI: 10.3390/vaccines9101050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 01/10/2023] Open
Abstract
The availability and adequate balance of deoxyribonucleoside triphosphate (dNTP) is an important determinant of both the fidelity and the processivity of DNA polymerases. Therefore, maintaining an optimal balance of the dNTP pool is critical for genomic stability in replicating and quiescent cells. Since DNA synthesis is required not only in genomic replication but also in DNA damage repair and recombination, the abnormalities in the dNTP pool affect a wide range of chromosomal activities. The generation of antibody diversity relies on antigen-independent V(D)J recombination, as well as antigen-dependent somatic hypermutation and class switch recombination. These processes involve diverse sets of DNA polymerases, which are affected by the dNTP pool imbalances. This review discusses the role of the optimal dNTP pool balance in the diversification of antibody encoding genes.
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Li M, Chen J, Liu S, Sun X, Xu H, Gao Q, Chen X, Xi C, Huang D, Deng Y, Zhang F, Gao S, Qiu S, Tao X, Zhai J, Wei H, Yao H, Chen W. Spermine-Related DNA Hypermethylation and Elevated Expression of Genes for Collagen Formation are Susceptible Factors for Chemotherapy-Induced Hand-Foot Syndrome in Chinese Colorectal Cancer Patients. Front Pharmacol 2021; 12:746910. [PMID: 34539419 PMCID: PMC8440935 DOI: 10.3389/fphar.2021.746910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/13/2021] [Indexed: 01/06/2023] Open
Abstract
Hand-foot syndrome (HFS) is a common capecitabine-based chemotherapy-related adverse event (CRAE) in patients with colorectal cancer (CRC). It is of great significance to comprehensively identify susceptible factors for HFS, and further to elucidate the biomolecular mechanism of HFS susceptibility. We performed an untargeted multi-omics analysis integrating DNA methylation, transcriptome, and metabolome data of 63 Chinese CRC patients who had complete CRAE records during capecitabine-based chemotherapy. We found that the metabolome changes for each of matched plasma, urine, and normal colorectal tissue (CRT) in relation to HFS were characterized by chronic tissue damage, which was indicated by reduced nucleotide salvage, elevated spermine level, and increased production of endogenous cytotoxic metabolites. HFS-related transcriptome changes of CRT showed an overall suppressed inflammation profile but increased M2 macrophage polarization. HFS-related DNA methylation of CRT presented gene-specific hypermethylation on genes mainly for collagen formation. The hypermethylation was accumulated in the opensea and shore regions, which elicited a positive effect on gene expression. Additionally, we developed and validated models combining relevant biomarkers showing reasonably good discrimination performance with the area under the receiver operating characteristic curve values from 0.833 to 0.955. Our results demonstrated that the multi-omics variations associated with a profibrotic phenotype were closely related to HFS susceptibility. HFS-related biomolecular variations in CRT contributed more to the relevant biomolecular mechanism of HFS than in plasma and urine. Spermine-related DNA hypermethylation and elevated expression of genes for collagen formation were closely associated with HFS susceptibility. These findings provided new insights into the susceptible factors for chemotherapy-induced HFS, which can promote the implementation of individualized treatment against HFS.
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Affiliation(s)
- Mingming Li
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jiani Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Shaoqun Liu
- Department of Gastric Intestinal Surgery, Minhang Hospital, Fudan University, Shanghai, China
| | - Xiaomeng Sun
- Research Institute, GloriousMed Clinical Laboratory Co., Ltd., Shanghai, China
| | - Huilin Xu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qianmin Gao
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Xintao Chen
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Chaowen Xi
- Research Institute, GloriousMed Clinical Laboratory Co., Ltd., Shanghai, China
| | - Doudou Huang
- Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Deng
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Feng Zhang
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Shouhong Gao
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Shi Qiu
- Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xia Tao
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jingwen Zhai
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Hua Wei
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China.,Department of Pharmacy, 905th Hospital of PLA Navy, Naval Medical University, Shanghai, China
| | - Houshan Yao
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Wansheng Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China.,Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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26
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Li C, Li K, Xu X, Qi W, Hu X, Jin P. A pilot study for colorectal carcinoma screening by instant metabolomic profiles using conductive polymer spray ionization mass spectrometry. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166210. [PMID: 34246751 DOI: 10.1016/j.bbadis.2021.166210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/17/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The rapid and accurate discrimination of colorectal carcinoma (CRC) and polyps at the molecular level enables early intervention of CRC, which can greatly improve the 5-year survival rate of patients. Here we reported the potential of conductive polymer spray ionization mass spectrometry (CPSI-MS) in successfully screening CRC according to the serum metabolic profile. METHODS Trace intravenous blood (50 μL) was collected from 60 colorectal carcinoma (CRC) and 60 polyp patients, respectively. After centrifugation, serum (2 μL) was loaded onto the tip of conductive polymer to form a dried serum spot. When the 5 μL methanol-water (1:1, v/v) extraction solvent was spiked onto the dried serum spot followed with +4.5 kV high voltage applied on the polymer tip, the extracted components will be ionized and carried into the MS system for direct metabolic profiling. FINDINGS There were 51 metabolites discovered to be significantly changed in CRC serum compared to polyps. Combining these metabolites as the characteristic panel, the ideal diagnostic performance was achieved by Lasso regression model with the accuracy of 88.3%. INTERPRETATION This pilot study demonstrated the potential of CPSI-MS as a cost-effective tool in large-scale CRC screening in the high-risk population.
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Affiliation(s)
- Chao Li
- Department of Pharmacy, Beijing Hospital, Beijing 100730, China; National Center of Gerontology, Beijing 100730, China; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory of Assessment of Clinical Drugs Risk and Individual Application (Beijing Hospital), Beijing 100730, China
| | - Kexin Li
- National Center of Gerontology, Beijing 100730, China; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China; Clinical Trial Center, Beijing Hospital, Beijing 100730, China
| | - Xiaoyu Xu
- National Center of Gerontology, Beijing 100730, China; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China; Clinical Trial Center, Beijing Hospital, Beijing 100730, China
| | - Wenyuan Qi
- National Center of Gerontology, Beijing 100730, China; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China; Clinical Trial Center, Beijing Hospital, Beijing 100730, China
| | - Xin Hu
- Department of Pharmacy, Beijing Hospital, Beijing 100730, China; National Center of Gerontology, Beijing 100730, China; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory of Assessment of Clinical Drugs Risk and Individual Application (Beijing Hospital), Beijing 100730, China
| | - Pengfei Jin
- Department of Pharmacy, Beijing Hospital, Beijing 100730, China; National Center of Gerontology, Beijing 100730, China; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory of Assessment of Clinical Drugs Risk and Individual Application (Beijing Hospital), Beijing 100730, China.
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27
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Kundu D, Dubey VK. Purines and Pyrimidines: Metabolism, Function and Potential as Therapeutic Options in Neurodegenerative Diseases. Curr Protein Pept Sci 2021; 22:170-189. [PMID: 33292151 DOI: 10.2174/1389203721999201208200605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/01/2020] [Accepted: 09/25/2020] [Indexed: 11/22/2022]
Abstract
Various neurodegenerative disorders have various molecular origins but some common molecular mechanisms. In the current scenario, there are very few treatment regimens present for advanced neurodegenerative diseases. In this context, there is an urgent need for alternate options in the form of natural compounds with an ameliorating effect on patients. There have been individual scattered experiments trying to identify potential values of various intracellular metabolites. Purines and Pyrimidines, which are vital molecules governing various aspects of cellular biochemical reactions, have been long sought as crucial candidates for the same, but there are still many questions that go unanswered. Some critical functions of these molecules associated with neuromodulation activities have been identified. They are also known to play a role in foetal neurodevelopment, but there is a lacuna in understanding their mechanisms. In this review, we have tried to assemble and identify the importance of purines and pyrimidines, connecting them with the prevalence of neurodegenerative diseases. The leading cause of this class of diseases is protein misfolding and the formation of amyloids. A direct correlation between loss of balance in cellular homeostasis and amyloidosis is yet an unexplored area. This review aims at bringing the current literature available under one umbrella serving as a foundation for further extensive research in this field of drug development in neurodegenerative diseases.
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Affiliation(s)
- Debanjan Kundu
- School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP - 221005, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP - 221005, India
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28
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Li J, Zhang Y, Wang X, Walk ST, Wang G. Integrated Metabolomics and Targeted Gene Transcription Analysis Reveal Global Bacterial Antimonite Resistance Mechanisms. Front Microbiol 2021; 12:617050. [PMID: 33584619 PMCID: PMC7876068 DOI: 10.3389/fmicb.2021.617050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/12/2021] [Indexed: 11/17/2022] Open
Abstract
Antimony (Sb)-resistant bacteria have potential applications in the remediation of Sb-contaminated sites. However, the effect of Sb(III) exposure on whole-cell metabolic change has not been studied. Herein, we combined untargeted metabolomics with a previous proteomics dataset and confirmatory gene transcription analysis to identify metabolic responses to Sb(III) exposure in Agrobacterium tumefaciens GW4. Dynamic changes in metabolism between control and Sb(III)-exposed groups were clearly shown. KEGG pathway analysis suggested that with Sb(III) exposure: (1) the branching pathway of gluconeogenesis is down-regulated, resulting in the up-regulation of pentose phosphate pathway to provide precursors of anabolism and NADPH; (2) glycerophospholipid and arachidonic acid metabolisms are down-regulated, resulting in more acetyl-CoA entry into the TCA cycle and increased capacity to produce energy and macromolecular synthesis; (3) nucleotide and fatty acid synthesis pathways are all increased perhaps to protect cells from DNA and lipid peroxidation; (4) nicotinate metabolism increases which likely leads to increased production of co-enzymes (e.g., NAD+ and NADP+) for the maintenance of cellular redox and Sb(III) oxidation. Expectedly, the total NADP+/NADPH content, total glutathione, and reduced glutathione contents were all increased after Sb(III) exposure in strain GW4, which contribute to maintaining the reduced state of the cytoplasm. Our results provide novel information regarding global bacterial responses to Sb(III) exposure from a single gene level to the entire metabolome and provide specific hypotheses regarding the metabolic change to be addressed in future research.
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Affiliation(s)
- Jingxin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuxiao Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xing Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Seth T Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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29
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Müller‐Nedebock AC, Westhuizen FH, Kõks S, Bardien S. Nuclear Genes Associated with Mitochondrial
DNA
Processes as Contributors to Parkinson's Disease Risk. Mov Disord 2021; 36:815-831. [DOI: 10.1002/mds.28475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022] Open
Affiliation(s)
- Amica C. Müller‐Nedebock
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | | | - Sulev Kõks
- Perron Institute for Neurological and Translational Science Nedlands Western Australia Australia
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch Western Australia Australia
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
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30
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Maiuri T, Hung CL, Suart C, Begeja N, Barba-Bazan C, Peng Y, Savic N, Wong T, Truant R. DNA Repair in Huntington's Disease and Spinocerebellar Ataxias: Somatic Instability and Alternative Hypotheses. J Huntingtons Dis 2021; 10:165-173. [PMID: 33579859 PMCID: PMC7990435 DOI: 10.3233/jhd-200414] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The use of genome wide association studies (GWAS) in Huntington's disease (HD) research, driven by unbiased human data analysis, has transformed the focus of new targets that could affect age at onset. While there is a significant depth of information on DNA damage repair, with many drugs and drug targets, most of this development has taken place in the context of cancer therapy. DNA damage repair in neurons does not rely on DNA replication correction mechanisms. However, there is a strong connection between DNA repair and neuronal metabolism, mediated by nucleotide salvaging and the poly ADP-ribose (PAR) response, and this connection has been implicated in other age-onset neurodegenerative diseases. Validation of leads including the mismatch repair protein MSH3, and interstrand cross-link repair protein FAN1, suggest the mechanism is driven by somatic CAG instability, which is supported by the protective effect of CAA substitutions in the CAG tract. We currently do not understand: how somatic instability is triggered; the state of DNA damage within expanding alleles in the brain; whether this damage induces mismatch repair and interstrand cross-link pathways; whether instability mediates toxicity, and how this relates to human ageing. We discuss DNA damage pathways uncovered by HD GWAS, known roles of other polyglutamine disease proteins in DNA damage repair, and a panel of hypotheses for pathogenic mechanisms.
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Affiliation(s)
- Tamara Maiuri
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Claudia L.K. Hung
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Celeste Suart
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Nola Begeja
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Carlos Barba-Bazan
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Yi Peng
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Natasha Savic
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Timothy Wong
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Ray Truant
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
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31
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Grotegut P, Perumal N, Kuehn S, Smit A, Dick HB, Grus FH, Joachim SC. Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model. J Neuroinflammation 2020; 17:375. [PMID: 33317557 PMCID: PMC7737388 DOI: 10.1186/s12974-020-02012-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Previous studies noted that intravitreal injection of S100B triggered a glaucoma-like degeneration of retina and optic nerve as well as microglia activation after 14 days. The precise role of microglia in our intravitreal S100B model is still unclear. Hence, microglia were inhibited through minocycline. The aim is to investigate whether microglia have a significant influence on the degeneration process or whether they are only a side effect in the model studied here. METHODS Minocycline was applied daily in rats by intraperitoneal injection using two different concentrations (13.5 mg/kg body weight, 25 mg/kg body weight). One day after treatment start, S100B or PBS was intravitreally injected in one eye per rat. The naïve groups received no injections. This resulted in a total of five groups (naïve n = 14, PBS n = 14, S100B n = 13, 13.5 mg/kg mino n = 15, 25 mg/kg mino n = 15). At day 14, electroretinogram measurements were performed, followed by immunofluorescence and label-free quantitative proteomics analysis. The focus of these investigations was on the survival of RGCs as well as their axons, the response of the microglia, and the identification of further pathological modes of action of S100B. RESULTS The best signal transmission was detected via ERG in the 13.5 mg/kg mino group. The inhibition of the microglia protected optic nerve neurofilaments and decreased the negative impact of S100B on RGCs. However, the minocycline treatment could not trigger complete protection of RGCs. Furthermore, in retina and optic nerve, the minocycline treatment reduced the number and activity of S100B-triggered microglia in a concentration-dependent manner. Proteomics analysis showed that S100B application led to numerous metabolic functions and cellular stress, mainly an increased inflammatory response, glycolysis, and mitochondrial dysfunction, which caused oxidative stress in the retina. Importantly, the protective capability of lower dose of minocycline was unraveled by suppressing the apoptotic, inflammatory, and the altered metabolic processes caused by S100B insult in the retina. CONCLUSION Intravitreally injected S100B not only led to a pro-inflammatory microglial reaction, but also a mitochondrial and metabolic dysfunction. Also, these results suggest that an excessive microglial response may be a significant degenerative factor, but not the only trigger for increased cell death.
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Affiliation(s)
- Pia Grotegut
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - Natarajan Perumal
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sandra Kuehn
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - Andreas Smit
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - H Burkhard Dick
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - Franz H Grus
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stephanie C Joachim
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892, Bochum, Germany.
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Li Z, Rasmussen LJ. TIP60 in aging and neurodegeneration. Ageing Res Rev 2020; 64:101195. [PMID: 33091598 DOI: 10.1016/j.arr.2020.101195] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/29/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023]
Abstract
Epigenetic modification of chromatin, including histone methylation and acetylation, plays critical roles in eukaryotic cells and has a significant impact on chromatin structure/accessibility, gene regulation and, susceptibility to aging, neurodegenerative disease, cancer, and other age-related diseases. This article reviews the current advances on TIP60/KAT5, a major histone acetyltransferase with diverse functions in eukaryotes, with emphasis on its regulation of autophagy, proteasome-dependent protein turnover, RNA transcription, DNA repair, circadian rhythms, learning and memory, and other neurological functions implicated in aging and neurodegeneration. Moreover, the promising therapeutic potential of TIP60 is discussed to target Alzheimer's disease and other neurological diseases.
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Zhang Y, Tian Y, Zhang H, Xu B, Chen H. Potential pathways of zinc deficiency-promoted tumorigenesis. Biomed Pharmacother 2020; 133:110983. [PMID: 33190036 DOI: 10.1016/j.biopha.2020.110983] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/11/2022] Open
Abstract
Zinc (Zn) is the second most abundant necessary trace element in the human body. It is reported that zinc deficiency (ZD) promotes many types of cancer progression through multiple signal pathways. It is well known that oxidative stress, DNA damage, DNA repair, cell cycle, cell apoptosis, metabolic alterations, microRNAs abnormal expression, and inflammation level are closely related to cancer development. Cumulative evidence suggests that ZD influences these biological functions. This review explores the latest advances in understanding the role of ZD in tumorigenesis. Fully comprehending the potential mechanisms of ZD-induced tumors may provide novel clues for prevention and clinical treatment of cancers.
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Affiliation(s)
- Yuting Zhang
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Yuyang Tian
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Haowen Zhang
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Baohua Xu
- Department of Experimental Animals, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China; Jiangxi Key Laboratory of Experimental Animals, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Hongping Chen
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China; Jiangxi Key Laboratory of Experimental Animals, Nanchang University, Nanchang, Jiangxi, 330006, PR China.
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Yatsuka H, Hada K, Shiraishi H, Umeda R, Morisaki I, Urushibata H, Shimizu N, Sebastian WA, Hikida T, Ishitani T, Hanada R, Shimada T, Kimoto K, Kubota T, Hanada T. Exosc2 deficiency leads to developmental disorders by causing a nucleotide pool imbalance in zebrafish. Biochem Biophys Res Commun 2020; 533:1470-1476. [PMID: 33333712 DOI: 10.1016/j.bbrc.2020.10.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/17/2020] [Indexed: 02/07/2023]
Abstract
Exosc2 is one of the components of the exosome complex involved in RNA 3' end processing and degradation of various RNAs. Recently, EXOSC2 mutation has been reported in German families presenting short stature, hearing loss, retinitis pigmentosa, and premature aging. However, the in vivo function of EXOSC2 has been elusive. Herein, we generated Exosc2 knockout (exosc2-/-) zebrafish that showed larval lethality 13 days post fertilization, with microcephaly, loss of spinal motor neurons, myelin deficiency, and retinitis pigmentosa. Mechanistically, Exosc2 deficiency caused impaired mRNA turnover, resulting in a nucleotide pool imbalance. Rapamycin, which modulated mRNA turnover by inhibiting the mTOR pathway, improved nucleotide pool imbalance in exosc2-/- zebrafish, resulting in prolonged survival and partial rescue of neuronal defects. Taken together, our findings offer new insights into the disease pathogenesis caused by Exosc2 deficiency, and might help explain fundamental molecular mechanisms in neuronal diseases, such as Alzheimer's disease, amyotrophic lateral sclerosis, and spinal muscular atrophy.
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Affiliation(s)
- Hiroyuki Yatsuka
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan; Department of Ophthalmology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Kazumasa Hada
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Hiroshi Shiraishi
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Ryohei Umeda
- Department of Neurophysiology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Ikuko Morisaki
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Hirotaro Urushibata
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Nobuyuki Shimizu
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Wulan Apridita Sebastian
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan; Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Takatoshi Hikida
- Laboratory for Advanced Brain Functions, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Tohru Ishitani
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Reiko Hanada
- Department of Neurophysiology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Tatsuo Shimada
- Oita Medical Technology School, Japan College of Judo-Therapy, Acupuncture & Moxibustion Therapy, Oita, Japan
| | - Kenichi Kimoto
- Department of Ophthalmology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Toshiaki Kubota
- Department of Ophthalmology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Toshikatsu Hanada
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu, Oita, Japan.
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Birder LA, Wolf-Johnston A, Wein AJ, Cheng F, Grove-Sullivan M, Kanai AJ, Watson AM, Stoltz D, Watkins SC, Robertson AM, Newman D, Dmochowski RR, Jackson EK. Purine nucleoside phosphorylase inhibition ameliorates age-associated lower urinary tract dysfunctions. JCI Insight 2020; 5:140109. [PMID: 32910805 PMCID: PMC7605521 DOI: 10.1172/jci.insight.140109] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/04/2020] [Indexed: 12/29/2022] Open
Abstract
In the aging population, lower urinary tract (LUT) dysfunction is common and often leads to storage and voiding difficulties classified into overlapping symptom syndromes. Despite prevalence and consequences of these syndromes, LUT disorders continue to be undertreated simply because there are few therapeutic options. LUT function and structure were assessed in aged (>25 months) male and female Fischer 344 rats randomized to oral treatment with a purine nucleoside phosphorylase (PNPase inhibitor) 8-aminoguanine (8-AG) or vehicle for 6 weeks. The bladders of aged rats exhibited multiple abnormalities: tactile insensitivity, vascular remodeling, reduced collagen-fiber tortuosity, increased bladder stiffness, abnormal smooth muscle morphology, swelling of mitochondria, and increases in urodamaging purine metabolites. Treatment of aged rats with 8-AG restored all evaluated histological, ultrastructural, and physiological abnormalities toward that of a younger state. 8-AG is an effective treatment that ameliorates key age-related structural and physiologic bladder abnormalities. Because PNPase inhibition blocks metabolism of inosine to hypoxanthine and guanosine to guanine, likely uroprotective effects of 8-AG are mediated by increased bladder levels of uroprotective inosine and guanosine and reductions in urodamaging hypoxanthine and xanthine. These findings demonstrate that 8-AG has translational potential for treating age-associated LUT dysfunctions and resultant syndromes in humans.
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Affiliation(s)
- Lori A Birder
- Department of Medicine, Renal-Electrolyte Division, and.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Alan J Wein
- Division of Urology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fangzhou Cheng
- Department of Mechanical Engineering and Materials Science, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mara Grove-Sullivan
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anthony J Kanai
- Department of Medicine, Renal-Electrolyte Division, and.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alan M Watson
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Donna Stoltz
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anne M Robertson
- Department of Mechanical Engineering and Materials Science, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Diane Newman
- Division of Urology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Roger R Dmochowski
- Department of Urology, Vanderbilt Medical Center, Nashville, Tennessee, USA
| | - Edwin K Jackson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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36
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Roci I, Watrous JD, Lagerborg KA, Jain M, Nilsson R. Mapping metabolic oscillations during cell cycle progression. Cell Cycle 2020; 19:2676-2684. [PMID: 33016215 PMCID: PMC7644150 DOI: 10.1080/15384101.2020.1825203] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Proliferating cells must synthesize a wide variety of macromolecules while progressing through the cell cycle, but the coordination between cell cycle progression and cellular metabolism is still poorly understood. To identify metabolic processes that oscillate over the cell cycle, we performed comprehensive, non-targeted liquid chromatography-high resolution mass spectrometry (LC-HRMS) based metabolomics of HeLa cells isolated in the G1 and SG2M cell cycle phases, capturing thousands of diverse metabolite ions. When accounting for increased total metabolite abundance due to cell growth throughout the cell cycle, 18% of the observed LC-HRMS peaks were at least twofold different between the stages, consistent with broad metabolic remodeling throughout the cell cycle. While most amino acids, phospholipids, and total ribonucleotides were constant across cell cycle phases, consistent with the view that total macromolecule synthesis does not vary across the cell cycle, certain metabolites were oscillating. For example, ribonucleotides were highly phosphorylated in SG2M, indicating an increase in energy charge, and several phosphatidylinositols were more abundant in G1, possibly indicating altered membrane lipid signaling. Within carbohydrate metabolism, pentose phosphates and methylglyoxal metabolites were associated with the cycle. Interestingly, hundreds of yet uncharacterized metabolites similarly oscillated between cell cycle phases, suggesting previously unknown metabolic activities that may be synchronized with cell cycle progression, providing an important resource for future studies.
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Affiliation(s)
- Irena Roci
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet , Stockholm, Sweden.,Division of Cardiovascular Medicine, Karolinska University Hospital , Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Jeramie D Watrous
- , Department of Medicine & Pharmacology University of California, San Diego , La Jolla, CA, USA
| | - Kim A Lagerborg
- , Department of Medicine & Pharmacology University of California, San Diego , La Jolla, CA, USA
| | - Mohit Jain
- , Department of Medicine & Pharmacology University of California, San Diego , La Jolla, CA, USA
| | - Roland Nilsson
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet , Stockholm, Sweden.,Division of Cardiovascular Medicine, Karolinska University Hospital , Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
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Zhang R, Engel AL, Wang Y, Li B, Shen W, Gillies MC, Chao JR, Du J. Inhibition of Mitochondrial Respiration Impairs Nutrient Consumption and Metabolite Transport in Human Retinal Pigment Epithelium. J Proteome Res 2020; 20:909-922. [PMID: 32975122 DOI: 10.1021/acs.jproteome.0c00690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mitochondrial respiration in mammalian cells not only generates ATP to meet their own energy needs but also couples with biosynthetic pathways to produce metabolites that can be exported to support neighboring cells. However, how defects in mitochondrial respiration influence these biosynthetic and exporting pathways remains poorly understood. Mitochondrial dysfunction in retinal pigment epithelium (RPE) cells is an emerging contributor to the death of their neighboring photoreceptors in degenerative retinal diseases including age-related macular degeneration. In this study, we used targeted-metabolomics and 13C tracing to investigate how inhibition of mitochondrial respiration influences the intracellular and extracellular metabolome. We found inhibition of mitochondrial respiration strikingly influenced both the intracellular and extracellular metabolome in primary RPE cells. Intriguingly, the extracellular metabolic changes sensitively reflected the intracellular changes. These changes included substantially enhanced glucose consumption and lactate production; reduced release of pyruvate, citrate, and ketone bodies; and massive accumulation of multiple amino acids and nucleosides. In conclusion, these findings reveal a metabolic signature of nutrient consumption and release in mitochondrial dysfunction in RPE cells. Testing medium metabolites provides a sensitive and noninvasive method to assess mitochondrial function in nutrient utilization and transport.
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Affiliation(s)
- Rui Zhang
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States.,Save Sight Institute, Sydney Medical School, University of Sydney, Sydney, NSW 2000, Australia
| | - Abbi L Engel
- Department of Ophthalmology, University of Washington, Seattle, Washington 98109, United States
| | - Yekai Wang
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Bo Li
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Weiyong Shen
- Save Sight Institute, Sydney Medical School, University of Sydney, Sydney, NSW 2000, Australia
| | - Mark C Gillies
- Save Sight Institute, Sydney Medical School, University of Sydney, Sydney, NSW 2000, Australia
| | - Jennifer R Chao
- Department of Ophthalmology, University of Washington, Seattle, Washington 98109, United States
| | - Jianhai Du
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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38
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Li Y, Guo J, Zhang H, Lam CW, Luo W, Zhou H, Zhang W. Protective Effect of Thymidine on DNA Damage Induced by Hydrogen Peroxide in Human Hepatocellular Cancer Cells. ACS OMEGA 2020; 5:21796-21804. [PMID: 32905386 PMCID: PMC7469367 DOI: 10.1021/acsomega.0c02843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Intracellular ribonucleotide (RN) and deoxyribonucleotide (dRN) pool sizes are critical for the fidelity of DNA synthesis. They are likely to be severely perturbed by many factors which disrupt the integrity and stability of DNA, leading to DNA damage. Exogenously supplied nucleosides are able to increase the deoxynucleoside triphosphate pools, then reverse the DNA damage, and decrease the oncogene-induced transformation dramatically. In this study, the impact of thymidine on the hydrogen peroxide (H2O2)-induced DNA damage was investigated in HepG2 liver cancer cells. From the result of the comet assay, the tail length of cells in the thymidine 600 μM + H2O2 1.0 mM group was dramatically decreased from 42.1 ± 10.8 to 21.9 ± 2.4 μm compared to that exposed with 1.0 mM H2O2 (p < 0.05), suggesting that pretreatment of thymidine reduced the DNA damage of HepG2 cells. Although the RN and dRN contents decreased in the damage group, most of them presented increasing tendency when pretreated with thymidine, especially the key metabolites dCTP, which was mainly related with the decline in the rate of DNA synthesis. The restoration also showed a significant G0/G1 phase arrest of cell cycle progression from 44.6 ± 2.2 to 56.6 ± 0.4% after pretreated with thymidine (p < 0.05). In conclusion, our data demonstrated that the pretreatment with thymidine had a potential protective ability against oxidative damage for DNA in HepG2 cells through the perturbation of RN and dRN pools as well as cell cycle arrest, which should provide new insights into the molecular basis of preventing H2O2-induced oxidative DNA damage in mammalian cells.
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39
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Kundu D, Umesh, Dubey VK. Interaction of selected biomolecules and metabolites with amyloidogenic proteins. J Biomol Struct Dyn 2020; 39:3061-3070. [PMID: 32329418 DOI: 10.1080/07391102.2020.1760138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The current manuscript reports docking and molecular interaction analyses of three FDA approved acetylcholinesterase inhibitors, nitrogenous bases and nucleotides with amyloidogenic proteins like hen egg white lysozyme (HEWL) and amyloid β peptide. After prediction of aggregation-prone regions in hen egg-white lysozyme and amyloid β peptide, grid boxes were defined for docking purposes covering these regions. We analyzed vital interactions and binding modes of molecules that dock near aggregation-prone regions of these proteins with acceptable statistics. The data hints toward the possibility that these molecules may bind to aggregation-prone regions and prevent amyloid/aggregation formation. We have also compared the binding energy and interactions of these molecules with certain other natural molecules viz. Curcumin, Coumarin and Resveratrol that have been previously reported to show anti-amyloidogenic activity as positive controls.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debanjan Kundu
- School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP, India
| | - Umesh
- School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP, India
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40
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Kundu D, Prerna K, Chaurasia R, Bharty MK, Dubey VK. Advances in protein misfolding, amyloidosis and its correlation with human diseases. 3 Biotech 2020; 10:193. [PMID: 32269898 PMCID: PMC7128022 DOI: 10.1007/s13205-020-2166-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/11/2020] [Indexed: 12/24/2022] Open
Abstract
Protein aggregation, their mechanisms and trends in the field of neurodegenerative diseases is still far from completely being decoded. It is mainly attributed to the complexity surrounding the interaction between proteins which includes various regulatory mechanisms involved with the presentation of abnormal conditions. Although most proteins are functional in their soluble form, they have also been reported to convert themselves into insoluble aggregates under certain conditions naturally. Misfolded protein forms aggregates which are mostly unwanted by the cellular system and are mostly involved in various pathophysiologies including Alzheimer's, Type II Diabetes mellitus, Kurus's etc. Challenges lie in understanding the complex mechanism of protein misfolding and its correlation with clinical evidence. It is often understood that due to the slowness of the process and its association with ageing, timely intervention with drugs or preventive measures will play an essential role in lowering the rate of dementia causing diseases and associated ailments in the future. Today approximately more than 35 proteins have been identified capable of forming amyloids under defined conditions, and nearly all of them have been associated with disease outcomes. This review incorporates a major understanding from the history of diseases associated with protein misfolding, to the current state of neurodegenerative diseases globally, highlighting challenges in drug development and current state of research in a comprehensive manner in the field of protein misfolding diseases. There is increasing clinical association of protein misfolding with regards to amyloids compelling us to thread questions solved and further helping us design possible solutions by generating a pathway-based research on which future work in this field could be driven.
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Affiliation(s)
- Debanjan Kundu
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, UP 221005 India
| | - Kumari Prerna
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, UP 221005 India
| | - Rahul Chaurasia
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Manoj Kumar Bharty
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, UP 221005 India
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41
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Yamada S, Sato A, Sakakibara SI. Nwd1 Regulates Neuronal Differentiation and Migration through Purinosome Formation in the Developing Cerebral Cortex. iScience 2020; 23:101058. [PMID: 32344379 PMCID: PMC7186558 DOI: 10.1016/j.isci.2020.101058] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/09/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
Abstract
Engagement of neural stem/progenitor cells (NSPCs) into proper neuronal differentiation requires the spatiotemporally regulated generation of metabolites. Purines are essential building blocks for many signaling molecules. Enzymes that catalyze de novo purine synthesis are assembled as a huge multienzyme complex called “purinosome.” However, there is no evidence of the formation or physiological function of the purinosome in the brain. Here, we showed that a signal transduction ATPases with numerous domains (STAND) protein, NACHT and WD repeat domain-containing 1 (Nwd1), interacted with Paics, a purine-synthesizing enzyme, to regulate purinosome assembly in NSPCs. Altered Nwd1 expression affected purinosome formation and induced the mitotic exit and premature differentiation of NSPCs, repressing neuronal migration and periventricular heterotopia. Overexpression/knockdown of Paics or Fgams, other purinosome enzymes, in the developing brain resulted in a phenocopy of Nwd1 defects. These findings indicate that strict regulation of purinosome assembly/disassembly is crucial for maintaining NSPCs and corticogenesis. STAND protein Nwd1 interacts with Paics to regulate the purinosome formation Dysregulated expression of Nwd1 induced the premature differentiation of NSPCs Nwd1 KD repressed the neuronal migration, causing the periventricular heterotopia Tightly regulated assembly of purinosome components is crucial for corticogenesis
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Affiliation(s)
- Seiya Yamada
- Laboratory for Molecular Neurobiology, Graduate School of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan
| | - Ayaka Sato
- Laboratory for Molecular Neurobiology, Graduate School of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan
| | - Shin-Ichi Sakakibara
- Laboratory for Molecular Neurobiology, Graduate School of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan.
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42
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Rezvani A, Taherifard E, Mokhtari M, Feili A, Movahed H. H syndrome with a possibly new immunological phenotype. Int J Dermatol 2020; 59:e248-e251. [PMID: 32227473 DOI: 10.1111/ijd.14867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/22/2020] [Accepted: 03/04/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Alireza Rezvani
- Hematology and oncology, Shiraz Hematology Research Center, Shiraz, Fars, Iran
| | | | - Maral Mokhtari
- Pathology Department, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Afrooz Feili
- Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Hamed Movahed
- Shiraz University of Medical Sciences, Shiraz, Fars, Iran
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Davideit H, Becker S, Müller J, Becker NP, Göttel P, Abay A, Sinn A, Grossmann M, Mallek M, Haberland A, Weisshoff H. In-Vivo Degradation of DNA-Based Therapeutic BC 007 in Humans. Eur J Drug Metab Pharmacokinet 2019; 44:567-578. [PMID: 30674038 PMCID: PMC6617257 DOI: 10.1007/s13318-019-00541-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND AND OBJECTIVES Since there is no clear evidence in the literature to show how non-modified single-stranded DNA (ssDNA) drugs are metabolized in humans, we assessed the metabolism of BC 007, an ssDNA therapeutic, under development as a neutralizer of autoantibodies against G-protein-coupled receptors. In-vitro, investigating its stability in monkey plasma and serum, a successive 3'-exonuclease degradation resulting in several n-x degradation products has been previously reported. Here, we investigated the metabolism of BC 007 in humans after intravenous application to autoantibody-positive healthy subjects, in line with Phase I safety testing. METHODS 1H-NMR was applied for n-x degradation product search and beta-aminoisobutyric acid (bAIBA) measurement in urine; ultra-performance liquid chromatography-mass spectrometry was also used for the latter. Colorimetric assays were used for quantification of uric acid in serum and urine. RESULTS Fast degradation prohibited the detection of the intermediate n-x degradation products in urine using 1H-NMR. Instead, NMR revealed a further downstream degradation product, bAIBA, which was also detected in serum shortly after initial application. The purine degradation product, uric acid, confirmed this finding of fast metabolism. CONCLUSION Fast and full degradation of BC 007, shown by nucleic bases degradation products, is one of the first reports about the fate of a ssDNA product in humans.
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Affiliation(s)
- Hanna Davideit
- Berlin Cures GmbH, Robert-Rössle-Str. 10, Laboratory, 13125, Berlin, Germany
| | - Susanne Becker
- Department of Clinical Affairs, Berlin Cures GmbH, Knesebeckstr. 59-61, 10719, Berlin, Germany
| | - Johannes Müller
- Management, Berlin Cures GmbH, Knesebeckstr. 59-61, 10719, Berlin, Germany
| | - Niels-Peter Becker
- Department of Regulatory Affairs, Berlin Cures GmbH, Knesebeckstr. 59-61, 10719, Berlin, Germany
| | - Peter Göttel
- Management, Berlin Cures GmbH, Knesebeckstr. 59-61, 10719, Berlin, Germany
| | - Ayşe Abay
- Department of Clinical Affairs, Berlin Cures GmbH, Knesebeckstr. 59-61, 10719, Berlin, Germany
| | - Angela Sinn
- PAREXEL-PAREXEL International GmbH, Early Phase Clinical Unit, Klinikum Westend, Spandauer Damm 130, 14050, Berlin, Germany
| | - Matthias Grossmann
- PAREXEL-PAREXEL International GmbH, Early Phase Clinical Unit, Klinikum Westend, Spandauer Damm 130, 14050, Berlin, Germany
| | - Markus Mallek
- Department of Toxicology and Drug-Monitoring, Medizinisches Versorgungszentrum Dr. Eberhard & Partner Dortmund, Brauhausstr. 4, 44137, Dortmund, Germany
| | | | - Hardy Weisshoff
- Department of Chemistry, NMR Facility, Humboldt University of Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
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44
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Irony-Tur Sinai M, Salamon A, Stanleigh N, Goldberg T, Weiss A, Wang YH, Kerem B. AT-dinucleotide rich sequences drive fragile site formation. Nucleic Acids Res 2019; 47:9685-9695. [PMID: 31410468 PMCID: PMC6765107 DOI: 10.1093/nar/gkz689] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/18/2019] [Accepted: 08/04/2019] [Indexed: 12/29/2022] Open
Abstract
Common fragile sites (CFSs) are genomic regions prone to breakage under replication stress conditions recurrently rearranged in cancer. Many CFSs are enriched with AT-dinucleotide rich sequences (AT-DRSs) which have the potential to form stable secondary structures upon unwinding the double helix during DNA replication. These stable structures can potentially perturb DNA replication progression, leading to genomic instability. Using site-specific targeting system, we show that targeted integration of a 3.4 kb AT-DRS derived from the human CFS FRA16C into a chromosomally stable region within the human genome is able to drive fragile site formation under conditions of replication stress. Analysis of >1300 X chromosomes integrated with the 3.4 kb AT-DRS revealed recurrent gaps and breaks at the integration site. DNA sequences derived from the integrated AT-DRS showed in vitro a significantly increased tendency to fold into branched secondary structures, supporting the predicted mechanism of instability. Our findings clearly indicate that intrinsic DNA features, such as complexed repeated sequence motifs, predispose the human genome to chromosomal instability.
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Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University of Jerusalem, 9190401, Israel
| | - Anita Salamon
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, 229080733, USA
| | - Noemie Stanleigh
- Department of Genetics, The Life Sciences Institute, The Hebrew University of Jerusalem, 9190401, Israel
| | - Tchelet Goldberg
- Department of Genetics, The Life Sciences Institute, The Hebrew University of Jerusalem, 9190401, Israel
| | - Aryeh Weiss
- Faculty of Engineering, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, 229080733, USA
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University of Jerusalem, 9190401, Israel
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45
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Nguyen JH, Chung JD, Lynch GS, Ryall JG. The Microenvironment Is a Critical Regulator of Muscle Stem Cell Activation and Proliferation. Front Cell Dev Biol 2019; 7:254. [PMID: 31737625 PMCID: PMC6828616 DOI: 10.3389/fcell.2019.00254] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022] Open
Abstract
Skeletal muscle has a remarkable capacity to regenerate following injury, a property conferred by a resident population of muscle stem cells (MuSCs). In response to injury, MuSCs must double their cellular content to divide, a process requiring significant new biomass in the form of nucleotides, phospholipids, and amino acids. This new biomass is derived from a series of intracellular metabolic cycles and alternative routing of carbon. In this review, we examine the link between metabolism and skeletal muscle regeneration with particular emphasis on the role of the cellular microenvironment in supporting the production of new biomass and MuSC proliferation.
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Affiliation(s)
- John H Nguyen
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Jin D Chung
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Gordon S Lynch
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - James G Ryall
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
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Vogel M, Moehrle B, Brown A, Eiwen K, Sakk V, Geiger H. HPRT and Purine Salvaging Are Critical for Hematopoietic Stem Cell Function. Stem Cells 2019; 37:1606-1614. [PMID: 31574190 DOI: 10.1002/stem.3087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/23/2019] [Indexed: 12/17/2022]
Abstract
Adult hematopoietic stem cells (HSCs) maintain tissue homeostasis and regenerative capacity of the hematopoietic system through self-renewal and differentiation. Metabolism is recognized as an important regulatory entity controlling stem cells. As purine nucleotides are essential for metabolic functions, we analyzed the role of hypoxanthine guanine phosphoribosyl transferase (HPRT)-associated purine salvaging in HSCs. Here, we demonstrate that hematopoietic stem and progenitor cells (HSPCs) show a strong dependence on HPRT-associated purine salvaging. HSPCs with lower HPRT activity had a severely reduced competitive repopulation ability upon transplantation. Strikingly, HPRT deficiency resulted in altered cell-cycle progression, proliferation kinetics and mitochondrial membrane potential primarily in the HSC compartment, whereas more committed progenitors were less affected. Our data thus imply a unique and important role of HPRT and the purine salvage pathway for HSC function. Stem Cells 2019;37:1606-1614.
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Affiliation(s)
- Mona Vogel
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Bettina Moehrle
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Andreas Brown
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Karina Eiwen
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Vadim Sakk
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, Ulm, Germany.,Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio, USA
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Maiuri T, Suart CE, Hung CLK, Graham KJ, Barba Bazan CA, Truant R. DNA Damage Repair in Huntington's Disease and Other Neurodegenerative Diseases. Neurotherapeutics 2019; 16:948-956. [PMID: 31364066 PMCID: PMC6985310 DOI: 10.1007/s13311-019-00768-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Recent genome-wide association studies of Huntington's disease (HD) primarily highlighted genes involved in DNA damage repair mechanisms as modifiers of age at onset and disease severity, consistent with evidence that more DNA repair genes are being implicated in late age-onset neurodegenerative diseases. This provides an exciting opportunity to advance therapeutic development in HD, as these pathways have already been under intense investigation in cancer research. Also emerging are the roles of other polyglutamine disease proteins in DNA damage repair mechanisms. A potential universal trigger of oxidative DNA damage shared in these late age-onset diseases is the increase of reactive oxygen species (ROS) in human aging, defining an age-related mechanism that has defied other hypotheses of neurodegeneration. We discuss the potential commonality of DNA damage repair pathways in HD and other neurodegenerative diseases. Potential targets for therapy that may prove beneficial across many of these diseases are also identified, defining nodes in the ataxia telangiectasia-mutated (ATM) complex, mismatch repair, and poly ADP-ribose polymerases (PARPs).
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Affiliation(s)
- T Maiuri
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - C E Suart
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - C L K Hung
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - K J Graham
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - C A Barba Bazan
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada
| | - R Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, HSC 4N54, 1200 Main Street West, Hamilton, Ontario, L8N3Z5, Canada.
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Lipowska J, Miks CD, Kwon K, Shuvalova L, Zheng H, Lewiński K, Cooper DR, Shabalin IG, Minor W. Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae. Int J Biol Macromol 2019; 136:1176-1187. [PMID: 31207330 PMCID: PMC6686667 DOI: 10.1016/j.ijbiomac.2019.05.149] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/01/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
Abstract
The de novo pyrimidine biosynthesis pathway is essential for the proliferation of many pathogens. One of the pathway enzymes, dihydroorotase (DHO), catalyzes the reversible interconversion of N-carbamoyl-l-aspartate to 4,5-dihydroorotate. The substantial difference between bacterial and mammalian DHOs makes it a promising drug target for disrupting bacterial growth and thus an important candidate to evaluate as a response to antimicrobial resistance on a molecular level. Here, we present two novel three-dimensional structures of DHOs from Yersinia pestis (YpDHO), the plague-causing pathogen, and Vibrio cholerae (VcDHO), the causative agent of cholera. The evaluations of these two structures led to an analysis of all available DHO structures and their classification into known DHO types. Comparison of all the DHO active sites containing ligands that are listed in DrugBank was facilitated by a new interactive, structure-comparison and presentation platform. In addition, we examined the genetic context of characterized DHOs, which revealed characteristic patterns for different types of DHOs. We also generated a homology model for DHO from Plasmodium falciparum.
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Affiliation(s)
- Joanna Lipowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA; Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Poland
| | - Charles Dylan Miks
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Keehwan Kwon
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Ludmilla Shuvalova
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA
| | | | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA.
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA.
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49
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Jeon RH, Lee WJ, Son YB, Bharti D, Shivakumar SB, Lee SL, Rho GJ. PPIA, HPRT1, and YWHAZ Genes Are Suitable for Normalization of mRNA Expression in Long-Term Expanded Human Mesenchymal Stem Cells. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3093545. [PMID: 31240211 PMCID: PMC6556274 DOI: 10.1155/2019/3093545] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/09/2019] [Indexed: 12/15/2022]
Abstract
Long-term expansion of mesenchymal stem cells (MSCs) under defined culture conditions is necessary in human stem cell therapy. However, it alters the characteristics of MSCs. Since quantitative real time polymerase chain reaction (qRT-PCR) is widely used as one of the key analytical methods for comparative characterization, the validation of reference genes (RGs) for normalization under each experimental condition is important to achieve reliable qRT-PCR results. Therefore, the most stable RGs for long-term expanded bone marrow- and umbilical cord blood-derived MSCs (BM-MSCs and UCB-MSCs) under defined culture conditions for up to 20 passages were evaluated. The more apparent alterations in characteristics such as differentiation capacity, proliferation, senescence, and the expression of RGs were noted in BM-MSCs than UCB-MSCs during long-term expansion. The RG validation programs (GeNorm and NormFinder) suggested that PPIA, HPRT1, and YWHAZ were suitable for normalization in qRT-PCR regardless of MSC types and long-term culture expansion, and the traditional RGs (ACTB and GAPDH) were less stable in long-term expanded MSCs. In addition, the use of these RGs for normalization of OCT4 expression in long-term expanded BM-MSCs showed that a less stable RG (GAPDH) showed contrasting data compared to other RGs. Therefore, the use of RGs such as PPIA, HPRT1, and YWHAZ for normalization in qRT-PCR experiments is highly recommended for long-term expanded MSCs to generate accurate and reliable data.
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Affiliation(s)
- Ryoung-Hoon Jeon
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Won-Jae Lee
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Young-Bum Son
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Dinesh Bharti
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | | | - Sung-Lim Lee
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyu-Jin Rho
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
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Du J, An J, Linton JD, Wang Y, Hurley JB. How Excessive cGMP Impacts Metabolic Proteins in Retinas at the Onset of Degeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1074:289-295. [PMID: 29721955 DOI: 10.1007/978-3-319-75402-4_35] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Aryl-hydrocarbon receptor interacting protein-like 1 (AIPL1) is essential to stabilize cGMP phosphodiesterase 6 (PDE6) in rod photoreceptors. Mutation of AIPL1 leads to loss of PDE6, accumulation of intracellular cGMP, and rapid degeneration of rods. To understand the metabolic basis for the photoreceptor degeneration caused by excessive cGMP, we performed proteomics and phosphoproteomics analyses on retinas from AIPL1-/- mice at the onset of rod cell death. AIPL1-/- retinas have about 18 times less than normal PDE6a and no detectable PDE6b. We identified twelve other proteins and thirty-nine phosphorylated proteins related to cell metabolism that are significantly altered preceding the massive degeneration of rods. They include transporters, kinases, phosphatases, transferases, and proteins involved in mitochondrial bioenergetics and metabolism of glucose, lipids, amino acids, nucleotides, and RNA. In AIPLI-/- retinas mTOR and proteins involved in mitochondrial energy production and lipid synthesis are more dephosphorylated, but glycolysis proteins and proteins involved in leucine catabolism are more phosphorylated than in normal retinas. Our findings indicate that elevating cGMP rewires cellular metabolism prior to photoreceptor degeneration and that targeting metabolism may be a productive strategy to prevent or slow retinal degeneration.
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Affiliation(s)
- Jianhai Du
- Departments of Ophthalmology, and Biochemistry, West Virginia University, Morgantown, WV, USA
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Jie An
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jonathan D Linton
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Yekai Wang
- Departments of Ophthalmology, and Biochemistry, West Virginia University, Morgantown, WV, USA
| | - James B Hurley
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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