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Hao B, Chen K, Zhai L, Liu M, Liu B, Tan M. Substrate and Functional Diversity of Protein Lysine Post-translational Modifications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae019. [PMID: 38862432 DOI: 10.1093/gpbjnl/qzae019] [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: 01/01/2023] [Revised: 11/11/2023] [Accepted: 01/08/2024] [Indexed: 06/13/2024]
Abstract
Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.
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Affiliation(s)
- Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kaifeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Muyin Liu
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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2
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Sukjoi W, Young C, Acland M, Siritutsoontorn S, Roytrakul S, Klingler-Hoffmann M, Hoffmann P, Jitrapakdee S. Proteomic analysis of holocarboxylase synthetase deficient-MDA-MB-231 breast cancer cells revealed the biochemical changes associated with cell death, impaired growth signaling, and metabolism. Front Mol Biosci 2024; 10:1250423. [PMID: 38283944 PMCID: PMC10812114 DOI: 10.3389/fmolb.2023.1250423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024] Open
Abstract
We have previously shown that the holocarboxylase synthetase (HLCS) is overexpressed in breast cancer tissue of patients, and silencing of its expression in triple-negative cancer cell line inhibits growth and migration. Here we investigated the global biochemical changes associated with HLCS knockdown in MDA-MB-231 cells to discern the pathways that involve HLCS. Proteomic analysis of two independent HLCS knockdown cell lines identified 347 differentially expressed proteins (DEPs) whose expression change > 2-fold (p < 0.05) relative to the control cell line. GO enrichment analysis showed that these DEPs were mainly associated with the cellular process such as cellular metabolic process, cellular response to stimulus, and cellular component organization or biogenesis, metabolic process, biological regulation, response to stimuli, localization, and signaling. Among the 347 identified DEPs, 64 proteins were commonly found in both HLCS knockdown clones, confirming their authenticity. Validation of some of these DEPs by Western blot analysis showed that plasminogen activator inhibitor type 2 (SerpinB2) and interstitial collagenase (MMP1) were approximately 90% decreased in HLCS knockdown cells, consistent with a 50%-60% decrease in invasion ability of knockdown cells. Notably, argininosuccinate synthase 1 (ASS1), one of the enzymes in the urea cycle, showed approximately a 10-fold increase in the knockdown cells, suggesting the crucial role of HLCS in supporting the urea cycle in the triple-negative cancer cell line. Collectively, our proteomic data provide biochemical insights into how suppression of HLCS expression perturbs global changes in cellular processes and metabolic pathways, impairing cell growth and invasion.
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Affiliation(s)
- Witchuda Sukjoi
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Clifford Young
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Mitchell Acland
- Adelaide Proteomics Centre, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | | | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Agency, Pathumthani, Thailand
| | | | - Peter Hoffmann
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
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3
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Yang N, Zhang Y, Huang Y, Yan J, Qian Z, Li H, Luo P, Yang Z, Luo M, Wei X, Nie H, Ruan L, Hao Y, Gao S, Zheng K, Zhang C, Zhang L. FGF21 at physiological concentrations regulates vascular endothelial cell function through multiple pathways. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166558. [PMID: 36174877 DOI: 10.1016/j.bbadis.2022.166558] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/05/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022]
Abstract
Cardiovascular diseases are closely associated with dysfunction of vascular endothelial cells (VECs), which can be influenced by various intrinsic and extrinsic factors, including fibroblast growth factor 21 (FGF21), but the effects of serum FGF21 on VECs remain unclear. We performed a cross-sectional study nested within a prospective cohort to assess the range of physiological concentrations of fasting serum FGF21 in 212 healthy individuals. We also treated human umbilical VECs (HUVECs) with recombinant FGF21 at different concentrations. The effects of FGF21 treatment on glycolysis, nitric oxide release and reduction of intracellular reactive oxygen species were assessed. The cells were also collected for RNA transcriptomic sequencing to investigate the potential mechanisms induced by FGF21 treatment. In addition, the roles of SIRT1 in the regulation of FGF21 were evaluated by SIRT1 knockdown. The results showed that the serum FGF21 concentration in healthy individuals ranged from 15.70 to 499.96 pg/mL and was positively correlated with age and pulse wave velocity. FGF21 at 400 pg/mL was sufficient to enhance glycolysis, increase nitric oxide release and protect cells from H2O2-induced oxidative damage. The upregulated genes after FGF21 treatment were mostly enriched in metabolic pathways, whereas the downregulated genes were mostly enriched in inflammation and apoptosis signaling pathways. Moreover, SIRT1 may be involved in the regulation of some genes by FGF21. In conclusion, our data indicate that FGF21 at a level within the physiological concentration range has a beneficial effect on HUVECs and that this effect may partly depend on the regulation of SIRT1.
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Affiliation(s)
- Ni Yang
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yucong Zhang
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Huang
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinhua Yan
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zonghao Qian
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Han Li
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pengcheng Luo
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhen Yang
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mandi Luo
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiuxian Wei
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Nie
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Ruan
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Hao
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shangbang Gao
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Zheng
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cuntai Zhang
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Le Zhang
- Department of Geriatrics, Institute of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Pan C, Zhao A, Li M. Atopic Dermatitis-like Genodermatosis: Disease Diagnosis and Management. Diagnostics (Basel) 2022; 12:diagnostics12092177. [PMID: 36140582 PMCID: PMC9498295 DOI: 10.3390/diagnostics12092177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/23/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Eczema is a classical characteristic not only in atopic dermatitis but also in various genodermatosis. Patients suffering from primary immunodeficiency diseases such as hyper-immunoglobulin E syndromes, Wiskott-Aldrich syndrome, immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome, STAT5B deficiency, Omenn syndrome, atypical complete DiGeorge syndrome; metabolic disorders such as acrodermatitis enteropathy, multiple carboxylase deficiency, prolidase deficiency; and other rare syndromes like severe dermatitis, multiple allergies and metabolic wasting syndrome, Netherton syndrome, and peeling skin syndrome frequently perform with eczema-like lesions. These genodermatosis may be misguided in the context of eczematous phenotype. Misdiagnosis of severe disorders unavoidably affects appropriate treatment and leads to irreversible outcomes for patients, which underlines the importance of molecular diagnosis and genetic analysis. Here we conclude clinical manifestations, molecular mechanism, diagnosis and management of several eczema-related genodermatosis and provide accessible advice to physicians.
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Affiliation(s)
- Chaolan Pan
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Anqi Zhao
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Ming Li
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Department of Dermatology, The Children’s Hospital of Fudan University, Shanghai 200092, China
- Correspondence: ; Tel.: +86-2125078571
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Cheng T, Cao J, Wu T, Jiang X, Yarmolenko MA, Rogachev AA, Rogachev AV. Study on osteoinductive activity of biotin film by low-energy electron beam deposition. BIOMATERIALS ADVANCES 2022; 135:212730. [PMID: 35929224 DOI: 10.1016/j.bioadv.2022.212730] [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: 10/02/2021] [Revised: 01/29/2022] [Accepted: 02/20/2022] [Indexed: 06/15/2023]
Abstract
Biotin film was prepared by low-energy electron beam deposition (LEBD). The molecular structure, chemical composition and micromorphology of the biotin film were investigated by 1HNMR, FTIR, XPS, AFM and SEM. The results showed the molecular structure of a monolayer of biotin film is fully consistent with the molecular structure of the initial biotin powders. The contact angle test showed that the biotin film exhibit good hydrophilicity. The release kinetics of biotin film was tested by UV-Vis method. It was found that the film was almost completely released in about two weeks. The cell viability of MC3T3-E1 cells on the surface of the biotin film was attaining 100.54 ± 1.7% (P < 0.05), showing excellent biocompatibility and biosafety. Titanium implant with surface of biotin film was implanted into the femoral head of rabbits as experimental group. The animals were euthanized after four weeks. Compared with the control group, mature lamellar bone formation was observed with dense trabecular bone, and the expression of Coll-I, Runx2 and BMP-2 was better. The results showed that the repair effect of bone defect in the experimental group was excellent.
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Affiliation(s)
- Tongfei Cheng
- Nanjing University of Science and Technology, 200, Xiaolingwei Street, Nanjing 210094, China
| | - Jinxing Cao
- Nanjing University of Science and Technology, 200, Xiaolingwei Street, Nanjing 210094, China
| | - Tiantian Wu
- Nanjing University of Science and Technology, 200, Xiaolingwei Street, Nanjing 210094, China
| | - Xiaohong Jiang
- Nanjing University of Science and Technology, 200, Xiaolingwei Street, Nanjing 210094, China.
| | - M A Yarmolenko
- Francisk Skorina Gomel State University, 104, Sovetskaya Street, Gomel 246019, Belarus
| | - A A Rogachev
- Francisk Skorina Gomel State University, 104, Sovetskaya Street, Gomel 246019, Belarus
| | - A V Rogachev
- Francisk Skorina Gomel State University, 104, Sovetskaya Street, Gomel 246019, Belarus
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Siritutsoontorn S, Sukjoi W, Polyak SW, Akekawatchai C, Jitrapakdee S. Differential growth inhibition, cell cycle arrest and apoptosis of MCF-7 and MDA-MB-231 cells to holocarboxylase synthetase suppression. Biochem Biophys Res Commun 2022; 593:108-115. [PMID: 35063765 DOI: 10.1016/j.bbrc.2022.01.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/12/2022] [Indexed: 11/02/2022]
Abstract
Holocarboxylase synthetase (HLCS) catalyzes the covalent attachment of biotin onto the biotin-dependent carboxylases. Recent studies have shown that HLCS is over-expressed in breast cancer patients. Here we investigated the functional roles of free biotin and HLCS in supporting growth and migration of breast cancer cell lines. Depletion of biotin from culture medium markedly reduced biotinylation of the two most abundant biotin-carboxylases, acetyl-CoA carboxylase and pyruvate carboxylase. This was accompanied by a marked decrease in cell growth. Suppression of HLCS expression in the low invasive breast cancer cell line MCF-7 resulted in an 80% reduction of biotinylated ACC, but not PC. HLCS knockdown MCF-7 cell lines showed 40-50% reduction of proliferation and 35% reduction of migration, accompanied by G1 cell cycle-arrest-induced apoptosis. In contrast, knockdown of HLCS expression in the highly invasive cell line MDA-MB-231 resulted in only marginal reduction of biotinylation of both ACC and PC, accompanied by 30% reduction of proliferation and 30% reduction of migration. Our studies provide new insights to use HLCS as a novel anti-cancer drug target.
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Affiliation(s)
| | - Witchuda Sukjoi
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Steven W Polyak
- Clinical and Health Sciences, University of South Australia, Adelaide, Australia, 5001
| | - Chareeporn Akekawatchai
- Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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Biotin rescues mitochondrial dysfunction and neurotoxicity in a tauopathy model. Proc Natl Acad Sci U S A 2020; 117:33608-33618. [PMID: 33318181 DOI: 10.1073/pnas.1922392117] [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] [Indexed: 12/26/2022] Open
Abstract
Mitochondrial and metabolic dysfunction are often implicated in neurological disease, but effective mechanism-based therapies remain elusive. We performed a genome-scale forward genetic screen in a Drosophila model of tauopathy, a class of neurodegenerative disorders characterized by the accumulation of the protein tau, and identified manipulation of the B-vitamin biotin as a potential therapeutic approach in tauopathy. We show that tau transgenic flies have an innate biotin deficiency due to tau-mediated relaxation of chromatin and consequent aberrant expression of multiple biotin-related genes, disrupting both carboxylase and mitochondrial function. Biotin depletion alone causes mitochondrial pathology and neurodegeneration in both flies and human neurons, implicating mitochondrial dysfunction as a mechanism in biotin deficiency. Finally, carboxylase biotin levels are reduced in mammalian tauopathies, including brains of human Alzheimer's disease patients. These results provide insight into pathogenic mechanisms of human biotin deficiency, the resulting effects on neuronal health, and a potential therapeutic pathway in the treatment of tau-mediated neurotoxicity.
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Liu H, Jeffery CJ. Moonlighting Proteins in the Fuzzy Logic of Cellular Metabolism. Molecules 2020; 25:molecules25153440. [PMID: 32751110 PMCID: PMC7435893 DOI: 10.3390/molecules25153440] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/09/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
The numerous interconnected biochemical pathways that make up the metabolism of a living cell comprise a fuzzy logic system because of its high level of complexity and our inability to fully understand, predict, and model the many activities, how they interact, and their regulation. Each cell contains thousands of proteins with changing levels of expression, levels of activity, and patterns of interactions. Adding more layers of complexity is the number of proteins that have multiple functions. Moonlighting proteins include a wide variety of proteins where two or more functions are performed by one polypeptide chain. In this article, we discuss examples of proteins with variable functions that contribute to the fuzziness of cellular metabolism.
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Affiliation(s)
- Haipeng Liu
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, IL 60607, USA;
| | - Constance J. Jeffery
- Department of Biological Sciences, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, IL 60607, USA
- Correspondence: ; Tel.: +1-312-996-3168
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Xiong Z, Zhang G, Luo X, Zhang N, Zheng J. Case report of holocarboxylase synthetase deficiency (late-onset) in 2 Chinese patients. Medicine (Baltimore) 2020; 99:e19964. [PMID: 32358368 PMCID: PMC7440356 DOI: 10.1097/md.0000000000019964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE Holocarboxylase synthetase (HCLS) deficiency, especially the late-onset type, is a rare disease. Affected patients can present with irreversible metabolic acidosis and may be misdiagnosed with a glucose metabolic disorder. Prompt and correct diagnosis and treatment can reduce mortality to a great extent. PATIENT CONCERNS We report 2 Chinese patients who were diagnosed with late-onset HCLS deficiency. The age of onset of the 2 patients was approximately 8 months. The 2 patients had skin lesions, severe profound metabolic acidosis, dyspnea, and hyperglycemia. DIAGNOSES The results of urinary and blood organic acid analysis with gas chromatography/mass spectrometry revealed multiple carboxylase deficiency. Maple syrup urine disease and diabetic ketoacidosis could not be excluded. This finding is different from those of hypoglycemic complications reported in previous reports. Human genetic analysis eventually provided a definite diagnosis. INTERVENTIONS Prompt oral treatment with biotin dramatically corrected the metabolic imbalances of the 2 patients, and continued oral biotin therapy was essential to the improvement of their prognoses. OUTCOMES Their metabolic disorders were corrected within 48 hours. During long-term follow-up, the patients achieved developmental milestones. LESSONS Late-onset HCLS deficiency may present with obvious hyperglycemia. Human genetic analysis eventually provided a definite diagnosis. Prompt treatment with biotin is vital to correct metabolic imbalances, and continued therapy is essential to the improving long-term prognoses. Their mutations were p.R508W and c.1088T > A, and these mutations might represent hot-spot genes in Chinese populations with HCLS deficiency. The variants c.1484T > G(p.L495*) and c.835G > T(p.E279x) are likely pathogenic, and more studies are needed to confirm these results.
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Astorkia M, Hernández M, Bocs S, Ponce K, León O, Morales S, Quezada N, Orellana F, Wendra F, Sembiring Z, Asmono D, Ritter E. Detection of significant SNP associated with production and oil quality traits in interspecific oil palm hybrids using RARSeq. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110366. [PMID: 31928673 DOI: 10.1016/j.plantsci.2019.110366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
A RARSeq based Association mapping study was performed in a population of 104 Elaeis oleifera x E. guineensis hybrids of five origins with the aim of finding functional markers associated to six productive and 19 oil quality traits. For this purpose mRNA of each genotype was isolated and double stranded cDNA was synthesized. Following digestion with two restriction enzymes and adapter ligation, a size selected pool of barcoded amplicons was produced and sequenced using Illumina MiSeq. The obtained sequences were processed with a "snakemake" pipeline, filtered and missing values were imputed. For all traits except two significant effects of the origin was observed. Genetic diversity analyses revealed high variability within origins and an excess of heterozygosity in the population. Two GLM models with Q matrix or PCA matrix as covariates and two MLM models incorporating in addition a Kinship matrix were tested for genotype-phenotype associations using GAPIT software. Using unadjusted p values (< 0.01) 78 potential associations were detected involving 25 SNP and 20 traits. When applying FDR multiple testing with p < 0.05, 25 significant associations remained involving eight SNP and six quality traits. Four SNP were located in genes with a potential relevant biological meaning.
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Affiliation(s)
- Maider Astorkia
- NEIKER Tecnalia, Campus Agroalimentario De Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain.
| | - Mónica Hernández
- NEIKER Tecnalia, Campus Agroalimentario De Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, F-34398, Montpellier, France; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France; South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, Montpellier, France
| | - Kevin Ponce
- La Fabril SA, Km 5.5 via Manta, Montecristi, Avenida 113, 130902, Manta, Ecuador
| | - Olga León
- Energy & Palma SA, Av. Atahualpa E3-49 y Juan Gonzales, Ed. Fundación Pérez Pallarez, Officina 4ª, 170507, Quito, Ecuador
| | - Shone Morales
- La Fabril SA, Km 5.5 via Manta, Montecristi, Avenida 113, 130902, Manta, Ecuador
| | - Nathalie Quezada
- La Fabril SA, Km 5.5 via Manta, Montecristi, Avenida 113, 130902, Manta, Ecuador
| | - Francisco Orellana
- Energy & Palma SA, Av. Atahualpa E3-49 y Juan Gonzales, Ed. Fundación Pérez Pallarez, Officina 4ª, 170507, Quito, Ecuador
| | - Fahmi Wendra
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788, Palembang, 30127, Indonesia
| | - Zulhermana Sembiring
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788, Palembang, 30127, Indonesia
| | - Dwi Asmono
- Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788, Palembang, 30127, Indonesia
| | - Enrique Ritter
- NEIKER Tecnalia, Campus Agroalimentario De Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain
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León-Del-Río A. Biotin in metabolism, gene expression, and human disease. J Inherit Metab Dis 2019; 42:647-654. [PMID: 30746739 DOI: 10.1002/jimd.12073] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/05/2019] [Indexed: 12/16/2022]
Abstract
Biotin is a water-soluble vitamin that belongs to the vitamin B complex and which is an essential nutrient of all living organisms from bacteria to man. In eukaryotic cells biotin functions as a prosthetic group of enzymes, collectively known as biotin-dependent carboxylases that catalyze key reactions in gluconeogenesis, fatty acid synthesis, and amino acid catabolism. Enzyme-bound biotin acts as a vector to transfer a carboxyl group between donor and acceptor molecules during carboxylation reactions. In recent years, evidence has mounted that biotin also regulates gene expression through a mechanism beyond its role as a prosthetic group of carboxylases. These activities may offer a mechanistic background to a developing literature on the action of biotin in neurological disorders. This review summarizes the role of biotin in activating carboxylases and proposed mechanisms associated with a role in gene expression and in ameliorating neurological disease.
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Affiliation(s)
- Alfonso León-Del-Río
- Programa de Investigación en Cáncer de Mama and Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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12
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Abstract
Inborn errors of metabolism, also known as inherited metabolic diseases, constitute an important group of conditions presenting with neurologic signs in newborns. They are individually rare but collectively common. Many are treatable through restoration of homeostasis of a disrupted metabolic pathway. Given their frequency and potential for treatment, the clinician should be aware of this group of conditions and learn to identify the typical manifestations of the different inborn errors of metabolism. In this review, we summarize the clinical, laboratory, electrophysiologic, and neuroimaging findings of the different inborn errors of metabolism that can present with florid neurologic signs and symptoms in the neonatal period.
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MESH Headings
- Adult
- Female
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/diagnosis
- Infant, Newborn, Diseases/diagnostic imaging
- Infant, Newborn, Diseases/physiopathology
- Infant, Newborn, Diseases/therapy
- Metabolism, Inborn Errors/diagnosis
- Metabolism, Inborn Errors/diagnostic imaging
- Metabolism, Inborn Errors/physiopathology
- Metabolism, Inborn Errors/therapy
- Neuroimaging
- Pregnancy
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Affiliation(s)
- Carlos R Ferreira
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Rare Disease Institute, Children's National Health System, Washington, DC, United States
| | - Clara D M van Karnebeek
- Departments of Pediatrics and Clinical Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands; Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada.
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13
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Parr LS, Sriram G, Nazarian R, Rahib L, Dipple KM. The ATP-stimulated translocation promoter (ASTP) activity of glycerol kinase plays central role in adipogenesis. Mol Genet Metab 2018; 124:254-265. [PMID: 29960856 DOI: 10.1016/j.ymgme.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 11/16/2022]
Abstract
Glycerol kinase (GK) is a multifunctional enzyme located at the interface of carbohydrate and fat metabolism. It contributes to both central carbon metabolism and adipogenesis; specifically, through its role as the ATP-stimulated translocation promoter (ASTP). GK overexpression leads to increased ASTP activity and increased fat storage in H4IIE cells. We performed metabolic flux analysis in human GK-overexpressing H4IIE cells and found that overexpressing cells had significantly altered fluxes through central carbon and lipid metabolism including increased flux through the pentose phosphate pathway and increased production of lipids. We also observed an equal contribution of glycerol to carbohydrate metabolism in all cell lines, suggesting that GK's alternate functions rather than its enzymatic function are important for these processes. To further elucidate the contributions of the enzymatic (phosphorylation) and alternative (ASTP) functions of GK in adipogenesis, we performed experiments on mammalian GK and E. coli GK. We determined that the ASTP function of GK (which is absent in E. coli GK) plays a greater role than the enzymatic activity in these processes. These studies further emphasize GK's diverse functionality and provides fundamental insights into the multiple protein functions of glycerol kinase.
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Affiliation(s)
- Lilly S Parr
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Los Angeles, CA 90095-7088, USA
| | - Ganesh Sriram
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Los Angeles, CA 90095-7088, USA; Department of Chemical and Biomolecular Engineering, Henry Samueli School of Engineering and Applied Science at UCLA, 420 Westwood Plaza, Los Angeles, CA 90095, USA; Department of Chemical and Biomolecular Engineering, 1208D Building 90, Chemical and Nuclear Engineering Bldg, University of Maryland, College Park, MD 20742-2111, USA
| | - Ramin Nazarian
- Department of Medicine/Dermatology, David Geffen School of Medicine at UCLA, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Lola Rahib
- Biomedical Engineering, Interdepartmental Program, Henry Samueli School of Engineering and Applied Science at UCLA, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Katrina M Dipple
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Los Angeles, CA 90095-7088, USA; Biomedical Engineering, Interdepartmental Program, Henry Samueli School of Engineering and Applied Science at UCLA, 420 Westwood Plaza, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine at UCLA, Mattel Children's Hospital at UCLA, 10833 Le Conte Avenue, Los Angeles, CA 90095-1782, USA; University of Washington, Department of Pediatrics, Seattle Children's Hospital, Division of Genetic Medicine, 4800 Sand Point Way NE, Seattle, WA 98105, USA.
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14
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Wongkittichote P, Ah Mew N, Chapman KA. Propionyl-CoA carboxylase - A review. Mol Genet Metab 2017; 122:145-152. [PMID: 29033250 PMCID: PMC5725275 DOI: 10.1016/j.ymgme.2017.10.002] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 12/20/2022]
Abstract
Propionyl-CoA carboxylase (PCC) is the enzyme which catalyzes the carboxylation of propionyl-CoA to methylmalonyl-CoA and is encoded by the genes PCCA and PCCB to form a hetero-dodecamer. Dysfunction of PCC leads to the inherited metabolic disorder propionic acidemia, which can result in an affected individual presenting with metabolic acidosis, hyperammonemia, lethargy, vomiting and sometimes coma and death if not treated. Individuals with propionic acidemia also have a number of long term complications resulting from the dysfunction of the PCC enzyme. Here we present an overview of the current knowledge about the structure and function of PCC. We review an updated list of human variants which are published and provide an overview of the disease.
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Affiliation(s)
- Parith Wongkittichote
- Children's National Health System, Division of Genetics and Metabolism, United States
| | - Nicholas Ah Mew
- Children's National Health System, Division of Genetics and Metabolism, United States; Rare Diseases Institute, Division of Genetics and Metabolism, United States
| | - Kimberly A Chapman
- Children's National Health System, Division of Genetics and Metabolism, United States; Rare Diseases Institute, Division of Genetics and Metabolism, United States.
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