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Scalise A, Aggarwal A, Sangwan N, Hamer A, Guntupalli S, Park HE, Aleman JO, Cameron SJ. A Divergent Platelet Transcriptome in Patients with Lipedema and Lymphedema. Genes (Basel) 2024; 15:737. [PMID: 38927673 PMCID: PMC11202821 DOI: 10.3390/genes15060737] [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: 04/26/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Lipedema and lymphedema are physically similar yet distinct diseases that are commonly misdiagnosed. We previously reported that lipedema and lymphedema are associated with increased risk for venous thromboembolism (VTE). The underlying etiology of the prothrombotic profile observed in lipedema and lymphedema is unclear, but may be related to alterations in platelets. Our objective was to analyze the platelet transcriptome to identify biological pathways that may provide insight into platelet activation and thrombosis. The platelet transcriptome was evaluated in patients with lymphedema and lipedema, then compared to control subjects with obesity. Patients with lipedema were found to have a divergent transcriptome from patients with lymphedema. The platelet transcriptome and impacted biological pathways in lipedema were surprisingly similar to weight-matched comparators, yet different when compared to overweight individuals with a lower body mass index (BMI). Differences in the platelet transcriptome for patients with lipedema and lymphedema were found in biological pathways required for protein synthesis and degradation, as well as metabolism. Key differences in the platelet transcriptome for patients with lipedema compared to BMI-matched subjects involved metabolism and glycosaminoglycan processing. These inherent differences in the platelet transcriptome warrant further investigation, and may contribute to the increased risk of thrombosis in patients with lipedema and lymphedema.
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Affiliation(s)
- Alliefair Scalise
- Heart Vascular and Thoracic Institute, Department of Cardiovascular Medicine, Section of Vascular Medicine, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Anu Aggarwal
- Lerner Research Institute, Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Naseer Sangwan
- Lerner Research Institute, Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Annelise Hamer
- Heart Vascular and Thoracic Institute, Department of Cardiovascular Medicine, Section of Vascular Medicine, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Suman Guntupalli
- Lerner Research Institute, Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Huijun Edelyn Park
- Lerner Research Institute, Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Jose O. Aleman
- Holman Division of Endocrinology, New York University, New York, NY 10012, USA;
| | - Scott J. Cameron
- Heart Vascular and Thoracic Institute, Department of Cardiovascular Medicine, Section of Vascular Medicine, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
- Lerner Research Institute, Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
- Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Department of Hematology, Taussig Cancer Center, Cleveland, OH 44195, USA
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Ye Z, Liu Y, Jin X, Wu Y, Zhao H, Gao T, Deng Q, Cheng J, Lin J, Tong Z. Aβ-binding with alcohol dehydrogenase drives Alzheimer's disease pathogenesis: A review. Int J Biol Macromol 2024; 264:130580. [PMID: 38432266 DOI: 10.1016/j.ijbiomac.2024.130580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/17/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Although Alzheimer's disease (AD) characterized with senile plaques and neurofibrillary tangles has been found for over 100 years, its molecular mechanisms are ambiguous. More worsely, the developed medicines targeting amyloid-beta (Aβ) and/or tau hyperphosphorylation did not approach the clinical expectations in patients with moderate or severe AD until now. This review unveils the role of a vicious cycle between Aβ-derived formaldehyde (FA) and FA-induced Aβ aggregation in the onset course of AD. Document evidence has shown that Aβ can bind with alcohol dehydrogenase (ADH) to form the complex of Aβ/ADH (ABAD) and result in the generation of reactive oxygen species (ROS) and aldehydes including malondialdehyde, hydroxynonenal and FA; in turn, ROS-derived H2O2 and FA promotes Aβ self-aggregation; subsequently, this vicious cycle accelerates neuron death and AD occurrence. Especially, FA can directly induce neuron death by stimulating ROS generation and tau hyper hyperphosphorylation, and impair memory by inhibiting NMDA-receptor. Recently, some new therapeutical methods including inhibition of ABAD activity by small molecules/synthetic polypeptides, degradation of FA by phototherapy or FA scavengers, have been developed and achieved positive effects in AD transgenic models. Thus, breaking the vicious loop may be promising interventions for halting AD progression.
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Affiliation(s)
- Zuting Ye
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yanming Liu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xingjiang Jin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yiqing Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hang Zhao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tingting Gao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qiangfeng Deng
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianhua Cheng
- Department of neurology, the first affiliated hospital of Wenzhou medical University, Wenzhou 325035. China
| | - Jing Lin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Zhiqian Tong
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, China.
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He XY, Frackowiak J, Dobkin C, Brown WT, Yang SY. Involvement of Type 10 17β-Hydroxysteroid Dehydrogenase in the Pathogenesis of Infantile Neurodegeneration and Alzheimer's Disease. Int J Mol Sci 2023; 24:17604. [PMID: 38139430 PMCID: PMC10743717 DOI: 10.3390/ijms242417604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/02/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Type 10 17β-hydroxysteroid dehydrogenase (17β-HSD10) is the HSD17B10 gene product playing an appreciable role in cognitive functions. It is the main hub of exercise-upregulated mitochondrial proteins and is involved in a variety of metabolic pathways including neurosteroid metabolism to regulate allopregnanolone homeostasis. Deacetylation of 17β-HSD10 by sirtuins helps regulate its catalytic activities. 17β-HSD10 may also play a critical role in the control of mitochondrial structure, morphology and dynamics by acting as a member of the Parkin/PINK1 pathway, and by binding to cyclophilin D to open mitochondrial permeability pore. 17β-HSD10 also serves as a component of RNase P necessary for mitochondrial tRNA maturation. This dehydrogenase can bind with the Aβ peptide thereby enhancing neurotoxicity to brain cells. Even in the absence of Aβ, its quantitative and qualitative variations can result in neurodegeneration. Since elevated levels of 17β-HSD10 were found in brain cells of Alzheimer's disease (AD) patients and mouse AD models, it is considered to be a key factor in AD pathogenesis. Since data underlying Aβ-binding-alcohol dehydrogenase (ABAD) were not secured from reported experiments, ABAD appears to be a fabricated alternative term for the HSD17B10 gene product. Results of this study would encourage researchers to solve the question why elevated levels of 17β-HSD10 are present in brains of AD patients and mouse AD models. Searching specific inhibitors of 17β-HSD10 may find candidates to reduce senile neurodegeneration and open new approaches for the treatment of AD.
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Affiliation(s)
- Xue-Ying He
- Department of Molecular Biology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - Jannusz Frackowiak
- Department of Developmental Neurobiology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - Carl Dobkin
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - William Ted Brown
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - Song-Yu Yang
- Department of Molecular Biology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
- Ph.D. Program in Biology-Neuroscience, Graduate Center of the City, University of New York, New York, NY 10016, USA
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He XY, Dobkin C, Brown WT, Yang SY. Infantile Neurodegeneration Results from Mutants of 17β-Hydroxysteroid Dehydrogenase Type 10 Rather Than Aβ-Binding Alcohol Dehydrogenase. Int J Mol Sci 2023; 24:ijms24108487. [PMID: 37239833 DOI: 10.3390/ijms24108487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Type 10 17β-hydroxysteroid dehydrogenase (17β-HSD10), a homo-tetrameric multifunctional protein with 1044 residues encoded by the HSD17B10 gene, is necessary for brain cognitive function. Missense mutations result in infantile neurodegeneration, an inborn error in isoleucine metabolism. A 5-methylcytosine hotspot underlying a 388-T transition leads to the HSD10 (p.R130C) mutant to be responsible for approximately half of all cases suffering with this mitochondrial disease. Fewer females suffer with this disease due to X-inactivation. The binding capability of this dehydrogenase to Aβ-peptide may play a role in Alzheimer's disease, but it appears unrelated to infantile neurodegeneration. Research on this enzyme was complicated by reports of a purported Aβ-peptide-binding alcohol dehydrogenase (ABAD), formerly referred to as endoplasmic-reticulum-associated Aβ-binding protein (ERAB). Reports concerning both ABAD and ERAB in the literature reflect features inconsistent with the known functions of 17β-HSD10. It is clarified here that ERAB is reportedly a longer subunit of 17β-HSD10 (262 residues). 17β-HSD10 exhibits L-3-hydroxyacyl-CoA dehydrogenase activity and is thus also referred to in the literature as short-chain 3-hydorxyacyl-CoA dehydrogenase or type II 3-hydorxyacyl-CoA dehydrogenase. However, 17β-HSD10 is not involved in ketone body metabolism, as reported in the literature for ABAD. Reports in the literature referring to ABAD (i.e., 17β-HSD10) as a generalized alcohol dehydrogenase, relying on data underlying ABAD's activities, were found to be unreproducible. Furthermore, the rediscovery of ABAD/ERAB's mitochondrial localization did not cite any published research on 17β-HSD10. Clarification of the purported ABAD/ERAB function derived from these reports on ABAD/ERAB may invigorate this research field and encourage new approaches to the understanding and treatment of HSD17B10-gene-related disorders. We establish here that infantile neurodegeneration is caused by mutants of 17β-HSD10 but not ABAD, and so we conclude that ABAD represents a misnomer employed in high-impact journals.
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Affiliation(s)
- Xue-Ying He
- Department of Molecular Biology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - Carl Dobkin
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - William Ted Brown
- Central Clinical School, University of Sydney, Sydney 2006, Australia
| | - Song-Yu Yang
- Department of Molecular Biology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
- Ph.D. Program in Biology-Neuroscience, Graduate Center, City University of New York, New York, NY 10016, USA
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Deacetylation of HSD17B10 by SIRT3 regulates cell growth and cell resistance under oxidative and starvation stresses. Cell Death Dis 2020; 11:563. [PMID: 32703935 PMCID: PMC7378191 DOI: 10.1038/s41419-020-02763-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022]
Abstract
17-beta-hydroxysteroid dehydrogenase 10 (HSD17B10) plays an important role in mitochondrial fatty acid metabolism and is also involved in mitochondrial tRNA maturation. HSD17B10 missense mutations cause HSD10 mitochondrial disease (HSD10MD). HSD17B10 with mutations identified from cases of HSD10MD show loss of function in dehydrogenase activity and mitochondrial tRNA maturation, resulting in mitochondrial dysfunction. It has also been implicated to play roles in the development of Alzheimer disease (AD) and tumorigenesis. Here, we found that HSD17B10 is a new substrate of NAD-dependent deacetylase Sirtuin 3 (SIRT3). HSD17B10 is acetylated at lysine residues K79, K99 and K105 by the acetyltransferase CBP, and the acetylation is reversed by SIRT3. HSD17B10 acetylation regulates its enzymatic activity and the formation of mitochondrial RNase P. Furthermore, HSD17B10 acetylation regulates the intracellular functions, affecting cell growth and cell resistance in response to stresses. Our results demonstrated that acetylation is an important regulation mechanism for HSD17B10 and may provide insight into interrupting the development of AD.
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Vinklarova L, Schmidt M, Benek O, Kuca K, Gunn-Moore F, Musilek K. Friend or enemy? Review of 17β-HSD10 and its role in human health or disease. J Neurochem 2020; 155:231-249. [PMID: 32306391 DOI: 10.1111/jnc.15027] [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: 12/04/2019] [Revised: 03/26/2020] [Accepted: 04/10/2020] [Indexed: 12/17/2022]
Abstract
17β-hydroxysteroid dehydrogenase (17β-HSD10) is a multifunctional human enzyme with important roles both as a structural component and also as a catalyst of many metabolic pathways. This mitochondrial enzyme has important functions in the metabolism, development and aging of the neural system, where it is involved in the homeostasis of neurosteroids, especially in regard to estradiol, changes in which make it an essential part of neurodegenerative pathology. These roles therefore, indicate that 17β-HSD10 may be a possible druggable target for neurodegenerative diseases including Alzheimer's disease (AD), and in hormone-dependent cancer. The objective of this review was to provide a summary about physiological functions and pathological roles of 17β-HSD10 and the modulators of its activity.
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Affiliation(s)
- Lucie Vinklarova
- Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Monika Schmidt
- Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ondrej Benek
- Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kamil Kuca
- Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | | | - Kamil Musilek
- Faculty of Science, Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czech Republic
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Antunes A, Ramos MJ. Gathering Computational Genomics and Proteomics to Unravel Adaptive Evolution. Evol Bioinform Online 2017. [DOI: 10.1177/117693430700300004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A recent editorial in PLoS Biology by MacCallum and Hill (2006) pointed out the inappropriateness of studies evaluating signatures of positive selection based solely in single-site analyses. Therefore the rising number of articles claiming positive selection that have been recently published urges the question of how to improve the bioinformatics standards for reliably unravel positive selection? Deeper integrative efforts using state-of-the-art methodologies at the gene-level and protein-level are improving positive selection studies. Here we provide some computational guidelines to thoroughly document molecular adaptation.
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Affiliation(s)
- Agostinho Antunes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687; 4169-007 Porto, Portugal
| | - Maria João Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687; 4169-007 Porto, Portugal
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Yang SY, He XY, Isaacs C, Dobkin C, Miller D, Philipp M. Roles of 17β-hydroxysteroid dehydrogenase type 10 in neurodegenerative disorders. J Steroid Biochem Mol Biol 2014; 143:460-72. [PMID: 25007702 DOI: 10.1016/j.jsbmb.2014.07.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 01/24/2023]
Abstract
17β-Hydroxysteroid dehydrogenase type 10 (17β-HSD10) is encoded by the HSD17B10 gene mapping at Xp11.2. This homotetrameric mitochondrial multifunctional enzyme catalyzes the oxidation of neuroactive steroids and the degradation of isoleucine. This enzyme is capable of binding to other peptides, such as estrogen receptor α, amyloid-β, and tRNA methyltransferase 10C. Missense mutations of the HSD17B10 gene result in 17β-HSD10 deficiency, an infantile neurodegeneration characterized by progressive psychomotor regression and alteration of mitochondria morphology. 17β-HSD10 exhibits only a negligible alcohol dehydrogenase activity, and is not localized in the endoplasmic reticulum or plasma membrane. Its alternate name - Aβ binding alcohol dehydrogenase (ABAD) - is a misnomer predicated on the mistaken belief that this enzyme is an alcohol dehydrogenase. Misconceptions about the localization and function of 17β-HSD10 abound. 17β-HSD10's proven location and function must be accurately identified to properly assess this enzyme's important role in brain metabolism, especially the metabolism of allopregnanolone. The brains of individuals with Alzheimer's disease (AD) and of animals in an AD mouse model exhibit abnormally elevated levels of 17β-HSD10. Abnormal expression, as well as mutations of the HSD17B10 gene leads to impairment of the structure, function, and dynamics of mitochondria. This may underlie the pathogenesis of the synaptic and neuronal deficiency exhibited in 17β-HSD10 related diseases, including 17β-HSD10 deficiency and AD. Restoration of steroid homeostasis could be achieved by the supplementation of neuroactive steroids with a proper dosing and treatment regimen or by the adjustment of 17β-HSD10 activity to protect neurons. The discovery of this enzyme's true function has opened a new therapeutic avenue for treating AD.
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Affiliation(s)
- Song-Yu Yang
- Department of Developmental Biochemistry, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA; Neuroscience Doctoral Program, Graduate Center of the City University of New York, 365 Fifth Avenue, NY 10016, USA.
| | - Xue-Ying He
- Department of Developmental Biochemistry, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA
| | - Charles Isaacs
- Department of Developmental Biochemistry, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA
| | - Carl Dobkin
- Department of Molecular Genetics, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA; Neuroscience Doctoral Program, Graduate Center of the City University of New York, 365 Fifth Avenue, NY 10016, USA
| | - David Miller
- Department of Molecular Biology, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA
| | - Manfred Philipp
- Department of Chemistry, Lehman College of CUNY, 250 Bedford Park Boulevard West, Bronx, NY 10468, USA; Biochemistry Doctoral Program, Graduate Center of the City University of New York, 365 Fifth Avenue, NY 10016, USA
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Tomasco IH, Lessa EP. Two mitochondrial genes under episodic positive selection in subterranean octodontoid rodents. Gene 2014; 534:371-8. [DOI: 10.1016/j.gene.2013.09.097] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 08/28/2013] [Accepted: 09/26/2013] [Indexed: 11/27/2022]
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Abstract
Background Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Methods Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Results Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Conclusions Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.
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Wiwanitkit V. Physiological genomics analysis for Alzheimer's disease. Ann Indian Acad Neurol 2013; 16:72-4. [PMID: 23661967 PMCID: PMC3644786 DOI: 10.4103/0972-2327.107711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 01/26/2012] [Accepted: 06/21/2012] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease is a common kind of dementia. This disorder can be detected in all countries around the world. This neurological disorder affects millions of population and becomes an important concern in modern neurology. There are many researches on the pathogenesis of Alzheimer's disease. Although it has been determined for a long time, there is no clear-cut that this is a case with genetic disorder or not. A physiological genomics is a new application that is useful for track function to genes within the human genome and can be applied for answering the problem of underlying pathobiology of complex diseases. The physiogenomics can be helpful for study of systemic approach on the pathophysiology, and genomics might provide useful information to better understand the pathogenesis of Alzheimer's disease. The present advent in genomics technique makes it possible to trace for the underlying genomics of disease. In this work, physiological genomics analysis for Alzheimer's disease was performed. The standard published technique is used for assessment. According to this work, there are 20 identified physiogenomics relationship on several chromosomes. Considering the results, the HADH2 gene on chromosome X, APBA1 gene on chromosome 9, AGER gene on chromosome 6, GSK3B gene on chromosome 3, CDKHR1 gene on chromosome 17, APPBP1 gene on chromosome 16, APBA2 gene on chromosome 15, GAL gene on chromosome 11, and APLP2 gene on chromosome 11 have the highest physiogenomics score (9.26) while the CASP3 gene on chromosome 4 and the SNCA gene on chromosome 4 have the lowest physiogenomics score (7.44). The results from this study confirm that Alzheimer's disease has a polygenomic origin.
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Lim YA, Grimm A, Giese M, Mensah-Nyagan AG, Villafranca JE, Ittner LM, Eckert A, Götz J. Inhibition of the mitochondrial enzyme ABAD restores the amyloid-β-mediated deregulation of estradiol. PLoS One 2011; 6:e28887. [PMID: 22174920 PMCID: PMC3236223 DOI: 10.1371/journal.pone.0028887] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 11/16/2011] [Indexed: 11/25/2022] Open
Abstract
Alzheimer's disease (AD) is a conformational disease that is characterized by amyloid-β (Aβ) deposition in the brain. Aβ exerts its toxicity in part by receptor-mediated interactions that cause down-stream protein misfolding and aggregation, as well as mitochondrial dysfunction. Recent reports indicate that Aβ may also interact directly with intracellular proteins such as the mitochondrial enzyme ABAD (Aβ binding alcohol dehydrogenase) in executing its toxic effects. Mitochondrial dysfunction occurs early in AD, and Aβ's toxicity is in part mediated by inhibition of ABAD as shown previously with an ABAD decoy peptide. Here, we employed AG18051, a novel small ABAD-specific compound inhibitor, to investigate the role of ABAD in Aβ toxicity. Using SH-SY5Y neuroblastoma cells, we found that AG18051 partially blocked the Aβ-ABAD interaction in a pull-down assay while it also prevented the Aβ42-induced down-regulation of ABAD activity, as measured by levels of estradiol, a known hormone and product of ABAD activity. Furthermore, AG18051 is protective against Aβ42 toxicity, as measured by LDH release and MTT absorbance. Specifically, AG18051 reduced Aβ42-induced impairment of mitochondrial respiration and oxidative stress as shown by reduced ROS (reactive oxygen species) levels. Guided by our previous finding of shared aspects of the toxicity of Aβ and human amylin (HA), with the latter forming aggregates in Type 2 diabetes mellitus (T2DM) pancreas, we determined whether AG18051 would also confer protection from HA toxicity. We found that the inhibitor conferred only partial protection from HA toxicity indicating distinct pathomechanisms of the two amyloidogenic agents. Taken together, our results present the inhibition of ABAD by compounds such as AG18051 as a promising therapeutic strategy for the prevention and treatment of AD, and suggest levels of estradiol as a suitable read-out.
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Affiliation(s)
- Yun-An Lim
- Alzheimer's & Parkinson's Disease Laboratory, Brain & Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - Amandine Grimm
- Neurobiology Laboratory, Psychiatric University Clinics Basel, University of Basel, Basel, Switzerland
| | - Maria Giese
- Neurobiology Laboratory, Psychiatric University Clinics Basel, University of Basel, Basel, Switzerland
| | - Ayikoe Guy Mensah-Nyagan
- Equipe Steroïdes, Neuromodulateurs et Neuropathologies, Université de Strasbourg, Strasbourg, France
| | | | - Lars M. Ittner
- Alzheimer's & Parkinson's Disease Laboratory, Brain & Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - Anne Eckert
- Neurobiology Laboratory, Psychiatric University Clinics Basel, University of Basel, Basel, Switzerland
- * E-mail: (JG); (AE)
| | - Jürgen Götz
- Alzheimer's & Parkinson's Disease Laboratory, Brain & Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia
- * E-mail: (JG); (AE)
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Yang SY, He XY, Miller D. Hydroxysteroid (17β) dehydrogenase X in human health and disease. Mol Cell Endocrinol 2011; 343:1-6. [PMID: 21708223 DOI: 10.1016/j.mce.2011.06.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 06/13/2011] [Indexed: 12/24/2022]
Abstract
Hydroxysteroid (17β) dehydrogenase 10 (HSD10), the HSD17B10 gene product, is a mitochondrial NAD(+)-dependent dehydrogenase. There are two outstanding features of this vital enzyme: (a) the versatility of its catalytic endowment is attributed to the flexibility of its active site to accommodate diverse substrates such as steroids, fatty acids, bile acid, and xenobiotics; (b) its capacity to bind other proteins and peptides. For example, it tightly binds with three identical subunits to compose a homotetramer. The homotetramer then binds with two other proteins, namely, RNA (guanine-9-)methyl-transferase domain containing-1 and KIAA0391, to form mitochondrial RNase P. Furthermore, various HSD10 functions are inhibited when the enzyme is bound by amyloid-β peptide or estrogen receptor alpha. Missense mutations of HSD10 may cause neurodegeneration related to HSD10 deficiency, whereas a silent mutation of HSD10 results in mental retardation, choreoathetosis and abnormal behavior (MRXS10). The clinical condition of some HSD10 patients mimics mitochondrial disorders. Since normal HSD10 function is essential for brain cognitive activity, elevated levels of HSD10 found in brains of Alzheimer disease (AD) patients and mouse AD model might counterbalance the inhibition of HSD10 by amyloid-β peptide. The investigation of HSD10 may lead to a better understanding of AD pathogenesis.
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Affiliation(s)
- Song-Yu Yang
- Department of Neurochemistry, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA.
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Pérez-Brocal V, Gil R, Moya A, Latorre A. New Insights on the Evolutionary History of Aphids and Their Primary Endosymbiont Buchnera aphidicola. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2011; 2011:250154. [PMID: 21350635 PMCID: PMC3042603 DOI: 10.4061/2011/250154] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 12/24/2010] [Indexed: 11/20/2022]
Abstract
Since the establishment of the symbiosis between the ancestor of modern aphids and their primary endosymbiont, Buchnera aphidicola, insects and bacteria have coevolved. Due to this parallel evolution, the analysis of bacterial genomic features constitutes a useful tool to understand their evolutionary history. Here we report, based on data from B. aphidicola, the molecular evolutionary analysis, the phylogenetic relationships among lineages and a comparison of sequence evolutionary rates of symbionts of four aphid species from three subfamilies. Our results support previous hypotheses of divergence of B. aphidicola and their host lineages during the early Cretaceous and indicate a closer relationship between subfamilies Eriosomatinae and Lachninae than with the Aphidinae. They also reveal a general evolutionary pattern among strains at the functional level. We also point out the effect of lifecycle and generation time as a possible explanation for the accelerated rate in B. aphidicola from the Lachninae.
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Affiliation(s)
- Vicente Pérez-Brocal
- Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Avenida de Cataluña 21, 46020 Valencia, Spain
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Jakob-Roetne R, Jacobsen H. Alzheimer's disease: from pathology to therapeutic approaches. Angew Chem Int Ed Engl 2009; 48:3030-59. [PMID: 19330877 DOI: 10.1002/anie.200802808] [Citation(s) in RCA: 486] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Mind how you go: The current strategies for the development of therapies for Alzheimer's disease are very diverse. Particular attention is given to the search for inhibitors (see picture for two examples) of the proteolytic enzyme beta- and gamma-secretase, which inhibits the cleavage of the amyloid precursor proteins into amyloid beta peptides, from which the disease-defining deposits of plaque in the brains of Alzheimer's patients originates.Research on senile dementia and Alzheimer's disease covers an extremely broad range of scientific activities. At the recent international meeting of the Alzheimer's Association (ICAD 2008, Chicago) more than 2200 individual scientific contributions were presented. The aim of this Review is to give an overview of the field and to outline its main areas, starting from behavioral abnormalities and visible pathological findings and then focusing on the molecular details of the pathology. The "amyloid hypothesis" of Alzheimer's disease is given particular attention, since the majority of the ongoing therapeutic approaches are based on its theoretical framework.
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Affiliation(s)
- Roland Jakob-Roetne
- F.Hoffmann-La Roche AG, Medicinal Chemistry, Bldg 92/8.10B, 4070 Basel, Switzerland.
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He X, Yang S. Comments on 'Significance of developmental expression of amphioxus Branchiostoma belcheri and zebrafish Danio rerio Hsd17b10 in biological and medical research'. JOURNAL OF FISH BIOLOGY 2009; 74:1689-1692. [PMID: 20735667 DOI: 10.1111/j.1095-8649.2009.02175.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The reported data on the developmental expression of Hsd17b10 gene in Danio rerio is crucial to the utilization of the D. rerio embryo as an animal model for human developmental disorders caused either by mutations on HSD17B10 (formerly HADH2) or by defective expression of the gene. Related diseases were summarized, and it was noticed that hyperinsulinaemic hypoglycaemia is not linked to HSD17B10. This inherited disease is actually caused by a deletion in the HADH gene on chromosome 4. Moreover, it was found by a revision of the reported phylogenetic tree that hydroxyacyl-CoA dehydrogenase II or rather hydroxysteroid (17beta) dehydrogenase 10 (HSD10) of amphioxus Branchiostoma belcheri-occupies a transition position from HSD10 orthologs of invertebrates to those of vertebrates.
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Affiliation(s)
- X He
- Department of Neurochemistry, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA
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Jakob-Roetne R, Jacobsen H. Die Alzheimer-Demenz: von der Pathologie zu therapeutischen Ansätzen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200802808] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Mindnich R, Adamski J. Zebrafish 17beta-hydroxysteroid dehydrogenases: an evolutionary perspective. Mol Cell Endocrinol 2009; 301:20-6. [PMID: 19111899 DOI: 10.1016/j.mce.2008.12.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 12/02/2008] [Accepted: 12/03/2008] [Indexed: 01/13/2023]
Abstract
The term 17beta-hydroxysteroid dehydrogenase (17beta-HSD) describes an enzyme that stereospecifically reduces or oxidizes a keto- or hydroxy group at C17 of the steroid scaffold, respectively. Fourteen mammalian 17beta-HSDs have been identified so far and nine sequence homologs are found in zebrafish. 17beta-HSDs additionally active in fatty acid metabolism display high sequence conservation and widespread tissue expression. Homologs of these multifunctional 17beta-HSDs have been identified in flies, worms and yeast, and steroid-converting activity was demonstrated in some cases. The "classical" 17beta-HSDs, types 1, 2 and 3, are steroid-specific enzymes expressed in few tissues. They may have arisen at the beginning of vertebrate evolution allowing new, differently controlled modes of steroid hormone action. These findings reflect on two aspects: (1) the evolutionary origin of steroid-specific enzymes and (2) a possible conservation of steroid hormone function in invertebrates through currently unknown mechanisms.
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Affiliation(s)
- R Mindnich
- University of Pennsylvania, School of Medicine, Department of Pharmacology, 3620 Hamilton Walk, 135 John Morgan Building, Philadelphia, PA 19104, USA.
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Osorio DS, Antunes A, Ramos MJ. Structural and functional implications of positive selection at the primate angiogenin gene. BMC Evol Biol 2007; 7:167. [PMID: 17883850 PMCID: PMC2194721 DOI: 10.1186/1471-2148-7-167] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 09/20/2007] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Angiogenesis, the formation of new blood vessels, is a primordial process in development and its dysregulation has a central role in the pathogenesis of many diseases. Angiogenin (ANG), a peculiar member of the RNase A superfamily, is a potent inducer of angiogenesis involved in many different types of cancer, amyotrophic lateral sclerosis and also with a possible role in the innate immune defense. The evolutionary path of this family has been a highly dynamic one, where positive selection has played a strong role. In this work we used a combined gene and protein level approach to determine the main sites under diversifying selection on the primate ANG gene and analyze its structural and functional implications. RESULTS We obtained evidence for positive selection in the primate ANG gene. Site specific analysis pointed out 15 sites under positive selection, most of which also exhibited drastic changes in amino acid properties. The mapping of these sites in the ANG 3D-structure described five clusters, four of which were located in functional regions: two in the active site region, one in the nucleolar location signal and one in the cell-binding site. Eight of the 15 sites under selection in the primate ANG gene were highly or moderately conserved in the RNase A family, suggesting a directed event and not a simple consequence of local structural or functional permissiveness. Moreover, 11 sites were exposed to the surface of the protein indicating that they may influence the interactions performed by ANG. CONCLUSION Using a maximum likelihood gene level analysis we identified 15 sites under positive selection in the primate ANG genes, that were further corroborated through a protein level analysis of radical changes in amino acid properties. These sites mapped onto the main functional regions of the ANG protein. The fact that evidence for positive selection is present in all ANG regions required for angiogenesis may be a good indication that angiogenesis is the process under selection. However, other possibilities to be considered arise from the possible involvement of ANG in innate immunity and the potential influence or co-evolution with its interacting proteins and ligands.
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Affiliation(s)
- Daniel S Osorio
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
- INSERM UMR S 787-Groupe Myologie, Faculté de Médecine – Pitié-Salpétrière, UPMC Paris VI, 105 bd. de l'Hôpital, 75634, Paris Cedex 13, France
| | - Agostinho Antunes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
- CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal
| | - Maria J Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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Antunes A, Ramos MJ. Gathering computational genomics and proteomics to unravel adaptive evolution. Evol Bioinform Online 2007; 3:207-9. [PMID: 19461985 PMCID: PMC2684141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
A recent editorial in PLoS Biology by MacCallum and Hill (2006) pointed out the inappropriateness of studies evaluating signatures of positive selection based solely in single-site analyses. Therefore the rising number of articles claiming positive selection that have been recently published urges the question of how to improve the bioinformatics standards for reliably unravel positive selection? Deeper integrative efforts using state-of-the-art methodologies at the gene-level and protein-level are improving positive selection studies. Here we provide some computational guidelines to thoroughly document molecular adaptation.
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Affiliation(s)
- Agostinho Antunes
- Correspondence: Antunes, CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal.
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Yang SY, He XY, Miller D. HSD17B10: a gene involved in cognitive function through metabolism of isoleucine and neuroactive steroids. Mol Genet Metab 2007; 92:36-42. [PMID: 17618155 DOI: 10.1016/j.ymgme.2007.06.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 06/06/2007] [Accepted: 06/06/2007] [Indexed: 12/20/2022]
Abstract
The HSD17B10 gene maps on chromosome Xp11.2, a region highly associated with X-linked mental retardation. This gene encodes HSD10, a mitochondrial multifunctional enzyme that plays a significant part in the metabolism of neuroactive steroids and the degradation of isoleucine. The HSD17B10 gene is composed of six exons and five introns. Its exon 5 is an alternative exon such that there are several HSD17B10 mRNA isoforms in brain. A silent mutation (c.605C-->A) and three missense mutations (c.395C-->G; c.419C-->T; c.771A-->G), respectively, cause the X-linked mental retardation, choreoathetosis, and abnormal behavior (MRXS10) and the hydroxyacyl-CoA dehydrogenase II deficiency. The latter condition seems to be a multifactorial disease due to the disturbance of more than one metabolic pathway by the HSD10 deficiency. HSD10 inactivates the positive modulators of GABAA receptors, and plays a role in the maintenance of GABAergic neuronal function. This working model may account for the mental retardation of these patients. The dehydrogenase activity is slightly inhibited by the binding of amyloid-beta peptide to the loop D of HSD10. Elevated levels of HSD10 were observed in hippocampi of Alzheimer disease patients so this multifunctional enzyme may be related to Alzheimer disease pathogenesis; however, the molecular mechanism of its involvement remains to be ascertained.
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Affiliation(s)
- Song-Yu Yang
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA.
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