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Graziano B, Wang L, White OR, Kaplan DH, Fernandez-Abascal J, Bianchi L. Glial KCNQ K + channels control neuronal output by regulating GABA release from glia in C. elegans. Neuron 2024:S0896-6273(24)00123-5. [PMID: 38460523 DOI: 10.1016/j.neuron.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/22/2024] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
KCNQs are voltage-gated K+ channels that control neuronal excitability and are mutated in epilepsy and autism spectrum disorder (ASD). KCNQs have been extensively studied in neurons, but their function in glia is unknown. Using voltage, calcium, and GABA imaging, optogenetics, and behavioral assays, we show here for the first time in Caenorhabditis elegans (C. elegans) that glial KCNQ channels control neuronal excitability by mediating GABA release from glia via regulation of the function of L-type voltage-gated Ca2+ channels. Further, we show that human KCNQ channels have the same role when expressed in nematode glia, underscoring conservation of function across species. Finally, we show that pathogenic loss-of-function and gain-of-function human KCNQ2 mutations alter glia-to-neuron GABA signaling in distinct ways and that the KCNQ channel opener retigabine exerts rescuing effects. This work identifies glial KCNQ channels as key regulators of neuronal excitability via control of GABA release from glia.
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Affiliation(s)
- Bianca Graziano
- Department Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lei Wang
- Department Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Olivia R White
- Department Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Daryn H Kaplan
- Department Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jesus Fernandez-Abascal
- Department Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Laura Bianchi
- Department Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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2
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Buneeva O, Medvedev A. Ubiquitin Carboxyl-Terminal Hydrolase L1 and Its Role in Parkinson's Disease. Int J Mol Sci 2024; 25:1303. [PMID: 38279302 PMCID: PMC10816476 DOI: 10.3390/ijms25021303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), also known as Parkinson's disease protein 5, is a highly expressed protein in the brain. It plays an important role in the ubiquitin-proteasome system (UPS), where it acts as a deubiquitinase (DUB) enzyme. Being the smallest member of the UCH family of DUBs, it catalyzes the reaction of ubiquitin precursor processing and the cleavage of ubiquitinated protein remnants, thus maintaining the level of ubiquitin monomers in the brain cells. UCHL1 mutants, containing amino acid substitutions, influence catalytic activity and its aggregability. Some of them protect cells and transgenic mice in toxin-induced Parkinson's disease (PD) models. Studies of putative protein partners of UCHL1 revealed about sixty individual proteins located in all major compartments of the cell: nucleus, cytoplasm, endoplasmic reticulum, plasma membrane, mitochondria, and peroxisomes. These include proteins related to the development of PD, such as alpha-synuclein, amyloid-beta precursor protein, ubiquitin-protein ligase parkin, and heat shock proteins. In the context of the catalytic paradigm, the importance of these interactions is not clear. However, there is increasing understanding that UCHL1 exhibits various effects in a catalytically independent manner through protein-protein interactions. Since this protein represents up to 5% of the soluble protein in the brain, PD-related changes in its structure will have profound effects on the proteomes/interactomes in which it is involved. Growing evidence is accumulating that the role of UCHL1 in PD is obviously determined by a balance of canonic catalytic activity and numerous activity-independent protein-protein interactions, which still need better characterization.
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Affiliation(s)
| | - Alexei Medvedev
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia;
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3
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Lou J, Chu X, Yang X, Jamil M, Zhu H. Deciphering DNA repair gene mutational landscape in uterine corpus endometrial carcinoma patients using next generation sequencing. Am J Cancer Res 2024; 14:210-226. [PMID: 38323278 PMCID: PMC10839304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/25/2023] [Indexed: 02/08/2024] Open
Abstract
Uterine Corpus Endometrial Carcinoma (UCEC) is a significant health concern with a complex genetic landscape impacting disease susceptibility and progression. This study aimed to unravel the spectrum of DNA repair gene mutations in Pakistani UCEC patients through Next Generation Sequencing (NGS) and explore their potential functional consequences via downstream analyses. NGS analysis of genomic DNA from 30 UCEC patients was conducted to identify clinically significant pathogenic mutations in DNA repair genes. This analysis revealed mutations in 4 key DNA repair genes: BRCA1, BRCA2, APC, and CDH1. Kaplan-Meier (KM) analysis was employed to assess the prognostic value of these mutations on patient overall survival (OS) in UCEC. To delve into the functional impact of these mutations, we performed RT-qPCR, immunohistochemistry (IHC), and western blot analyses on the mutated UCEC samples compared to their non-mutated counterparts. These results unveiled the up-regulation in the expression of the mutated genes, suggesting a potential association between the identified mutations and enhanced gene activity. Additionally, targeted bisulfite sequencing analysis was utilized to evaluate DNA methylation patterns in the promoters of the mutated genes. Strikingly, hypomethylation in the promoters of BRCA1, BRCA2, APC, and CDH1 was observed in the mutated UCEC samples relative to the non-mutated, indicating the involvement of epigenetic mechanisms in the altered gene expression. In conclusion, this study offers insights into the genetic landscape of DNA repair gene mutations in Pakistani UCEC patients. The presence of pathogenic mutations in BRCA1, BRCA2, APC, and CDH1, coupled with their down-regulation and hypermethylation, suggests a convergence of genetic and epigenetic factors contributing to genomic instability in UCEC cells. These findings enhance our understanding of UCEC susceptibility and provide potential avenues for targeted therapeutic interventions in Pakistani UCEC patients.
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Affiliation(s)
- Jun Lou
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Key Laboratory of Translational Research for CancerNanchang 330029, Jiangxi, China
| | - Xiaoyan Chu
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
| | - Xiaorong Yang
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Hong Zhu
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
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4
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Pitsillou E, Logothetis ANO, Liang JJ, El-Osta A, Hung A, AbuMaziad AS, Karagiannis TC. Identification of Potential Modulators of a Pathogenic G Protein-Gated Inwardly Rectifying K + Channel 4 Mutant: In Silico Investigation in the Context of Drug Discovery for Hypertension. Molecules 2023; 28:7946. [PMID: 38138436 PMCID: PMC10745636 DOI: 10.3390/molecules28247946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Genetic abnormalities have been associated with primary aldosteronism, a major cause of secondary hypertension. This includes mutations in the KCNJ5 gene, which encodes G protein-gated inwardly rectifying K+ channel 4 (GIRK4). For example, the substitution of glycine with glutamic acid gives rise to the pathogenic GIRK4G151E mutation, which alters channel selectivity, making it more permeable to Na+ and Ca2+. While tertiapin and tertiapin-Q are well-known peptide inhibitors of the GIRK4WT channel, clinically, there is a need for the development of selective modulators of mutated channels, including GIRK4G151E. Using in silico methods, including homology modeling, protein-peptide docking, ligand-binding site prediction, and molecular docking, we aimed to explore potential modulators of GIRK4WT and GIRK4G151E. Firstly, protein-peptide docking was performed to characterize the binding site of tertiapin and its derivative to the GIRK4 channels. In accordance with previous studies, the peptide inhibitors preferentially bind to the GIRK4WT channel selectivity filter compared to GIRK4G151E. A ligand-binding site analysis was subsequently performed, resulting in the identification of two potential regions of interest: the central cavity and G-loop gate. Utilizing curated chemical libraries, we screened over 700 small molecules against the central cavity of the GIRK4 channels. Flavonoids, including luteolin-7-O-rutinoside and rutin, and the macrolides rapamycin and troleandomycin bound strongly to the GIRK4 channels. Similarly, xanthophylls, particularly luteoxanthin, bound to the central cavity with a strong preference towards the mutated GIRK4G151E channel compared to GIRK4WT. Overall, our findings suggest potential lead compounds for further investigation, particularly luteoxanthin, that may selectively modulate GIRK4 channels.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Alexander N. O. Logothetis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Julia J. Liang
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32 Ngan Shing Street, Sha Tin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Biomedical Laboratory Science, Department of Technology, Faculty of Health, University College Copenhagen, 1799 Copenhagen, Denmark
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Asmaa S. AbuMaziad
- Department of Pediatrics, College of Medicine Tucson, The University of Arizona, Tucson, AZ 85724, USA
| | - Tom C. Karagiannis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
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5
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Giudice V, Serio B, Errichiello S, Ferrara I, Galdiero A, Bertolini A, Visconti R, De Novellis D, Guariglia R, Luponio S, Morini D, Della Corte AM, Sessa AM, Verdesca F, Langella M, Izzo B, Selleri C. Subclones with variants of uncertain clinical significance might contribute to ineffective hemopoiesis and leukemia predisposition. Eur J Haematol 2023; 111:729-741. [PMID: 37501402 DOI: 10.1111/ejh.14069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Splicing modifications, genomic instability, and hypomethylation are central mechanisms promoting myelodysplasia and acute myeloid leukemia (AML). In this real-life retrospective study, to elucidate pathophysiology of clonal hemopoiesis in hematological malignancies, we investigated clinical significance of mutations in leukemia-related genes of known pathogenetic significance and of variants of uncertain clinical significance (VUS) in a cohort of patients with MDS and AML. METHODS A total of 59 consecutive subjects diagnosed with MDS, 48 with AML, and 17 with clonal cytopenia with unknown significance were screened for somatic mutations in AML-related genes by next-generation sequencing. RESULTS We showed that TET2, SETBP1, ASXL1, EZH2, RUNX1, SRSF2, DNMT3A, and IDH1/2 were commonly mutated. MDS patients also showed a high genetic complexity, especially for SETBP1. Moreover, the presence of SETBP1 wild-type or two or more simultaneous VUS variants identified a subgroup of AML and MDS patients with better outcome, while the presence of single SETBP1 VUS variant was related to a worse prognosis, regardless TET2 mutational status. CONCLUSIONS In conclusions, we linked both pathogenic and VUS variants in AML-related genes to clonal hematopoiesis; therefore, we proposed to consider those variants as prognostic markers in leukemia and myelodysplasia. However, further studies in larger prospective cohorts are required to validate our results.
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Affiliation(s)
- Valentina Giudice
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
| | - Bianca Serio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Santa Errichiello
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Idalucia Ferrara
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Alessandra Galdiero
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Angela Bertolini
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Roberta Visconti
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Danilo De Novellis
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
| | - Roberto Guariglia
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Serena Luponio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Denise Morini
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Anna Maria Della Corte
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Anna Maria Sessa
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Francesco Verdesca
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Maddalena Langella
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Barbara Izzo
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Carmine Selleri
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
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6
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Davyt M, Bharti N, Ignatova Z. Effect of mRNA/tRNA mutations on translation speed: Implications for human diseases. J Biol Chem 2023; 299:105089. [PMID: 37495112 PMCID: PMC10470029 DOI: 10.1016/j.jbc.2023.105089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Recent discoveries establish tRNAs as central regulators of mRNA translation dynamics, and therefore cotranslational folding and function of the encoded protein. The tRNA pool, whose composition and abundance change in a cell- and tissue-dependent manner, is the main factor which determines mRNA translation velocity. In this review, we discuss a group of pathogenic mutations, in the coding sequences of either protein-coding genes or in tRNA genes, that alter mRNA translation dynamics. We also summarize advances in tRNA biology that have uncovered how variations in tRNA levels on account of genetic mutations affect protein folding and function, and thereby contribute to phenotypic diversity in clinical manifestations.
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Affiliation(s)
- Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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7
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Abstract
DNA sequencing has revolutionized medicine over recent decades. However, analysis of large structural variation and repetitive DNA, a hallmark of human genomes, has been limited by short-read technology, with read lengths of 100-300 bp. Long-read sequencing (LRS) permits routine sequencing of human DNA fragments tens to hundreds of kilobase pairs in size, using both real-time sequencing by synthesis and nanopore-based direct electronic sequencing. LRS permits analysis of large structural variation and haplotypic phasing in human genomes and has enabled the discovery and characterization of rare pathogenic structural variants and repeat expansions. It has also recently enabled the assembly of a complete, gapless human genome that includes previously intractable regions, such as highly repetitive centromeres and homologous acrocentric short arms. With the addition of protocols for targeted enrichment, direct epigenetic DNA modification detection, and long-range chromatin profiling, LRS promises to launch a new era of understanding of genetic diversity and pathogenic mutations in human populations.
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Affiliation(s)
- Peter E Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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8
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Pasquadibisceglie A, Bonaccorsi di Patti MC, Musci G, Polticelli F. Membrane Transporters Involved in Iron Trafficking: Physiological and Pathological Aspects. Biomolecules 2023; 13:1172. [PMID: 37627237 PMCID: PMC10452680 DOI: 10.3390/biom13081172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Iron is an essential transition metal for its involvement in several crucial biological functions, the most notable being oxygen storage and transport. Due to its high reactivity and potential toxicity, intracellular and extracellular iron levels must be tightly regulated. This is achieved through transport systems that mediate cellular uptake and efflux both at the level of the plasma membrane and on the membranes of lysosomes, endosomes and mitochondria. Among these transport systems, the key players are ferroportin, the only known transporter mediating iron efflux from cells; DMT1, ZIP8 and ZIP14, which on the contrary, mediate iron influx into the cytoplasm, acting on the plasma membrane and on the membranes of lysosomes and endosomes; and mitoferrin, involved in iron transport into the mitochondria for heme synthesis and Fe-S cluster assembly. The focus of this review is to provide an updated view of the physiological role of these membrane proteins and of the pathologies that arise from defects of these transport systems.
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Affiliation(s)
| | | | - Giovanni Musci
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy;
| | - Fabio Polticelli
- Department of Sciences, University Roma Tre, 00146 Rome, Italy;
- National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy
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9
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Mian A, Wei J, Shi Z, Rifkin AS, Zheng SL, Glaser AP, Kearns JT, Helfand BT, Xu J. Systematic review of reported association studies of monogenic genes and bladder cancer risk and confirmation analysis in a large population cohort. BJUI Compass 2023; 4:156-163. [PMID: 36816149 PMCID: PMC9931534 DOI: 10.1002/bco2.206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/10/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Objectives To evaluate which of previously reported monogenic genes are associated with increased bladder cancer risk, we reviewed published papers on associations of genes and bladder cancer risk and performed a confirmation study of these genes in a large population-based cohort. Subjects and methods A systematic review of published papers prior to June 2022 was performed first to identify all genes where germline mutations were associated with bladder cancer risk. The associations of these candidate genes with bladder cancer risk were then tested among 1695 bladder cancer cases and 186 271 controls in the UK Biobank (UKB). The robust SKAT-O, a gene-based analysis that properly controls for type I error rates due to unbalanced case-control ratio, was used for association tests adjusting for age at recruitment, gender, smoking status, and genetic background. Results The systematic review identified nine genes that were significantly associated with bladder cancer risk in at least one study (p < 0.05), including MUTYH, MSH2, MSH6, MLH1, ATM, BRCA2, ERCC5, TGFB1 and CHEK2. When pathogenic/likely pathogenic mutations were aggregated within each gene, the association was confirmed for three genes in the UKB at p < 0.0056 (Bonferroni correction for nine tests), including CHEK2, ATM and BRCA2, all also known to be associated with hereditary breast cancer. Suggestive evidence of association was found for two other genes, including MLH1 (p = 0.006) and MSH2 (p = 0.007), both known to be associated with Lynch syndrome. Among these five genes, the bladder cancer risks range from 1.60 (ATM) to 4.88 (MLH1), and mutation carrier rates in cases range from 0.06% (MSH2) to 2.01% (CHEK2). Conclusion This study provides statistical evidence for association of previously reported genes and bladder cancer risk and has clinical utility for risk assessment and genetic counselling.
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Affiliation(s)
- Abrar Mian
- Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA.,Midwestern University Chicago College of Osteopathic Medicine Downers Grove Illinois
| | - Jun Wei
- Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA
| | - Zhuqing Shi
- Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA
| | - Andrew S Rifkin
- Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA
| | - Alexander P Glaser
- Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA.,Department of Surgery NorthShore University HealthSystem Evanston Illinois USA
| | - James T Kearns
- Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA.,Department of Surgery NorthShore University HealthSystem Evanston Illinois USA
| | - Brian T Helfand
- Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA.,Department of Surgery NorthShore University HealthSystem Evanston Illinois USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA.,Department of Surgery NorthShore University HealthSystem Evanston Illinois USA.,Department of Surgery University of Chicago Pritzker School of Medicine Chicago Illinois USA
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10
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Rosa P, De Falco E, Pacini L, Piazza A, Ciracì P, Ricciardi L, Fiorentino F, Trungu S, Miscusi M, Raco A, Calogero A. Next-Generation Sequencing Comparative Analysis of DNA Mutations between Blood-Derived Extracellular Vesicles and Matched Cancer Tissue in Patients with Grade 4 Glioblastoma. Biomedicines 2022; 10:biomedicines10102590. [PMID: 36289852 PMCID: PMC9599233 DOI: 10.3390/biomedicines10102590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 12/24/2022] Open
Abstract
The biological heterogeneity of glioblastoma, IDH-wildtype (GBM, CNS WHO grade 4), the most aggressive type of brain cancer, is a critical hallmark, caused by changes in the genomic mutational asset and influencing clinical progression over time. The understanding and monitoring of the mutational profile is important not only to reveal novel therapeutic targets in this set of patients, but also to ameliorate the clinical stratification of subjects and the prognostic significance. As neurosurgery represents the primary technique to manage GBM, it is of utmost importance to optimize alternative and less invasive methods to monitor the dynamic mutation profile of these patients. Extracellular vesicles (EVs) are included in the liquid biopsy analysis and have emerged as the biological mirror of escaping and surviving mechanisms by many tumors, including glioblastoma. Very few studies have investigated the technical feasibility to detect and analyze the genomic profile by Next-Generation Sequencing (UMI system) in circulating EVs of patients with grade IV glioblastoma. Here, we attempted to characterize and to compare the corresponding matched tissue samples and potential variants with pathogenic significance of the DNA contained in peripheral-blood-derived EVs. The NGS analysis has revealed that patients with grade IV glioblastoma exhibited lesser DNA content in EVs than controls and that, both in EVs and matched cancer tissues, the NF1 gene was consistently mutated in all patients, with the c.2568C>G as the most common pathogenic variant expressed. This study supports the clinical utility of circulating EVs in glioblastoma as an eligible tool for personalized medicine.
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Affiliation(s)
- Paolo Rosa
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.so Della Repubblica 79, 04100 Latina, Italy
- Correspondence: (P.R.); (M.M.)
| | - Elena De Falco
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.so Della Repubblica 79, 04100 Latina, Italy
- Mediterranea Cardiocentro, 80122 Naples, Italy
| | - Luca Pacini
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.so Della Repubblica 79, 04100 Latina, Italy
| | - Amedeo Piazza
- Operative Unit of Neurosurgery, Department of NESMOS, Sapienza University of Rome, 00185 Rome, Italy
| | - Paolo Ciracì
- Operative Unit of Neurosurgery, Department of NESMOS, Sapienza University of Rome, 00185 Rome, Italy
| | - Luca Ricciardi
- Operative Unit of Neurosurgery, Department of NESMOS, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Fiorentino
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Sokol Trungu
- Operative Unit of Neurosurgery, Department of NESMOS, Sapienza University of Rome, 00185 Rome, Italy
- UO di Neurochirurgia, Azienda Ospedaliera Cardinal G. Panico, 73039 Tricase, Italy
| | - Massimo Miscusi
- Operative Unit of Neurosurgery, Department of NESMOS, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: (P.R.); (M.M.)
| | - Antonino Raco
- Operative Unit of Neurosurgery, Department of NESMOS, Sapienza University of Rome, 00185 Rome, Italy
| | - Antonella Calogero
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.so Della Repubblica 79, 04100 Latina, Italy
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11
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Halman A, Dolzhenko E, Oshlack A. STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data. Hum Mutat 2022; 43:859-868. [PMID: 35395114 PMCID: PMC9541159 DOI: 10.1002/humu.24382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/01/2021] [Accepted: 04/06/2022] [Indexed: 11/22/2022]
Abstract
Expansions of short tandem repeats (STRs) have been implicated as the causal variant in over 50 diseases known to date. There are several tools which can genotype STRs from high‐throughput sequencing (HTS) data. However, running these tools out of the box only allows around half of the known disease‐causing loci to be genotyped. Furthermore, the genotypes estimated at these loci are often underestimated with maximum lengths limited to either the read or fragment length, which is less than the pathogenic cutoff for some diseases. Although analysis tools can be customized to genotype extra loci, this requires proficiency in bioinformatics to set up, limiting their widespread usage by other researchers and clinicians. To address these issues, we have developed a new software called STRipy, which is able to target all known disease‐causing STRs from HTS data. We created an intuitive graphical interface for STRipy and significantly simplified the detection of STRs expansions. Moreover, we genotyped all disease loci for over two and half thousand samples to provide population‐wide distributions to assist with interpretation of results. We believe the simplicity and breadth of STRipy will increase the genotyping of STRs in sequencing data resulting in further diagnoses of rare STR diseases.
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Affiliation(s)
- Andreas Halman
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, 3052, Australia.,Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3010, Australia.,School of Natural Sciences and Health, Tallinn University, 10120, Tallinn, Estonia
| | | | - Alicia Oshlack
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia.,School of BioSciences, University of Melbourne, Parkville, Victoria, 3052, Australia
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12
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Sienkiewicz K, Yang C, Paschal BM, Ratan A. Genomic analyses of the metastasis-derived prostate cancer cell lines LNCaP, VCaP, and PC3-AR. Prostate 2022; 82:442-451. [PMID: 34951700 PMCID: PMC8792310 DOI: 10.1002/pros.24290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/11/2021] [Accepted: 12/07/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND The lymph node metastasis-derived LNCaP, the bone metastasis-derived PC3 (skull), and VCaP (vertebral) cell lines are widely used as preclinical models of human prostate cancer (CaP) and have been described in more than 19,000 publications. Here, we report on short-read whole-genome sequencing and genomic analyses of LNCaP, VCaP, and PC3 cells stably transduced with WT AR (PC3-AR). METHODS LNCaP, VCaP, and PC3-AR cell lines were sequenced to an average depth of more than 30-fold using Illumina short-read sequencing. Using various computational methods, we identified and compared the single-nucleotide variants, copy-number profiles, and the structural variants observed in the three cell lines. RESULTS LNCaP cells are composed of multiple subpopulations, which results in nonintegral copy number states and a high mutational load when the data is analyzed in bulk. All three cell lines contain pathogenic mutations and homozygous deletions in genes involved in DNA mismatch repair, along with deleterious mutations in cell-cycle, Wnt signaling, and other critical cellular processes. PC3-AR cells have a truncating mutation in TP53 and do not express the p53 protein. The VCaP cells contain a homozygous gain-of-function mutation in TP53 (p.R248W) that promotes cancer invasion, metastasis, and progression and has also been observed in prostate adenocarcinomas. In addition, we detect the signatures of chromothripsis of the q arms of chromosome 5 in both PC3-AR and VCaP cells, strengthening the association of TP53 inactivation with chromothripsis reported in other systems. CONCLUSIONS Our work provides a resource for genetic, genomic, and biological studies employing these commonly-used prostate cancer cell lines.
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Affiliation(s)
| | - Chunsong Yang
- Center for Cell Signaling, University of Virginia, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Virginia, USA
| | - Bryce M. Paschal
- Center for Cell Signaling, University of Virginia, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Virginia, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Virginia, USA
- Department of Public Health Sciences, University of Virginia, Virginia, USA
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13
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Bonaventura J, Polakova E, Vejtasova V, Veselka J. Genetic Testing in Patients with Hypertrophic Cardiomyopathy. Int J Mol Sci 2021; 22:10401. [PMID: 34638741 DOI: 10.3390/ijms221910401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a common inherited heart disease with an estimated prevalence of up to 1 in 200 individuals. In the majority of cases, HCM is considered a Mendelian disease, with mainly autosomal dominant inheritance. Most pathogenic variants are usually detected in genes for sarcomeric proteins. Nowadays, the genetic basis of HCM is believed to be rather complex. Thousands of mutations in more than 60 genes have been described in association with HCM. Nevertheless, screening large numbers of genes results in the identification of many genetic variants of uncertain significance and makes the interpretation of the results difficult. Patients lacking a pathogenic variant are now believed to have non-Mendelian HCM and probably have a better prognosis than patients with sarcomeric pathogenic mutations. Identifying the genetic basis of HCM creates remarkable opportunities to understand how the disease develops, and by extension, how to disrupt the disease progression in the future. The aim of this review is to discuss the brief history and recent advances in the genetics of HCM and the application of molecular genetic testing into common clinical practice.
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14
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Buneeva OA, Medvedev AE. DJ-1 Protein and Its Role in the Development of Parkinson's Disease: Studies on Experimental Models. Biochemistry (Mosc) 2021; 86:627-640. [PMID: 34225587 DOI: 10.1134/s000629792106002x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DJ-1, also known as Parkinson's disease protein 7, is a multifunctional protein ubiquitously expressed in cells and tissues. Interacting with proteins of various intracellular compartments, DJ-1 plays an important role in maintaining different cellular functions. Mutant DJ-1 forms containing amino acid substitutions (especially L166P), typical of Parkinson's disease, are characterized by impaired dimerization, stability, and folding. DJ-1 exhibits several types of catalytic activity; however, in the enzyme classification it exists as protein deglycase (EC 3.5.1.124). Apparently, in different cell compartments DJ-1 exhibits catalytic and non-catalytic functions, and their ratio still remains unknown. Oxidative stress promotes dissociation of cytoplasmic DJ-1 dimers into monomers, which are translocated to the nucleus, where this protein acts as a coactivator of various signaling pathways, preventing cell death. In mitochondria, DJ-1 is found in the synthasome, where it interacts with the β ATP synthase subunit. Downregulation of the DJ-1 gene under conditions of experimental PD increases sensitivity of the cells to neurotoxins, and introduction of the recombinant DJ-1 protein attenuates manifestation of this pathology. The thirteen-membered fragment of the DJ-1 amino acid sequence attached to the heptapeptide of the TAT protein penetrating into the cells exhibited neuroprotective properties in various PD models both in cell cultures and after administration to animals. Low molecular weight DJ-1 ligands also demonstrate therapeutic potential, providing neuroprotective effects seen during their incubation with cells and administration to animals.
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Affiliation(s)
- Olga A Buneeva
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
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15
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Vlad CE, Foia LG, Popescu R, Popa I, Aanicai R, Reurean-Pintilei D, Toma V, Florea L, Kanbay M, Covic A. Molecular Genetic Approach and Evaluation of Cardiovascular Events in Patients with Clinical Familial Hypercholesterolemia Phenotype from Romania. J Clin Med 2021; 10:jcm10071399. [PMID: 33807407 PMCID: PMC8036385 DOI: 10.3390/jcm10071399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 12/13/2022] Open
Abstract
This study identifies the genetic background of familial hypercholesterolemia (FH) patients in Romania and evaluates the association between mutations and cardiovascular events. We performed a prospective observational study of 61 patients with a clinical diagnosis of FH selected based on Dutch Lipid Clinic Network (DLCN) and Simon Broome score between 2017 and 2020. Two techniques were used to identify mutations: multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. The mutation rate was 37.7%, i.e., 23 patients with mutations were identified, of which 7 subjects had pathogenic mutations and 16 had polymorphisms. Moreover, 10 variants of the low-density lipoprotein receptor (LDLR) gene were identified in 22 patients, i.e., one variant of the proprotein convertase subtilisin/kexin type 9 (PCSK9) gene in six patients, and one variant of the apolipoprotein B (APOB) gene in three patients. Of the LDLR gene variants, four were LDLR pathogenic mutations (c.81C > G, c.502G > A, c.1618G > A mutations in exon 2, exon 4, exon 11, and exon 13–15 duplication). The PCSK9 and APOB gene variants were benign mutations. The pathogenic LDLR mutations were significant predictors of the new cardiovascular events, and the time interval for new cardiovascular events occurrence was significantly decreased, compared to FH patients without mutations. In total, 12 variants were identified, with four pathogenic variants identified in the LDLR gene, whereas 62.3% of the study population displayed no pathological mutations.
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Affiliation(s)
- Cristiana-Elena Vlad
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
- Department of Nephrology-Internal Medicine, “Dr. C.I. Parhon” Clinical Hospital, Carol I Street, No 50, 700503 Iasi, Romania
| | - Liliana Georgeta Foia
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
- Department of Biochemistry, “Sf. Spiridon” Clinical County Hospital, Independentei Street, 700111 Iasi, Romania
- Correspondence: ; Tel.: +40-744704452
| | - Roxana Popescu
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Ioana Popa
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Ruxandra Aanicai
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Delia Reurean-Pintilei
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Vasilica Toma
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
| | - Laura Florea
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
- Department of Nephrology-Internal Medicine, “Dr. C.I. Parhon” Clinical Hospital, Carol I Street, No 50, 700503 Iasi, Romania
| | - Mehmet Kanbay
- Department of Medicine, Division of Nephrology, Koc University School of Medicine, 34450 Istanbul, Turkey;
| | - Adrian Covic
- Faculty of Medicine, “Grigore T Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania; (C.-E.V.); (R.P.); (I.P.); (R.A.); (D.R.-P.); (V.T.); (L.F.); (A.C.)
- Department of Nephrology-Internal Medicine, “Dr. C.I. Parhon” Clinical Hospital, Carol I Street, No 50, 700503 Iasi, Romania
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16
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Zhang T, Yan C, Liu Y, Cao L, Ji K, Li D, Chi L, Zhao Y. Late-Onset Leukodystrophy Mimicking Hereditary Spastic Paraplegia without Diffuse Leukodystrophy on Neuroimaging. Neuropsychiatr Dis Treat 2021; 17:1451-1458. [PMID: 34012265 PMCID: PMC8126967 DOI: 10.2147/ndt.s296424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 04/12/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Leukodystrophies are frequently regarded as childhood disorders, but they can occur at any age, and the clinical and imaging patterns of the adult-onset form are usually different from the better-known childhood variants. Several reports have shown that various late-onset leukodystrophies, such as X-linked adrenoleukodystrophy and Krabbe disease, may present as spastic paraplegia with the absence of the characteristic white matter lesions on neuroimaging; this can be easily misdiagnosed as hereditary spastic paraplegia. The objective of this study was to investigate the frequency of late-onset leukodystrophies in patients with spastic paraplegia. PATIENTS AND METHODS We performed genetic analysis using a custom-designed gene panel for leukodystrophies in 112 hereditary spastic paraplegia-like patients. RESULTS We identified pathogenic mutations in 13 out of 112 patients, including five patients with adrenomyeloneuropathy, three with Krabbe disease, three with Alexander disease, and two with cerebrotendinous xanthomatosis. In terms of clinical manifestations, in addition to spastic paraplegia, three adrenomyeloneuropathy probands also had adrenocortical insufficiency, two Alexander disease probands developed urinary retention, one CTX proband developed cataracts and chronic diarrhea and the other presented with chronic diarrhea and mild tendon xanthomatosis. None of the patients had evidence of diffuse leukodystrophy on neuroimaging. CONCLUSION Patients with late-onset spastic paraplegia should be screened for underlying leukodystrophies, irrespective of the presence of additional complicating symptoms and neuroimaging abnormalities.
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Affiliation(s)
- Tongxia Zhang
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, People's Republic of China.,School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Chuanzhu Yan
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, People's Republic of China.,Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Shandong University, Qingdao, People's Republic of China
| | - Yiming Liu
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Lili Cao
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Kunqian Ji
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Duoling Li
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Lingyi Chi
- School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China.,Brain Science Research Institute, Qilu Hospital, Shandong University, Jinan, People's Republic of China.,Department of Neurosurgery, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Yuying Zhao
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, People's Republic of China
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17
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Snezhkina AV, Fedorova MS, Pavlov VS, Kalinin DV, Golovyuk AL, Pudova EA, Guvatova ZG, Melnikova NV, Dmitriev AA, Razmakhaev GS, Poloznikov AA, Alekseeva GS, Kaprin AD, Krasnov GS, Kudryavtseva AV. Mutation Frequency in Main Susceptibility Genes Among Patients With Head and Neck Paragangliomas. Front Genet 2020; 11:614908. [PMID: 33391357 PMCID: PMC7775293 DOI: 10.3389/fgene.2020.614908] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/26/2020] [Indexed: 11/13/2022] Open
Abstract
Head and neck paragangliomas (HNPGLs) are rare neuroendocrine tumors that have a high degree of heritability and are predominantly associated with mutations in ten genes, such as SDHx, SDHAF2, VHL, RET, NF1, TMEM127, MAX, FH, MEN2, and SLC25A11. Elucidating the mutation prevalence is crucial for the development of genetic testing. In this study, we identified pathogenic/likely pathogenic variants in the main susceptibility genes in 102 Russian patients with HNPGLs (82 carotid and 23 vagal paragangliomas) using whole exome sequencing. Pathogenic/likely pathogenic variants were detected in 43% (44/102) of patients. We identified the following variant distribution of the tested genes: SDHA (1%), SDHB (10%), SDHC (5%), SDHD (24.5%), and RET (5%). SDHD variants were observed in the majority of the patients with bilateral/multiple paragangliomas. Thus, among Russian patients with HNPGLs the most frequently mutated gene was SDHD followed by SDHB, SDHC, RET, and SDHA.
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Affiliation(s)
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladislav S Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander L Golovyuk
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Zulfiya G Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Razmakhaev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey A Poloznikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Galina S Alekseeva
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey D Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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18
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Abstract
Objective To reveal the distribution signature of cancer susceptibility genes in patients with gastric adenocarcinoma, offering a diagnostic and prognostic surrogate for disease risk management and therapeutic decisions. Methods A total of 282 patients with gastric adenocarcinoma (182 males and 100 females) were enrolled in this study, with peripheral blood genomic DNA extracted. Mutations of 69 canonical cancer susceptibility genes or presumably tumor-related genes were analyzed by targeted capture-based high-throughput sequencing. Candidate mutations were particularly selected for discussion on tumor pathogenesis according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results In this study, 7.1% (20/282) of patients with gastric adenocarcinoma were found to harbor mutations of canonical or presumable cancer susceptibility genes. The detection rate in male patients (3.8%, 7/182) was significantly lower than that in female patients (13%, 13/100) (P=0.004). The most recurrent mutations were in A-T mutated (ATM) (1.1%, 3/282), followed by BRCA1, BRIP1 and RAD51D, all showed a detection rate of 0.7% (2/282). Mutations in three genes associated with hereditary gastric cancer syndromes were detected, namely, PMS2 and EPCAM associated with Lynch syndrome and CDH1 associated with hereditary diffuse gastric cancer. The detection frequencies were all 0.4% (1/282). Notwithstanding no significant difference observed, the age of patients with pathogenic mutations or likely pathogenic mutations is slightly younger than that of non-carriers (median age: 58.5 vs. 60.5 years old), while the age of patients with ATM mutations was the youngest overall (median age: 49.3 years old).
Conclusions Our study shed more light on the distribution signature and pathogenesis of mutations in gastric cancer susceptibility genes, and found the detection rate of pathogenic and likely pathogenic mutations in male patients was significantly lower than that in female patients. Some known and unidentified mutations were found in gastric cancer, which allowed us to gain more insight into the hereditary gastric cancer syndromes from the molecular perspective.
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Affiliation(s)
- Ke Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Sheng Ao
- Department of Gastrointestinal Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Liu He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Lijiao Zhang
- Cadre Health Department, Shanxi Provincial Cancer Hospital, Taiyuan 030013, China
| | - Li Feng
- Abdominal Surgery Department, Affiliated People's Hospital of Inner Mongolia Medical College, Hohhot 010020, China
| | - Guoqing Lyu
- Department of Gastrointestinal Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
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19
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Peretz M, Tworowski D, Kartvelishvili E, Livingston J, Chrzanowska-Lightowlers Z, Safro M. Breaking a single hydrogen bond in the mitochondrial tRNA Phe -PheRS complex leads to phenotypic pleiotropy of human disease. FEBS J 2020; 287:3814-3826. [PMID: 32115907 PMCID: PMC7540514 DOI: 10.1111/febs.15268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/09/2020] [Accepted: 02/27/2020] [Indexed: 01/19/2023]
Abstract
Various pathogenic variants in both mitochondrial tRNAPhe and Phenylalanyl‐tRNA synthetase mitochondrial protein coding gene (FARS2) gene encoding for the human mitochondrial PheRS have been identified and associated with neurological and/or muscle‐related pathologies. An important Guanine‐34 (G34)A anticodon mutation associated with myoclonic epilepsy with ragged red fibers (MERRF) syndrome has been reported in hmit‐tRNAPhe. The majority of G34 contacts in available aaRSs‐tRNAs complexes specifically use that base as an important tRNA identity element. The network of intermolecular interactions providing its specific recognition also largely conserved. However, their conservation depends also on the invariance of the residues in the anticodon binding domain (ABD) of human mitochondrial Phenylalanyl‐tRNA synthetase (hmit‐PheRS). A defect in recognition of the anticodon of tRNAPhe may happen not only because of G34A mutation, but also due to mutations in the ABD. Indeed, a pathogenic mutation in FARS2 has been recently reported in a 9‐year‐old female patient harboring a p.Asp364Gly mutation. Asp364 is hydrogen bonded (HB) to G34 in WT hmit‐PheRS. Thus, there are two pathogenic variants disrupting HB between G34 and Asp364: one is associated with G34A mutation, and the other with Asp364Gly mutation. We have measured the rates of tRNAPhe aminoacylation catalyzed by WT hmit‐PheRS and mutant enzymes. These data ranked the residues making a HB with G34 according to their contribution to activity and the signal transduction pathway in the hmit‐PheRS‐tRNAPhe complex. Furthermore, we carried out extensive MD simulations to reveal the interdomain contact topology on the dynamic trajectories of the complex, and gaining insight into the structural and dynamic integrity effects of hmit‐PheRS complexed with tRNAPhe. Database Structural data are available in PDB database under the accession number(s): 3CMQ, 3TUP, 5MGH, 5MGV.
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Affiliation(s)
- Moshe Peretz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dmitry Tworowski
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | - Mark Safro
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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20
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Abstract
Non-small cell lung carcinoma (NSCLC) is a malignant tumour with poor prognosis and high mortality. Platinum-based dual-agent chemotherapy is the main therapeutic regimen for this disease. In recent years, because of the introduction of molecular targeted therapy, various targeted therapeutic agents against epidermal growth factor receptor (EGFR) have been rapidly developed, which has become a research hotspot for NSCLC treatment. Here, we review the latest studies describing the features and types of EGFR pathogenic mutations, currently established EGFR-tyrosine kinase inhibitors from the first to fourth generation, including their action mechanisms, acquired resistance, and clinical applications, and potential challenges and perspectives that current researchers should address.
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Affiliation(s)
- Rui Li
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, P. R. China
| | - Xiaofei Zhou
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, P. R. China
| | - Hongjuan Yao
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, P. R. China
| | - Liang Li
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, P. R. China
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21
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Yeung E, McFann S, Marsh L, Dufresne E, Filippi S, Harrington HA, Shvartsman SY, Wühr M. Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations. Curr Biol 2020; 30:877-882.e6. [PMID: 32059766 PMCID: PMC7085240 DOI: 10.1016/j.cub.2019.12.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/03/2019] [Accepted: 12/16/2019] [Indexed: 01/03/2023]
Abstract
Multisite protein phosphorylation plays a critical role in cell regulation [1-3]. It is widely appreciated that the functional capabilities of multisite phosphorylation depend on the order and kinetics of phosphorylation steps, but kinetic aspects of multisite phosphorylation remain poorly understood [4-6]. Here, we focus on what appears to be the simplest scenario, when a protein is phosphorylated on only two sites in a strict, well-defined order. This scenario describes the activation of ERK, a highly conserved cell-signaling enzyme. We use Bayesian parameter inference in a structurally identifiable kinetic model to dissect dual phosphorylation of ERK by MEK, a kinase that is mutated in a large number of human diseases [7-12]. Our results reveal how enzyme processivity and efficiencies of individual phosphorylation steps are altered by pathogenic mutations. The presented approach, which connects specific mutations to kinetic parameters of multisite phosphorylation mechanisms, provides a systematic framework for closing the gap between studies with purified enzymes and their effects in the living organism.
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Affiliation(s)
- Eyan Yeung
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Sarah McFann
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Engineering Quad, Princeton University, Princeton, NJ 08544, USA
| | - Lewis Marsh
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford OX2 6GG, UK
| | - Emilie Dufresne
- Department of Mathematics, James College, Campus West, University of York, York YO10 5DD, UK
| | - Sarah Filippi
- Department of Epidemiology and Biostatistics, Imperial College London, Medical School Building, St Mary's Campus, Norfolk Place, London W2 1PG, UK; Department of Mathematics, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Heather A Harrington
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford OX2 6GG, UK
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA; Flatiron Institute, Simons Foundation, New York, NY 10010, USA.
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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22
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Wang R, Han S, Liu H, Khan A, Xiaerbati H, Yu X, Huang J, Zhang X. Novel Compound Heterozygous Mutations in TTI2 Cause Syndromic Intellectual Disability in a Chinese Family. Front Genet 2019; 10:1060. [PMID: 31737043 PMCID: PMC6830114 DOI: 10.3389/fgene.2019.01060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 10/03/2019] [Indexed: 11/13/2022] Open
Abstract
Telomere maintenance 2 (TELO2)-interacting protein 2 (TTI2) interacts with TTI1 and TELO2 to form the Triple T complex, which is required for various cellular processes, including the double-strand DNA break response, nonsense-mediated mRNA decay, and telomerase assembly. Herein, we identified compound heterozygous mutations in TTI2 using whole-exome sequencing (WES) in a Chinese family with a recessive inheritance pattern of syndromic intellectual disability. The patients displayed intellectual disability, aggressive and self-injurious behaviors, facial dysmorphic features, microcephaly, and skeletal anomalies. In addition, one patient showed cerebral white matter abnormality. Maternal novel indel mutation resulted in a premature termination codon and nonsense-mediated mRNA decay. Paternal reported c.1100C > T mutation changed the highly conserved proline to leucine that located in the DUF2454 domain. Immunoblotting experiments showed significantly decreased TTI2, TTI1, and TELO2 in the patients' lymphocytes. These results indicated that TTI2 loss-of-function mutations might cause an autosomal-recessive syndromic intellectual disability by affecting the Triple T complex. Our report expands the genetic causes of syndromic intellectual disability in the Chinese population.
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Affiliation(s)
- Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Shirui Han
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Hongyan Liu
- Medical Genetics Institute, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Amjad Khan
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Habulieti Xiaerbati
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xue Yu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,Department of Pediatrics, the First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Jia Huang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
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23
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Bergendahl LT, Gerasimavicius L, Miles J, Macdonald L, Wells JN, Welburn JPI, Marsh JA. The role of protein complexes in human genetic disease. Protein Sci 2019; 28:1400-1411. [PMID: 31219644 DOI: 10.1002/pro.3667] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022]
Abstract
Many human genetic disorders are caused by mutations in protein-coding regions of DNA. Taking protein structure into account has therefore provided key insight into the molecular mechanisms underlying human genetic disease. Although most studies have focused on the intramolecular effects of mutations, the critical role of the assembly of proteins into complexes is being increasingly recognized. Here, we review multiple ways in which consideration of protein complexes can help us to understand and explain the effects of pathogenic mutations. First, we discuss disorders caused by mutations that perturb intersubunit interactions in homomeric and heteromeric complexes. Second, we address how protein complex assembly can facilitate a dominant-negative mechanism, whereby mutated subunits can disrupt the activity of wild-type protein. Third, we show how mutations that change protein expression levels can lead to damaging stoichiometric imbalances. Finally, we review how mutations affecting different subunits of the same heteromeric complex often cause similar diseases, whereas mutations in different interfaces of the same subunit can cause distinct phenotypes.
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Affiliation(s)
- L Therese Bergendahl
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Lukas Gerasimavicius
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Jamilla Miles
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Lewis Macdonald
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14850
| | - Julie P I Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
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24
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Villanueva R, Romero-Tamayo S, Laplaza R, Martínez-Olivan J, Velázquez-Campoy A, Sancho J, Ferreira P, Medina M. Redox- and Ligand Binding-Dependent Conformational Ensembles in the Human Apoptosis-Inducing Factor Regulate Its Pro-Life and Cell Death Functions. Antioxid Redox Signal 2019; 30:2013-2029. [PMID: 30450916 DOI: 10.1089/ars.2018.7658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aims: The human apoptosis-inducing factor (hAIF) supports OXPHOS biogenesis and programmed cell death, with missense mutations producing neurodegenerative phenotypes. hAIF senses the redox environment of cellular compartments, stabilizing a charge transfer complex (CTC) dimer that modulates the protein interaction network. In this context, we aimed to evaluate the subcellular pH, CTC formation, and pathogenic mutations effects on hAIF stability, and a thermal denaturation high-throughput screening (HTS) assay to discover AIF binders. Results: Apoptotic hAIFΔ1-101 is not stable at intermembrane mitochondrial space (IMS) pH, but the 77-101 residues confer stability to the mitochondrial isoform. hAIF and its CTC populate different conformational ensembles with redox switch to the CTC producing a less stable and compact protein. The pathogenic G308E, ΔR201, and E493V mutations modulate hAIF stability; particularly, ΔR201 causes a population shift to a less stable conformation that remodels active site structure and dynamics. We have identified new molecules that modulate the hAIF reduced nicotinamide adenine dinucleotide (NADH)/oxidized nicotinamide adenine dinucleotide (NAD+) association/dissociation equilibrium and regulate its catalytic efficiency. Innovation: Biophysical methods allow evaluating the regulation of hAIF functional ensembles and to develop an HTS assay to discover small molecules that might modulate hAIF stability and activities. Conclusions: The mitochondrial soluble 54-77 portion stabilizes hAIF at the IMS pH. NADH-redox-linked conformation changes course with strong NAD+ binding and protein dimerization, but they produce a negative impact in overall hAIF stability. Loss of functionality in the R201 deletion is due to distortion of the active site architecture. We report molecules that may serve as leads in the development of hAIF bioactive compounds.
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Affiliation(s)
- Raquel Villanueva
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Silvia Romero-Tamayo
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Ruben Laplaza
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,2 Departamento de Química Física, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan Martínez-Olivan
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,3 Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.,4 Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,5 Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Javier Sancho
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,4 Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Patricia Ferreira
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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25
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Marsiglia WM, Katigbak J, Zheng S, Mohammadi M, Zhang Y, Traaseth NJ. A Conserved Allosteric Pathway in Tyrosine Kinase Regulation. Structure 2019; 27:1308-1315.e3. [PMID: 31204250 DOI: 10.1016/j.str.2019.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/25/2019] [Accepted: 05/08/2019] [Indexed: 01/01/2023]
Abstract
An autoinhibitory network of hydrogen bonds located at the kinase hinge (referred to as the "molecular brake") regulates the activity of several receptor tyrosine kinases. The mechanism whereby mutational disengagement of the brake allosterically activates the kinase in human disease is incompletely understood. We used a combination of NMR, bioinformatics, and molecular dynamics simulation to show that mutational disruption of the molecular brake triggers localized conformational perturbations that propagate to the active site. This entails changes in interactions of an isoleucine, one of three hydrophobic residues that lock the phenylalanine of the DFG motif in an inactive conformation. Structural analysis of tyrosine kinases provides evidence that this allosteric control mechanism is shared across the tyrosine kinase family. We also show that highly activating mutations at the brake diminish the enzyme's thermostability, thereby explaining why these mutations cause milder skeletal syndromes compared with less-activating mutations in the activation loop.
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26
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Heyder N, Kleinau G, Szczepek M, Kwiatkowski D, Speck D, Soletto L, Cerdá-Reverter JM, Krude H, Kühnen P, Biebermann H, Scheerer P. Signal Transduction and Pathogenic Modifications at the Melanocortin-4 Receptor: A Structural Perspective. Front Endocrinol (Lausanne) 2019; 10:515. [PMID: 31417496 PMCID: PMC6685040 DOI: 10.3389/fendo.2019.00515] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022] Open
Abstract
The melanocortin-4 receptor (MC4R) can be endogenously activated by binding of melanocyte-stimulating hormones (MSH), which mediates anorexigenic effects. In contrast, the agouti-related peptide (AgRP) acts as an endogenous inverse agonist and suppresses ligand-independent basal signaling activity (orexigenic effects). Binding of ligands to MC4R leads to the activation of different G-protein subtypes or arrestin and concomitant signaling pathways. This receptor is a key protein in the hypothalamic regulation of food intake and energy expenditure and naturally-occurring inactivating MC4R variants are the most frequent cause of monogenic obesity. In general, obesity is a growing problem on a global scale and is of social, medical, and economic relevance. A significant goal is to develop optimized pharmacological tools targeting MC4R without adverse effects. To date, this has not been achieved because of inter alia non-selective ligands across the five functionally different MCR subtypes (MC1-5R). This motivates further investigation of (i) the three-dimensional MC4R structure, (ii) binding mechanisms of various ligands, and (iii) the molecular transfer process of signal transduction, with the aim of understanding how structural features are linked with functional-physiological aspects. Unfortunately, experimentally elucidated structural information is not yet available for the MC receptors, a group of class A G-protein coupled receptors (GPCRs). We, therefore, generated MC4R homology models and complexes with interacting partners to describe approximate structural properties associated with signaling mechanisms. In addition, molecular insights from pathogenic mutations were incorporated to discriminate more precisely their individual malfunction of the signal transfer mechanism.
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Affiliation(s)
- Nicolas Heyder
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- *Correspondence: Gunnar Kleinau
| | - Michal Szczepek
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dennis Kwiatkowski
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - David Speck
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lucia Soletto
- Departamento de Fisiología de Peces y Biotecnología, Consejo Superior de Investigaciones Científicas, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - José Miguel Cerdá-Reverter
- Departamento de Fisiología de Peces y Biotecnología, Consejo Superior de Investigaciones Científicas, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - Heiko Krude
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Kühnen
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Patrick Scheerer
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27
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Ming L, Wang Y, Lu W, Sun T. A Mutational Analysis of GJB2, SLC26A4, MT-RNA1, and GJB3 in Children with Nonsyndromic Hearing Loss in the Henan Province of China. Genet Test Mol Biomarkers 2018; 23:51-56. [PMID: 30589569 DOI: 10.1089/gtmb.2018.0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Hearing impairment is one of the most common neurosensory disorders afflicting humans. Approximately half of all cases have a genetic etiology. The distribution and frequency of genetic mutations that cause deafness differ significantly by ethnic group and geographic region. METHODS 130 sporadic nonsyndromic hearing loss (NSHL) children from the Henan province were subjected to microarray-based mutation detection. Nine pathogenic mutations were detected in four of the most common deafness-related genes (GJB2, GJB3, SLC26A4, and MT-RNA1). RESULTS Fifty percent of the analyzed patients (65/130) were shown to have genetic defects known to be related to deafness. Slightly >30% (41/130) had biallelic pathogenic mutations. One patient had pathogenic mutations in their mitochondrial genes (MT-RNA1); no mutations were detected in the GJB3 gene. Twenty-three (17.69%) patients were carriers of a single mutation in a recessive gene; these findings alone, however, cannot be interpreted as a cause of hearing loss. Utilizing this molecular strategy, we were able to arrive at a conclusive diagnosis for 42 of the NSHL children. CONCLUSION Genetic factors play a major role in sporadic NSHL patients from the Henan province, but it is clear that our screen needs to be expanded to include additional genes and alleles. Screening of potential pathogenic genes is important for patient risk assessment.
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Affiliation(s)
- Liang Ming
- 1 Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
| | - Yangxia Wang
- 1 Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
| | - Wei Lu
- 2 Department of Otology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
| | - Ting Sun
- 1 Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
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28
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Gianferante DM, Rotunno M, Dean M, Zhou W, Hicks BD, Wyatt K, Jones K, Wang M, Zhu B, Goldstein AM, Mirabello L. Whole-exome sequencing of nevoid basal cell carcinoma syndrome families and review of Human Gene Mutation Database PTCH1 mutation data. Mol Genet Genomic Med 2018; 6:1168-1180. [PMID: 30411536 PMCID: PMC6305672 DOI: 10.1002/mgg3.498] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/05/2018] [Accepted: 10/02/2018] [Indexed: 12/22/2022] Open
Abstract
Background Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder with variable expression and nearly complete penetrance. PTCH1 is the major susceptibility locus and has no known hot spots or genotype–phenotype relationships. Methods We evaluated 18 NBCCS National Cancer Institute (NCI) families plus PTCH1 data on 333 NBCCS disease‐causing mutations (DM) reported in the Human Gene Mutation Database (HGMD). National Cancer Institute families underwent comprehensive genomic evaluation, and clinical data were extracted from NCI and HGMD cases. Genotype–phenotype relationships were analyzed using Fisher's exact tests focusing on mutation type and PTCH1 domains. Results PTCH1 pathogenic mutations were identified in 16 of 18 NCI families, including three previously mutation‐negative families. PTCH1 mutations were spread across the gene with no hot spot. After adjustment for multiple tests, a statistically significant genotype–phenotype association was observed for developmental delay and gross deletion–insertions (p = 9.0 × 10−6), and suggestive associations between falx cerebri calcification and all transmembrane domains (p = 0.002) and severe outcomes and gross deletion–insertions (p = 4.0 × 10−4). Conclusion Overall, 89% of our NCI families had a pathogenic PTCH1 mutation. The identification of PTCH1 mutations in previously mutation‐negative families underscores the importance of repeated testing when new technologies become available. Additional clinical information linked to mutation databases would enhance follow‐up and future studies of genotype–phenotype relationships.
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Affiliation(s)
- D Matthew Gianferante
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Melissa Rotunno
- Division of Cancer Control and Population Science, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kathleen Wyatt
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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29
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Ebrahimi A, Rahim F. Crigler-Najjar Syndrome: Current Perspectives and the Application of Clinical Genetics. Endocr Metab Immune Disord Drug Targets 2018; 18:201-211. [PMID: 29237388 DOI: 10.2174/1871530318666171213153130] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 10/01/2017] [Accepted: 11/30/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Crigler-Najjar syndrome (CNS, OMIM: 218800) is the paradigm of an inborn error of metabolism and a rare genetic disease with an estimated incidence of 0.6-1.0 per million live births. Discrimination between CNS subtypes is usually done on the basis of the clinical criteria, such as response to phenobarbital treatment and other molecular and functional characteristics. METHODS The identification of four novel pathogenic mutations and the analysis of residual activity of missense in UGT1A1 gene are useful for clinical diagnosis, and may reveal a new insight in enzyme activity, whereas the identification of pathogenic mutations will accelerate genetic counseling for newly identified CNS patients. RESULTS Phototherapy, orthotropic liver transplantation, liver cell transplantation and gene therapy are treatment choices and candidates to fight back this syndrome. Due to the promising reports of gene therapy in small animal models, gene therapy approaches are expected to continue in preclinical research for developing safe and effective treatment of CNS. Gene transfer vectors using recombinant viruses, such as Adenovirus have been applied successfully in transferring UGT1A1 gene to the liver of Gunn rat model of CNS. CONCLUSION In spite of remaining safety and efficiency issues, gene therapy promises to be a realistic treatment modality for CNS during the future decade.
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Affiliation(s)
- Ammar Ebrahimi
- Department of Medical Biotechnology, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Fakher Rahim
- Health Research Institute, Thalassemia and Hemoglobinopathies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Al-Abbasi FA, Mohammed K, Sadath S, Banaganapalli B, Nasser K, Shaik NA. Computational Protein Phenotype Characterization of IL10RA Mutations Causative to Early Onset Inflammatory Bowel Disease (IBD). Front Genet 2018; 9:146. [PMID: 29755507 PMCID: PMC5934427 DOI: 10.3389/fgene.2018.00146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 04/09/2018] [Indexed: 01/08/2023] Open
Abstract
The deleterious amino acid substitution mutations in IL-10 receptor alpha gene are most frequently reported in several autoimmune diseases including early onset-inflammatory bowel disease (IBD). Despite the important role of IL-10 RA in maintaining immune homeostasis, the specific structural and functional implications of these mutations on protein phenotype, stability, ligand binding and post translational characteristics is not well explored. Therefore, this study performed the multidimensional computational analysis of IL10RA missense variations causative to pediatric or early onset inflammatory bowel disease (<5 years of age). Our computational algorithmic screening identified the deleterious nature of p. W45G, p. Y57C, p. W69G, p.T84I, p.Y91C, p.R101W, p.R117C, and p.R117H, IBD causative IL10-RA mutations. The sensitivity and specificity analysis of different computational methods showed that CADD outperform SIFT, PolyPhen 2.0, FATHMM, LRT, MetaLR, MetaSVM, PROVEAN and Condel in predicting the pathogenicity of IL10RA mutations. Our three-dimensional protein modeling assays showed that the point mutations cause major drifts in the structural plasticity of IL10 RA molecule and negatively influence its stability. Findings from molecular docking analysis have shown that these point mutations decrease the binding affinity of IL10RA toward IL10 and may likely to disturb the IL10 signaling pathway. This study provides an easy frame work for phenotypic characterization of mutant IL10RA molecule in terms of structure, flexibility and stability aspects. Our approach may also add a new dimension to conventional functional biology assays in quickly studying IL10 RA mutations and also for designing and developing inhibitors for mutant IL10RA molecule.
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Affiliation(s)
- Fahad A Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kaleemuddin Mohammed
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saida Sadath
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalidah Nasser
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor A Shaik
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Nadeem MS, Ahmad H, Mohammed K, Muhammad K, Ullah I, Baothman OAS, Ali N, Anwar F, Zamzami MA, Shakoori AR. Identification of variants in the mitochondrial lysine-tRNA (MT-TK) gene in myoclonic epilepsy-pathogenicity evaluation and structural characterization by in silico approach. J Cell Biochem 2018; 119:6258-6265. [PMID: 29663531 DOI: 10.1002/jcb.26857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 03/12/2018] [Indexed: 02/06/2023]
Abstract
Variations in mitochondrial genes have an established link with myoclonic epilepsy. In the present study we evaluated the nucleotide sequence of MT-TK gene of 52 individuals from 12 unrelated families and reported three variations in 2 of the 13 epileptic patients. The DNA sequences coding for MT-TK gene were sequenced and mutations were detected in all participants. The mutations were further analyzed by the in silico analysis and their structural and pathogenic effects were determined. All the investigated patients had symptoms of myoclonus, 61.5% were positive for ataxia, 23.07% were suffering from hearing loss, 15.38% were having mild to severe dementia, 69.23% were males, and 61.53% had cousin marriage in their family history. DNA extracted from saliva was used for the PCR amplification of a 440 bp DNA fragment encompassing complete MT-TK gene. The nucleotide sequence analysis revealed three mutations, m.8306T>C, m.8313G>C, and m.8362T>G that are divergent from available reports. The identified mutations designate the heteroplasmic condition. Furthermore, pathogenicity of the identified variants was predicted by in silico tools viz., PON-mt-tRNA and MitoTIP. Secondary structure of altered MT-TK was predicted by RNAStructure web server. Studies by MitoTIP and PON-mt-tRNA tools have provided strong evidences of pathogenic effects of these mutations. Single nucleotide variations resulted in disruptive secondary structure of mutant MT-TK models, as predicted by RNAStructure. In vivo confirmation of structural and pathogenic effects of identified mutations in the animal models can be prolonged on the basis of these findings.
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Affiliation(s)
- Muhammad S Nadeem
- Department of Biochemistry, Faculty of Science, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Habib Ahmad
- Department of Genetics, Faculty of Life Sciences, Hazara University, Mansehra, Pakistan
| | - Kaleemuddin Mohammed
- Department of Biochemistry, Faculty of Science, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Khushi Muhammad
- Department of Genetics, Faculty of Life Sciences, Hazara University, Mansehra, Pakistan
| | - Inam Ullah
- Department of Genetics, Faculty of Life Sciences, Hazara University, Mansehra, Pakistan
| | - Othman A S Baothman
- Department of Biochemistry, Faculty of Science, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Nasir Ali
- Department of Genetics, Faculty of Life Sciences, Hazara University, Mansehra, Pakistan
| | - Firoz Anwar
- Department of Biochemistry, Faculty of Science, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Abdul Rauf Shakoori
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, Pakistan
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32
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Khan A, Wang R, Han S, Ahmad W, Zhang X. Identification of a Novel Nonsense ASPM Mutation in a Large Consanguineous Pakistani Family Using Targeted Next-Generation Sequencing. Genet Test Mol Biomarkers 2018; 22:159-164. [PMID: 29431480 DOI: 10.1089/gtmb.2017.0229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS To identify the pathogenic mutation underlying microcephaly primary hereditary (MCPH) in a large consanguineous Pakistani family. METHODS A five-generation family with an autosomal recessive transmission of MCPH was recruited. Targeted next-generation DNA sequencing was carried out to analyze the genomic DNA sample from the proband with MCPH using a previously designed panel targeting 46 known microcephaly-causing genes. Sanger sequencing was performed to verify all identified variants. RESULTS We found a novel homozygous nonsense mutation, c.7543C>T, in the ASPM gene. This mutation led to the substitution of an arginine with a stop codon at amino acid residue 2515 (p.Arg2515Ter). The mutation cosegregated with the MCPH phenotype in all affected and obligate carrier family members, but was not present in public databases (dbSNP147, Exome Variant Server, the 1000 Genomes Project, Exome Aggregation Consortium, Human Gene Mutation Database, and ClinVar) or 200 control individuals. The c.7543C>T mutation in ASPM may activate nonsense-mediated mRNA decay pathways and could underlie the pathogenesis of MCPH through a loss-of-function mechanism. CONCLUSIONS The c.7543C>T (p.Arg2515Ter) mutation in ASPM is a novel pathogenic mutation for the typical MCPH phenotype in this family.
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Affiliation(s)
- Amjad Khan
- 1 The Research Center for Medical Genomics, China Medical University , Shenyang, China .,2 State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, McKusick-Zhang Center for Genetic Medicine, School of Basic Medicine Peking Union Medical College , Beijing, China .,3 Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University , Islamabad, Pakistan
| | - Rongrong Wang
- 2 State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, McKusick-Zhang Center for Genetic Medicine, School of Basic Medicine Peking Union Medical College , Beijing, China
| | - Shirui Han
- 1 The Research Center for Medical Genomics, China Medical University , Shenyang, China .,2 State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, McKusick-Zhang Center for Genetic Medicine, School of Basic Medicine Peking Union Medical College , Beijing, China
| | - Wasim Ahmad
- 3 Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University , Islamabad, Pakistan
| | - Xue Zhang
- 1 The Research Center for Medical Genomics, China Medical University , Shenyang, China .,2 State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, McKusick-Zhang Center for Genetic Medicine, School of Basic Medicine Peking Union Medical College , Beijing, China
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Kimble DC, Lach FP, Gregg SQ, Donovan FX, Flynn EK, Kamat A, Young A, Vemulapalli M, Thomas JW, Mullikin JC, Auerbach AD, Smogorzewska A, Chandrasekharappa SC. A comprehensive approach to identification of pathogenic FANCA variants in Fanconi anemia patients and their families. Hum Mutat 2018; 39:237-254. [PMID: 29098742 PMCID: PMC5762269 DOI: 10.1002/humu.23366] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/20/2017] [Accepted: 10/22/2017] [Indexed: 11/11/2022]
Abstract
Fanconi anemia (FA) is a rare recessive DNA repair deficiency resulting from mutations in one of at least 22 genes. Two-thirds of FA families harbor mutations in FANCA. To genotype patients in the International Fanconi Anemia Registry (IFAR) we employed multiple methodologies, screening 216 families for FANCA mutations. We describe identification of 57 large deletions and 261 sequence variants, in 159 families. All but seven families harbored distinct combinations of two mutations demonstrating high heterogeneity. Pathogenicity of the 18 novel missense variants was analyzed functionally by determining the ability of the mutant cDNA to improve the survival of a FANCA-null cell line when treated with MMC. Overexpressed pathogenic missense variants were found to reside in the cytoplasm, and nonpathogenic in the nucleus. RNA analysis demonstrated that two variants (c.522G > C and c.1565A > G), predicted to encode missense variants, which were determined to be nonpathogenic by a functional assay, caused skipping of exons 5 and 16, respectively, and are most likely pathogenic. We report 48 novel FANCA sequence variants. Defining both variants in a large patient cohort is a major step toward cataloging all FANCA variants, and permitting studies of genotype-phenotype correlations.
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Affiliation(s)
- Danielle C Kimble
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York
| | - Siobhan Q Gregg
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Elizabeth K Flynn
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Aparna Kamat
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Alice Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland
| | - Meghana Vemulapalli
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland
| | - James W Thomas
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland
| | - Arleen D Auerbach
- Human Genetics and Hematology Program, The Rockefeller University, New York, New York
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
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Ang C, Shields A, Xiu J, Gatalica Z, Reddy S, Salem ME, Farhangfar C, Hwang J, Astsaturov I, Marshall JL. Molecular characteristics of hepatocellular carcinomas from different age groups. Oncotarget 2017; 8:101591-101598. [PMID: 29254188 PMCID: PMC5731898 DOI: 10.18632/oncotarget.21353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/31/2017] [Indexed: 01/01/2023] Open
Abstract
While most patients in Western countries who are diagnosed with HCC are in their 50s and 60s, HCCs diagnosed at extremes of the age spectrum (i.e., < 40 years and ≥ 75 years) are less common and have been linked with distinct geographic locations and etiologies. Using multiplatform profiling, we identified differences in genetic alterations and protein expression in different age groups within a large cohort of HCC patients (N = 421). Young adult HCC patients (18-39 years' old) were more likely to be female, living in the West and Midwestern United States, and showed decreased androgen receptor, drug resistance and pro-angiogenic protein expression compared to older patients. TP53 mutations were the most frequent alteration in young adults (19%), whereas CTNNB1 mutations occurred in 30-33% of patients ≥ 40 years' old. The overall frequency of pathogenic and presumed pathogenic mutations was observed to increase significantly with advancing age. To our knowledge, these data represent one of the only studies to analyze age-specific molecular profiles in HCC, and provide a basis for further exploration and validation of these findings with respect to their clinical and therapeutic implications.
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Affiliation(s)
- Celina Ang
- Department of Medicine, Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anthony Shields
- Department of Oncology, Molecular Imaging & Diagnostics Program, Karmanos Cancer Center, Wayne State University, Detroit, MI, USA
| | - Joanne Xiu
- Department of Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Zoran Gatalica
- Department of Pathology, Caris Life Sciences, Phoenix, AZ, USA
| | - Sandeep Reddy
- Department of Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Mohamed E Salem
- Hematology/Oncology, Lombardi Comprehensive Cancer Center, Georgetown, University, Washington, DC, USA
| | - Carol Farhangfar
- Levine Cancer Institute, Carolinas Healthcare System, Charlotte, NC, USA
| | - Jimmy Hwang
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Igor Astsaturov
- Department of Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA.,Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - John L Marshall
- Hematology/Oncology, Lombardi Comprehensive Cancer Center, Georgetown, University, Washington, DC, USA
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35
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Dindo M, Conter C, Cellini B. Electrostatic interactions drive native-like aggregation of human alanine:glyoxylate aminostransferase. FEBS J 2017; 284:3739-3764. [PMID: 28906061 DOI: 10.1111/febs.14269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 08/04/2017] [Accepted: 09/11/2017] [Indexed: 11/28/2022]
Abstract
Protein aggregate formation is the basis of several misfolding diseases, including those displaying loss-of-function pathogenesis. Although aggregation is often attributed to the population of intermediates exposing hydrophobic surfaces, the contribution of electrostatic forces has recently gained attention. Here, we combined computational and in vitro studies to investigate the aggregation process of human peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme involved in glyoxylate detoxification. We demonstrated that AGT is susceptible to electrostatic aggregation due to its peculiar surface charge anisotropy and that PLP binding counteracts the self-association process. The two polymorphic mutations P11L and I340M exert opposite effects. The P11L substitution enhances the aggregation tendency, probably by increasing surface charge anisotropy, while I340M plays a stabilizing role. In light of these results, we examined the effects of the most common missense mutations leading to primary hyperoxaluria type I (PH1), a rare genetic disorder associated with abnormal calcium oxalate precipitation in the urinary tract. All of them endow AGT with a strong electrostatic aggregation propensity. Moreover, we predicted that pathogenic mutations of surface residues could alter charge distribution, thus inducing aggregation under physiological conditions. A global model describing the AGT aggregation process is provided. Overall, the results indicate that the contribution of electrostatic interactions in determining the fate of proteins and the effect of amino acid substitutions should not be underestimated and provide the basis for the development of new therapeutic strategies for PH1 aimed at increasing AGT stability.
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Affiliation(s)
- Mirco Dindo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Italy
| | - Carolina Conter
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Italy
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36
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Fischer J, Kleinau G, Müller A, Kühnen P, Zwanziger D, Kinne A, Rehders M, Moeller LC, Führer D, Grüters A, Krude H, Brix K, Biebermann H. Modulation of monocarboxylate transporter 8 oligomerization by specific pathogenic mutations. J Mol Endocrinol 2015; 54:39-50. [PMID: 25527620 DOI: 10.1530/jme-14-0272] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The monocarboxylate transporter 8 (MCT8) is a member of the major facilitator superfamily (MFS). These membrane-spanning proteins facilitate translocation of a variety of substrates, MCT8 specifically transports iodothyronines. Mutations in MCT8 are the underlying cause of severe X-linked psychomotor retardation. At the molecular level, such mutations led to deficiencies in substrate translocation due to reduced cell-surface expression, impaired substrate binding, or decreased substrate translocation capabilities. However, the causal relationships between genotypes, molecular features of mutated MCT8, and patient characteristics have not yet been comprehensively deciphered. We investigated the relationship between pathogenic mutants of MCT8 and their capacity to form dimers (presumably oligomeric structures) as a potential regulatory parameter of the transport function of MCT8. Fourteen pathogenic variants of MCT8 were investigated in vitro with respect to their capacity to form oligomers. Particular mutations close to the substrate translocation channel (S194F, A224T, L434W, and R445C) were found to inhibit dimerization of MCT8. This finding is in contrast to those for other transporters or transmembrane proteins, in which substitutions predominantly at the outer-surface inhibit oligomerization. Moreover, specific mutations of MCT8 located in transmembrane helix 2 (del230F, V235M, and ins236V) increased the capacity of MCT8 variants to dimerize. We analyzed the localization of MCT8 dimers in a cellular context, demonstrating differences in MCT8 dimer formation and distribution. In summary, our results add a new link between the functions (substrate transport) and protein organization (dimerization) of MCT8, and might be of relevance for other members of the MFS. Finally, the findings are discussed in relationship to functional data combined with structural-mechanistical insights into MCT8.
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Affiliation(s)
- Jana Fischer
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Gunnar Kleinau
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Anne Müller
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Peter Kühnen
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Denise Zwanziger
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Anita Kinne
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Maren Rehders
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Lars C Moeller
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Dagmar Führer
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Annette Grüters
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Heiko Krude
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Klaudia Brix
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Heike Biebermann
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
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Abstract
Short RNA molecules were considered to be junk for decades, but in recent years they have been shown to have important functional roles. MicroRNAs (miRNAs) in particular have attracted much attention. They have been assumed to be highly conserved in humans and other species; however, a recent study published in Genome Medicine reveals an unexpected level of variability in human miRNAs, including variations within the seed region. This challenges the current view of miRNAs, and may explain previous reports of pathogenic mutations in miRNAs. See research article http://genomemedicine.com/content/4/8/62/abstract.
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Affiliation(s)
- Stefano Volinia
- Data Mining for Analysis of Microarrays, Department of Morphology and Embryology, Università degli Studi di Ferrara, 44100 Ferrara, Italy ; Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA ; Biomedical Informatics, Ohio State University, Columbus, OH 43210, USA
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38
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Oppici E, Montioli R, Lorenzetto A, Bianconi S, Borri Voltattorni C, Cellini B. Biochemical analyses are instrumental in identifying the impact of mutations on holo and/or apo-forms and on the region(s) of alanine:glyoxylate aminotransferase variants associated with primary hyperoxaluria type I. Mol Genet Metab 2012; 105:132-40. [PMID: 22018727 PMCID: PMC3271384 DOI: 10.1016/j.ymgme.2011.09.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/28/2011] [Accepted: 09/28/2011] [Indexed: 10/27/2022]
Abstract
Primary Hyperoxaluria Type I (PH1) is a disorder of glyoxylate metabolism caused by mutations in the human AGXT gene encoding liver peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5'-phosphate (PLP) dependent enzyme. Previous investigations highlighted that, although PH1 is characterized by a significant variability in terms of enzymatic phenotype, the majority of the pathogenic variants are believed to share both structural and functional defects, as mainly revealed by data on AGT activity and expression level in crude cellular extracts. However, the knowledge of the defects of the AGT variants at a protein level is still poor. We therefore performed a side-by-side comparison between normal AGT and nine purified recombinant pathogenic variants in terms of catalytic activity, coenzyme binding mode and affinity, spectroscopic features, oligomerization, and thermal stability of both the holo- and apo-forms. Notably, we chose four variants in which the mutated residues are located in the large domain of AGT either within the active site and interacting with the coenzyme or in its proximity, and five variants in which the mutated residues are distant from the active site either in the large or in the small domain. Overall, this integrated analysis of enzymatic activity, spectroscopic and stability information is used to (i) reassess previous data obtained with crude cellular extracts, (ii) establish which form(s) (i.e. holoenzyme and/or apoenzyme) and region(s) (i.e. active site microenvironment, large and/or small domain) of the protein are affected by each mutation, and (iii) suggest the possible therapeutic approach for patients bearing the examined mutations.
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39
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Abstract
The association of amyloid fibril formation with a number of important diseases, and the extensive study of this process in vitro, has resulted in a large literature containing a vast amount of information about the fibril formation process. This includes mutations and experimental conditions that promote or protect against fibril formation. A database (fibril_one) was designed to hold information relating to the formation of fibrils. It was populated by extensive searches of the literature and other databases. A powerful World Wide Web query interface to the database was developed, enabling a simple and effective method to view amyloidogenic mutations associated with specific proteins. The Web interface was used to identify trends in the data. This revealed that mutations promoting fibril formation through altered folding tend to be associated with destabilization of the native fold. In particular, tendencies of mutations to disrupt the native secondary structure and packing in the hydrophobic core were discovered to be significant. Query access to the database is available freely on the World Wide Web at http://www.bioinformatics.leeds.ac.uk/group/online/fibril_one.
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Affiliation(s)
- Jennifer A Siepen
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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