1
|
Duardo RC, Guerra F, Pepe S, Capranico G. Non-B DNA structures as a booster of genome instability. Biochimie 2023; 214:176-192. [PMID: 37429410 DOI: 10.1016/j.biochi.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Non-canonical secondary structures (NCSs) are alternative nucleic acid structures that differ from the canonical B-DNA conformation. NCSs often occur in repetitive DNA sequences and can adopt different conformations depending on the sequence. The majority of these structures form in the context of physiological processes, such as transcription-associated R-loops, G4s, as well as hairpins and slipped-strand DNA, whose formation can be dependent on DNA replication. It is therefore not surprising that NCSs play important roles in the regulation of key biological processes. In the last years, increasing published data have supported their biological role thanks to genome-wide studies and the development of bioinformatic prediction tools. Data have also highlighted the pathological role of these secondary structures. Indeed, the alteration or stabilization of NCSs can cause the impairment of transcription and DNA replication, modification in chromatin structure and DNA damage. These events lead to a wide range of recombination events, deletions, mutations and chromosomal aberrations, well-known hallmarks of genome instability which are strongly associated with human diseases. In this review, we summarize molecular processes through which NCSs trigger genome instability, with a focus on G-quadruplex, i-motif, R-loop, Z-DNA, hairpin, cruciform and multi-stranded structures known as triplexes.
Collapse
Affiliation(s)
- Renée C Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy.
| |
Collapse
|
2
|
Papadopoulou E, Pepe G, Konitsiotis S, Chondrogiorgi M, Grigoriadis N, Kimiskidis VK, Tsivgoulis G, Mitsikostas DD, Chroni E, Domouzoglou E, Tsaousis G, Nasioulas G. The evolution of comprehensive genetic analysis in neurology: Implications for precision medicine. J Neurol Sci 2023; 447:120609. [PMID: 36905813 DOI: 10.1016/j.jns.2023.120609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
Technological advancements have facilitated the availability of reliable and thorough genetic analysis in many medical fields, including neurology. In this review, we focus on the importance of selecting the appropriate genetic test to aid in the accurate identification of disease utilizing currently employed technologies for analyzing monogenic neurological disorders. Moreover, the applicability of comprehensive analysis via NGS for various genetically heterogeneous neurological disorders is reviewed, revealing its efficiency in clarifying a frequently cloudy diagnostic picture and delivering a conclusive and solid diagnosis that is essential for the proper management of the patient. The feasibility and effectiveness of medical genetics in neurology require interdisciplinary cooperation among several medical specialties and geneticists, to select and perform the most relevant test according to each patient's medical history, using the most appropriate technological tools. The prerequisites for a comprehensive genetic analysis are discussed, highlighting the utility of appropriate gene selection, variant annotation, and classification. Moreover, genetic counseling and interdisciplinary collaboration could improve diagnostic yield further. Additionally, a sub-analysis is conducted on the 1,502,769 variation records with submitted interpretations in the Clinical Variation (ClinVar) database, with a focus on neurology-related genes, to clarify the value of suitable variant categorization. Finally, we review the current applications of genetic analysis in the diagnosis and personalized management of neurological patients and the advances in the research and scientific knowledge of hereditary neurological disorders that are evolving the utility of genetic analysis towards the individualization of the treatment strategy.
Collapse
Affiliation(s)
| | - Georgia Pepe
- GeneKor Medical SA, Spaton 52, Gerakas 15344, Greece
| | - Spiridon Konitsiotis
- Department of Neurology, University of Ioannina, Stavrou Niarchou Avenue, Ioannina 45500, Greece
| | - Maria Chondrogiorgi
- Department of Neurology, University of Ioannina, Stavrou Niarchou Avenue, Ioannina 45500, Greece
| | - Nikolaos Grigoriadis
- Second Department of Neurology, "AHEPA" University Hospital, Aristotle University of Thessaloniki, St. Kiriakidis 1, Thessaloniki 54636, Greece
| | - Vasilios K Kimiskidis
- First Department of Neurology, "AHEPA" University hospital, Aristotle University of Thessaloniki, St. Kiriakidis 1, Thessaloniki 54636, Greece
| | - Georgios Tsivgoulis
- Second Department of Neurology, School of Medicine, "Attikon" University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimos D Mitsikostas
- First Department of Neurology, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Elisabeth Chroni
- Department of Neurology, School of Medicine, University of Patras, Rio-Patras, Greece
| | - Eleni Domouzoglou
- Department of Pediatrics, University Hospital of Ioannina, Stavrou Niarchou Avenue, Ioannina 45500, Greece
| | | | | |
Collapse
|
3
|
Neuro-Ophthalmological Findings in Friedreich's Ataxia. J Pers Med 2021; 11:jpm11080708. [PMID: 34442352 PMCID: PMC8398238 DOI: 10.3390/jpm11080708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/08/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022] Open
Abstract
Friedreich ataxia (FRDA) is a progressive neurodegenerative disease caused by a severe autosomal recessive genetic disorder of the central nervous (CNS) and peripheral nervous system (PNS), affecting children and young adults. Its onset is before 25 years of age, with mean ages of onset and death between 11 and 38 years, respectively. The incidence is 1 in 30,000–50,000 persons. It is caused, in 97% of cases, by a homozygous guanine-adenine-adenine (GAA) trinucleotide mutation in the first intron of the frataxin (FXN) gene on chromosome 9 (9q13–q1.1). The mutation of this gene causes a deficiency of frataxin, which induces an altered inflow of iron into the mitochondria, increasing the nervous system’s vulnerability to oxidative stress. The main clinical signs include spinocerebellar ataxia with sensory loss and disappearance of deep tendon reflexes, cerebellar dysarthria, cardiomyopathy, and scoliosis. Diabetes, hearing loss, and pes cavus may also occur, and although most patients with FRDA do not present with symptomatic visual impairment, 73% present with clinical neuro-ophthalmological alterations such as optic atrophy and altered eye movement, among others. This review provides a brief overview of the main aspects of FRDA and then focuses on the ocular involvement of this pathology and the possible use of retinal biomarkers.
Collapse
|
4
|
Martinez HR, Beasley GS, Miller N, Goldberg JF, Jefferies JL. Clinical Insights Into Heritable Cardiomyopathies. Front Genet 2021; 12:663450. [PMID: 33995492 PMCID: PMC8113776 DOI: 10.3389/fgene.2021.663450] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
Cardiomyopathies (CMs) encompass a heterogeneous group of structural and functional abnormalities of the myocardium. The phenotypic characteristics of these myocardial diseases range from silent to symptomatic heart failure, to sudden cardiac death due to malignant tachycardias. These diseases represent a leading cause of cardiovascular morbidity, cardiac transplantation, and death. Since the discovery of the first locus associated with hypertrophic cardiomyopathy 30 years ago, multiple loci and molecular mechanisms have been associated with these cardiomyopathy phenotypes. Conversely, the disparity between the ever-growing landscape of cardiovascular genetics and the lack of awareness in this field noticeably demonstrates the necessity to update training curricula and educational pathways. This review summarizes the current understanding of heritable CMs, including the most common pathogenic gene variants associated with the morpho-functional types of cardiomyopathies: dilated, hypertrophic, arrhythmogenic, non-compaction, and restrictive. Increased understanding of the genetic/phenotypic associations of these heritable diseases would facilitate risk stratification to leveraging appropriate surveillance and management, and it would additionally provide identification of family members at risk of avoidable cardiovascular morbidity and mortality.
Collapse
Affiliation(s)
- Hugo R. Martinez
- The Heart Institute, Le Bonheur Children’s Hospital, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Gary S. Beasley
- The Heart Institute, Le Bonheur Children’s Hospital, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Noah Miller
- The Heart Institute, Le Bonheur Children’s Hospital, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jason F. Goldberg
- The Heart Institute, Le Bonheur Children’s Hospital, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - John L. Jefferies
- The Cardiovascular Institute, The University of Tennessee Health Science Center, Memphis, TN, United States
| |
Collapse
|
5
|
Lenhart B, Wei X, Zhang Z, Wang X, Wang Q, Liu C. Nanopore Fabrication and Application as Biosensors in Neurodegenerative Diseases. Crit Rev Biomed Eng 2020; 48:29-62. [PMID: 32749118 PMCID: PMC8020784 DOI: 10.1615/critrevbiomedeng.2020033151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Since its conception as an applied biomedical technology nearly 30 years ago, nanopore is emerging as a promising, high-throughput, biomarker-targeted diagnostic tool for clinicians. The attraction of a nanopore-based detection system is its simple, inexpensive, robust, user-friendly, high-throughput blueprint with minimal sample preparation needed prior to analysis. The goal of clinical-based nanopore biosensing is to go from sample acquisition to a meaningful readout quickly. The most extensive work in nanopore applications has been targeted at DNA, RNA, and peptide identification. Although, biosensing of pathological biomarkers, which is covered in this review, is on the rise. This review is broken into two major sections: (i) the current state of existing biological, solid state, and hybrid nanopore systems and (ii) the applications of nanopore biosensors toward detecting neurodegenerative biomarkers.
Collapse
Affiliation(s)
- Brian Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| |
Collapse
|
6
|
Chiara M, Zambelli F, Picardi E, Horner DS, Pesole G. Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data. Brief Bioinform 2019; 21:1971-1986. [DOI: 10.1093/bib/bbz099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/22/2019] [Accepted: 07/09/2019] [Indexed: 01/19/2023] Open
Abstract
Abstract
A number of studies have reported the successful application of single-molecule sequencing technologies to the determination of the size and sequence of pathological expanded microsatellite repeats over the last 5 years. However, different custom bioinformatics pipelines were employed in each study, preventing meaningful comparisons and somewhat limiting the reproducibility of the results. In this review, we provide a brief summary of state-of-the-art methods for the characterization of expanded repeats alleles, along with a detailed comparison of bioinformatics tools for the determination of repeat length and sequence, using both real and simulated data. Our reanalysis of publicly available human genome sequencing data suggests a modest, but statistically significant, increase of the error rate of single-molecule sequencing technologies at genomic regions containing short tandem repeats. However, we observe that all the methods herein tested, irrespective of the strategy used for the analysis of the data (either based on the alignment or assembly of the reads), show high levels of sensitivity in both the detection of expanded tandem repeats and the estimation of the expansion size, suggesting that approaches based on single-molecule sequencing technologies are highly effective for the detection and quantification of tandem repeat expansions and contractions.
Collapse
Affiliation(s)
- Matteo Chiara
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
| | - Federico Zambelli
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70126 Bari, Italy
| | - David S Horner
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70126 Bari, Italy
| |
Collapse
|
7
|
Indelicato E, Nachbauer W, Eigentler A, Rudzki D, Wanschitz J, Boesch S. Intraepidermal Nerve Fiber Density in Friedreich's Ataxia. J Neuropathol Exp Neurol 2019; 77:1137-1143. [PMID: 30358880 DOI: 10.1093/jnen/nly100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 09/27/2018] [Indexed: 01/11/2023] Open
Abstract
Friedreich's Ataxia (FRDA) is caused by a homozygous intronic GAA expansion in the FXN gene. FRDA affects primarily the peripheral nervous system (PNS) with cumulative evidence from postmortem studies and in vitro models suggesting a developmental component of its pathology. In the present study, we aimed at gaining further insight in the PNS involvement in FRDA by investigating small nerve fibers in vivo. For this purpose, we evaluated the intraepidermal nerve fiber (IENF) density in skin-biopsies of the lower leg and applied clinical assessments of small fiber function (painDETECT, quantitative sensory testing) in 17 FRDAs. Mean IENF density was significantly lower in FRDAs compared to controls (5.77 ± 4.68 vs 9.33 ± 1.41, p = 0.013). Clinically, cold detection threshold was decreased in FRDAs (FRDA = -3.47(-6.64; -3.14), controls = -1.71 (-3.43; -1.23), p = 0.001) while other measures of small fiber function such as warm and pain sensation thresholds did not differ from controls. Five patients had sensory complaints, but none was diagnosed with neuropathic pain at painDETECT. The degree of small fiber loss was markedly variable in our cohort and showed an inverse correlation with the GAA repeat length (R2 = 0.573, p = 0.001). Our findings support a genetically determined small fiber loss in FRDA.
Collapse
Affiliation(s)
| | | | - Andreas Eigentler
- Neurology Department, Innsbruck Medical University, Innsbruck, Austria
| | - Dagmar Rudzki
- Neurology Department, Innsbruck Medical University, Innsbruck, Austria
| | - Julia Wanschitz
- Neurology Department, Innsbruck Medical University, Innsbruck, Austria
| | - Sylvia Boesch
- Neurology Department, Innsbruck Medical University, Innsbruck, Austria
| |
Collapse
|
8
|
Ferreira GC, Oberstaller J, Fonseca R, Keller TE, Adapa SR, Gibbons J, Wang C, Liu X, Li C, Pham M, Dayhoff Ii GW, Duong LM, Reyes LT, Laratelli LE, Franz D, Fatumo S, Bari AG, Freischel A, Fiedler L, Dokur O, Sharma K, Cragun D, Busby B, Jiang RHY. Iron Hack - A symposium/hackathon focused on porphyrias, Friedreich's ataxia, and other rare iron-related diseases. F1000Res 2019; 8:1135. [PMID: 31824661 PMCID: PMC6894363 DOI: 10.12688/f1000research.19140.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 01/14/2023] Open
Abstract
Background: Basic and clinical scientific research at the University of South Florida (USF) have intersected to support a multi-faceted approach around a common focus on rare iron-related diseases. We proposed a modified version of the National Center for Biotechnology Information’s (NCBI) Hackathon-model to take full advantage of local expertise in building “Iron Hack”, a rare disease-focused hackathon. As the collaborative, problem-solving nature of hackathons tends to attract participants of highly-diverse backgrounds, organizers facilitated a symposium on rare iron-related diseases, specifically porphyrias and Friedreich’s ataxia, pitched at general audiences. Methods: The hackathon was structured to begin each day with presentations by expert clinicians, genetic counselors, researchers focused on molecular and cellular biology, public health/global health, genetics/genomics, computational biology, bioinformatics, biomolecular science, bioengineering, and computer science, as well as guest speakers from the American Porphyria Foundation (APF) and Friedreich’s Ataxia Research Alliance (FARA) to inform participants as to the human impact of these diseases. Results: As a result of this hackathon, we developed resources that are relevant not only to these specific disease-models, but also to other rare diseases and general bioinformatics problems. Within two and a half days, “Iron Hack” participants successfully built collaborative projects to visualize data, build databases, improve rare disease diagnosis, and study rare-disease inheritance. Conclusions: The purpose of this manuscript is to demonstrate the utility of a hackathon model to generate prototypes of generalizable tools for a given disease and train clinicians and data scientists to interact more effectively.
Collapse
Affiliation(s)
- Gloria C Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, MDC 7, Tampa, FL, 33612, USA
| | - Jenna Oberstaller
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Renée Fonseca
- Morsani College of Medicine, University of South Florida, 12901 Bruce B Downs Blvd, Tampa, FL, 33612, USA
| | - Thomas E Keller
- University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Swamy Rakesh Adapa
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Justin Gibbons
- Morsani College of Medicine, University of South Florida, 12901 Bruce B Downs Blvd, Tampa, FL, 33612, USA
| | - Chengqi Wang
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Xiaoming Liu
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Chang Li
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Minh Pham
- Center for Urban Transportation Research, University of South Florida, 4202 E. Fowler Avenue, CUT100, Tampa, FL, 33620, USA
| | - Guy W Dayhoff Ii
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE 205, Tampa, FL, 33620-5250, USA
| | - Linh M Duong
- College of Public Health, University of South Florida, 13201 Bruce B. Downs Blvd., MDC 56, Tampa, FL, 33612, USA.,Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Luis Tañón Reyes
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Ave, ISA 2015 Tampa, FL, 33620, USA
| | - Luciano Enrique Laratelli
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE 205, Tampa, FL, 33620-5250, USA
| | - Douglas Franz
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE 205, Tampa, FL, 33620-5250, USA
| | - Segun Fatumo
- MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda
| | - Atm Golam Bari
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL, USA
| | | | - Lindsey Fiedler
- College of Public Health, University of South Florida, 13201 Bruce B. Downs Blvd., MDC 56, Tampa, FL, 33612, USA
| | - Omkar Dokur
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL, USA
| | | | - Deborah Cragun
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Ben Busby
- National Library of Medicine, 8600 Rockville Pike, Bethesda, MD, 20894-6075, USA
| | - Rays H Y Jiang
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| |
Collapse
|
9
|
Yeast as a Tool for Deeper Understanding of Human Manganese-Related Diseases. Genes (Basel) 2019; 10:genes10070545. [PMID: 31319631 PMCID: PMC6678438 DOI: 10.3390/genes10070545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/26/2022] Open
Abstract
The biological importance of manganese lies in its function as a key cofactor for numerous metalloenzymes and as non-enzymatic antioxidant. Due to these two essential roles, it appears evident that disturbed manganese homeostasis may trigger the development of pathologies in humans. In this context, yeast has been extensively used over the last decades to gain insight into how cells regulate intra-organellar manganese concentrations and how human pathologies may be related to disturbed cellular manganese homeostasis. This review first summarizes how manganese homeostasis is controlled in yeast cells and how this knowledge can be extrapolated to human cells. Several manganese-related pathologies whose molecular mechanisms have been studied in yeast are then presented in the light of the function of this cation as a non-enzymatic antioxidant or as a key cofactor of metalloenzymes. In this line, we first describe the Transmembrane protein 165-Congenital Disorder of Glycosylation (TMEM165-CDG) and Friedreich ataxia pathologies. Then, due to the established connection between manganese cations and neurodegeneration, the Kufor–Rakeb syndrome and prion-related diseases are finally presented.
Collapse
|
10
|
Castro IH, Pignataro MF, Sewell KE, Espeche LD, Herrera MG, Noguera ME, Dain L, Nadra AD, Aran M, Smal C, Gallo M, Santos J. Frataxin Structure and Function. Subcell Biochem 2019; 93:393-438. [PMID: 31939159 DOI: 10.1007/978-3-030-28151-9_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mammalian frataxin is a small mitochondrial protein involved in iron sulfur cluster assembly. Frataxin deficiency causes the neurodegenerative disease Friedreich's Ataxia. Valuable knowledge has been gained on the structural dynamics of frataxin, metal-ion-protein interactions, as well as on the effect of mutations on protein conformation, stability and internal motions. Additionally, laborious studies concerning the enzymatic reactions involved have allowed for understanding the capability of frataxin to modulate Fe-S cluster assembly function. Remarkably, frataxin biological function depends on its interaction with some proteins to form a supercomplex, among them NFS1 desulfurase and ISCU, the scaffolding protein. By combining multiple experimental tools including high resolution techniques like NMR and X-ray, but also SAXS, crosslinking and mass-spectrometry, it was possible to build a reliable model of the structure of the desulfurase supercomplex NFS1/ACP-ISD11/ISCU/frataxin. In this chapter, we explore these issues showing how the scientific view concerning frataxin structure-function relationships has evolved over the last years.
Collapse
Affiliation(s)
- Ignacio Hugo Castro
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
| | - María Florencia Pignataro
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
| | - Karl Ellioth Sewell
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
| | - Lucía Daniela Espeche
- Departamento de Diagnóstico Genético, Centro Nacional de Genética Médica "Dr. Eduardo E. Castilla"-A.N.L.I.S, Av. Las Heras 2670, C1425ASQ, C.A.B.A, Argentina
| | - María Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
| | - Martín Ezequiel Noguera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Liliana Dain
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Departamento de Diagnóstico Genético, Centro Nacional de Genética Médica "Dr. Eduardo E. Castilla"-A.N.L.I.S, Av. Las Heras 2670, C1425ASQ, C.A.B.A, Argentina
| | - Alejandro Daniel Nadra
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Martín Aran
- Fundación Instituto Leloir E IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Clara Smal
- Fundación Instituto Leloir E IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Mariana Gallo
- IRBM Science Park S.p.A, Via Pontina km 30,600, 00071, Pomezia, RM, Italy
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160-Ciudad Universitaria, 1428EGA, C.A.B.A, Argentina.
- Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD, C.A.B.A, Argentina.
| |
Collapse
|
11
|
Hu K, Liu D, Salinger T, Oder D, Knop S, Ertl G, Weidemann F, Frantz S, Störk S, Nordbeck P. Value of cardiac biomarker measurement in the differential diagnosis of infiltrative cardiomyopathy patients with preserved left ventricular systolic function. J Thorac Dis 2018; 10:4966-4975. [PMID: 30233871 DOI: 10.21037/jtd.2018.07.56] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background This study aimed to explore the value of cardiac biomarker [serum high sensitive troponin T (hs-TNT) and N-terminal pro-brain natriuretic peptide (NT-proBNP)] measurement in the differential diagnosis of infiltrative cardiomyopathy patients [Friedreich's ataxia (FA), Fabry disease (FD) and light-chain (AL) cardiac amyloidosis (CA)] with preserved left ventricular (LV) systolic function. Methods Between 2012 and 2014, all consecutive patients presenting at our center with infiltrative cardiomyopathy and concomitant symmetrical LV hypertrophy as well as preserved LV systolic function were included in this study. Serum hs-TNT and NT-proBNP, morphologic and functional features derived from echocardiography and cardiac magnetic resonance imaging (cMRI) examinations were compared among these patients. Results A total of 57 patients (FA 20, FD 23 and CA 14) were included. Hs-TNT and NT-proBNP levels were significantly higher in the CA group [median: hs-TNT 98 pg/mL, NT-proBNP 4,110 pg/mL] than in the FA group [hs-TNT 14 pg/mL, NT-proBNP 40 pg/mL] and FD group [hs-TNT 18 pg/mL, NT-proBNP 131 pg/mL, both P<0.001]. There was a negative correlation between NT-proBNP and estimated glomerular filtration rate (eGFR) in CA patients (r=-0.72, P=0.012). Both hs-TNT >60 pg/mL (sensitivity 0.79, specificity 0.93) and NT-proBNP >1,000 pg/mL (sensitivity 0.91, specificity 0.93) excellently differentiated CA from FA and FD. Conclusions Increased hs-TNT and NT-proBNP levels are suggestive of CA diagnosis among patients with infiltrative cardiomyopathy and preserved LV ejection fraction.
Collapse
Affiliation(s)
- Kai Hu
- Department of Internal Medicine I, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| | - Dan Liu
- Department of Internal Medicine I, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| | - Tim Salinger
- Department of Internal Medicine I, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| | - Daniel Oder
- Department of Internal Medicine I, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| | - Stefan Knop
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Georg Ertl
- Department of Internal Medicine I, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| | - Frank Weidemann
- Medizinische Klinik I des Klinikum Vest, Recklinghausen, Germany
| | - Stefan Frantz
- Department of Internal Medicine I, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| | - Stefan Störk
- Department of Internal Medicine I, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| | - Peter Nordbeck
- Department of Internal Medicine I, Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| |
Collapse
|
12
|
Singh HN, Scheiber-Mojdehkar B, Rajeswari MR. DNA trinucleotide (GAA) repeats in human genome: hint for disease pathogenesis? J Biomol Struct Dyn 2018; 36:1958-1965. [PMID: 28605995 DOI: 10.1080/07391102.2017.1341336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Himanshu Narayan Singh
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
| | - Barbara Scheiber-Mojdehkar
- b Department of Medical Chemistry and Pathobiochemistry , Medical University of Vienna , Vienna , Austria
| | - Moganty R Rajeswari
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
| |
Collapse
|
13
|
Roy AR, Ahmed A, DiStefano PV, Chi L, Khyzha N, Galjart N, Wilson MD, Fish JE, Delgado-Olguín P. The transcriptional regulator CCCTC-binding factor limits oxidative stress in endothelial cells. J Biol Chem 2018; 293:8449-8461. [PMID: 29610276 PMCID: PMC5986204 DOI: 10.1074/jbc.m117.814699] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 03/28/2018] [Indexed: 12/22/2022] Open
Abstract
The CCCTC-binding factor (CTCF) is a versatile transcriptional regulator required for embryogenesis, but its function in vascular development or in diseases with a vascular component is poorly understood. Here, we found that endothelial Ctcf is essential for mouse vascular development and limits accumulation of reactive oxygen species (ROS). Conditional knockout of Ctcf in endothelial progenitors and their descendants affected embryonic growth, and caused lethality at embryonic day 10.5 because of defective yolk sac and placental vascular development. Analysis of global gene expression revealed Frataxin (Fxn), the gene mutated in Friedreich's ataxia (FRDA), as the most strongly down-regulated gene in Ctcf-deficient placental endothelial cells. Moreover, in vitro reporter assays showed that Ctcf activates the Fxn promoter in endothelial cells. ROS are known to accumulate in the endothelium of FRDA patients. Importantly, Ctcf deficiency induced ROS-mediated DNA damage in endothelial cells in vitro, and in placental endothelium in vivo Taken together, our findings indicate that Ctcf promotes vascular development and limits oxidative stress in endothelial cells. These results reveal a function for Ctcf in vascular development, and suggest a potential mechanism for endothelial dysfunction in FRDA.
Collapse
Affiliation(s)
- Anna R Roy
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Abdalla Ahmed
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Peter V DiStefano
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Lijun Chi
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Nadiya Khyzha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Genetics and Genome Biology Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Jason E Fish
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario M5G 2C4, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and
- Heart and Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Ontario M5S 3H2, Canada
| | - Paul Delgado-Olguín
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada,
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Heart and Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Ontario M5S 3H2, Canada
| |
Collapse
|
14
|
Byard RW, Gilbert JD. Mechanisms of unexpected death and autopsy findings in Friedreich ataxia. MEDICINE, SCIENCE, AND THE LAW 2017; 57:192-196. [PMID: 28803513 DOI: 10.1177/0025802417723809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A 36-year-old woman with a clinical history of Friedreich ataxia and hypertrophic cardiomyopathy was found unexpectedly dead at her home. The heart showed asymmetric left ventricular hypertrophy, with an interventricular septal thickness of 20-25 mm (the remainder of the left ventricular wall measured 15 mm). Histologically, both ventricles had irregular areas of marked myocyte hypertrophy with associated interstitial fibrosis and focal myofibre disarray. There was neuronal loss within the dentate nucleus of the cerebellum, with vacuolation and axonal loss in the dorsal columns and spinocerebellar tracts of the upper cervical spinal cord. Death was due to hypertrophic cardiomyopathy complicating Friedreich ataxia. Other causes of death in this condition include embolic stroke, cerebral haemorrhage, aspiration pneumonia, renal failure, diabetic ketoacidosis, myocardial infarction, generalised inanition and trauma. Sudden death due to cardiac disease, resulting in presentation for medicolegal autopsy, may be the presenting feature at all ages, including childhood.
Collapse
Affiliation(s)
- Roger W Byard
- 1 The University of Adelaide Medical School, Australia
- 2 Forensic Science SA, Australia
| | | |
Collapse
|
15
|
Dantham S, Srivastava AK, Gulati S, Rajeswari MR. Plasma circulating cell-free mitochondrial DNA in the assessment of Friedreich's ataxia. J Neurol Sci 2016; 365:82-8. [PMID: 27206881 DOI: 10.1016/j.jns.2016.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/14/2016] [Accepted: 04/11/2016] [Indexed: 12/11/2022]
Abstract
Friedreich's ataxia (FRDA) is one of the most devastating childhood onset neurodegenerative disease affecting multiple organs in the course of progression. FRDA is associated with mitochondrial dysfunction due to deficit in a nuclear encoded mitochondrial protein, frataxin. Identification of disease-specific biomarker for monitoring the severity remains to be a challenging topic. This study was aimed to identify whether circulating cell-free nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) in blood plasma can be a potential biomarker for FRDA. Clinical information was assessed using International Cooperative Ataxia Rating Scale and the disease was confirmed using Long-range PCR for GAA repeat expansion within the gene encoding frataxin. The frataxin expression was measured using Western blot. Plasma nDNA and mtDNA levels were quantified by Multiplex real-time PCR. The major observation is that the levels of nDNA found to be increased, whereas mtDNA levels were reduced significantly in the plasma of FRDA patients (n=21) as compared to healthy controls (n=21). Further, plasma mtDNA levels showed high sensitivity (90%) and specificity (76%) in distinguishing from healthy controls with optimal cutoff indicated at 4.1×10(5)GE/mL. Interestingly, a small group of follow-up patients (n=9) on intervention with, a nutrient supplement, omega-3 fatty acid (a known enhancer of mitochondrial metabolism) displayed a significant improvement in the levels of plasma mtDNA, supporting our hypothesis that plasma mtDNA can be a potential monitoring or prognosis biomarker for FRDA.
Collapse
Affiliation(s)
- Subrahamanyam Dantham
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India.
| | - Sheffali Gulati
- Paediatrics Neurology, All India Institute of Medical Sciences, New Delhi, India.
| | - Moganty R Rajeswari
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
16
|
Singh HN, Rajeswari MR. Identification of genes containing expanded purine repeats in the human genome and their apparent protective role against cancer. J Biomol Struct Dyn 2015; 34:689-704. [PMID: 25990537 DOI: 10.1080/07391102.2015.1049553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Purine repeat sequences present in a gene are unique as they have high propensity to form unusual DNA-triple helix structures. Friedreich's ataxia is the only human disease that is well known to be associated with DNA-triplexes formed by purine repeats. The purpose of this study was to recognize the expanded purine repeats (EPRs) in human genome and find their correlation with cancer pathogenesis. We developed "PuRepeatFinder.pl" algorithm to identify non-overlapping EPRs without pyrimidine interruptions in the human genome and customized for searching repeat lengths, n ≥ 200. A total of 1158 EPRs were identified in the genome which followed Wakeby distribution. Two hundred and ninety-six EPRs were found in geneic regions of 282 genes (EPR-genes). Gene clustering of EPR-genes was done based on their cellular function and a large number of EPR-genes were found to be enzymes/enzyme modulators. Meta-analysis of 282 EPR-genes identified only 63 EPR-genes in association with cancer, mostly in breast, lung, and blood cancers. Protein-protein interaction network analysis of all 282 EPR-genes identified proteins including those in cadherins and VEGF. The two observations, that EPRs can induce mutations under malignant conditions and that identification of some EPR-gene products in vital cell signaling-mediated pathways, together suggest the crucial role of EPRs in carcinogenesis. The new link between EPR-genes and their functionally interacting proteins throws a new dimension in the present understanding of cancer pathogenesis and can help in planning therapeutic strategies. Validation of present results using techniques like NGS is required to establish the role of the EPR genes in cancer pathology.
Collapse
Affiliation(s)
- Himanshu Narayan Singh
- a Department of Biochemistry , All India Institute of Medical Sciences , Room No: 3005A, New Delhi 110029 , India
| | - Moganty R Rajeswari
- a Department of Biochemistry , All India Institute of Medical Sciences , Room No: 3005A, New Delhi 110029 , India
| |
Collapse
|
17
|
Shimizu R, Lan NN, Tai TT, Adachi Y, Kawazoe A, Mu A, Taketani S. p53 directly regulates the transcription of the human frataxin gene and its lack of regulation in tumor cells decreases the utilization of mitochondrial iron. Gene 2014; 551:79-85. [PMID: 25158131 DOI: 10.1016/j.gene.2014.08.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/19/2014] [Accepted: 08/21/2014] [Indexed: 02/05/2023]
Abstract
Mitochondrial frataxin functions in iron homeostasis, biogenesis of iron-sulfur clusters, protection from oxidative stress and apoptosis, and as a tumor suppressor protein. We examined regulation of the expression of the human frataxin by p53. Pifithrin-α, an inhibitor of p53 function, and knockdown of p53 decreased the level of frataxin mRNA in human kidney HEK 293T cells. The transcriptional activity of the human frataxin gene is enhanced by the proximal promoter containing the p53-responsive element (p53RE) on the gene. Chromatin immunoprecipitation assay and electrophoretic mobility shift assay confirmed the binding of p53 to the human frataxin p53RE. The expression of wild-type p53 in human cancer HeLa cells increased the reporter activity carrying p53RE at the region of -209 to -200bp of the frataxin promoter. Finally, when the HeLa cells overexpressing frataxin were treated with 5-aminolevulinic acid (ALA), there was less accumulation of protoporphyrin than HeLa control cells, and it was sharply decreased by the addition of iron citrate, suggesting that the utilization of mitochondrial iron for heme biosynthesis can be dependent on the level of frataxin. Alternatively, the low expression of frataxin not regulated by p53 in tumor cells lowers the utilization of iron in mitochondria, causing the tumor-specific ALA-induced accumulation of protoporphyrin.
Collapse
Affiliation(s)
- Rina Shimizu
- Department of Biotechnology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Nguyen Ngoc Lan
- Department of Biotechnology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Tran Tien Tai
- Department of Biotechnology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Yuka Adachi
- Department of Biotechnology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Asako Kawazoe
- Department of Biotechnology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Anfeng Mu
- Department of Biotechnology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Shigeru Taketani
- Department of Biotechnology, Kyoto Institute of Technology, Kyoto 606-8585, Japan; Insect Biomedical Center, Kyoto Institute of Technology, Kyoto 606-8585, Japan.
| |
Collapse
|
18
|
Friedreich ataxia: executive control is related to disease onset and GAA repeat length. THE CEREBELLUM 2014; 13:9-16. [PMID: 23925595 DOI: 10.1007/s12311-013-0513-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Friedreich ataxia (FRDA) is the most frequent inherited ataxia. Neuropsychological studies suggest that FRDA may be associated with specific cognitive impairment. Very little is known about the relation between cognitive performance, demographics and disease-related parameters, such as GAA repeat size, age of onset and disease duration. The present investigation aimed at assessing cognitive functions in a representative sample of FRDA patients and at identifying the most relevant disease-related parameters. Twenty-nine adult FRDA patients underwent neuropsychological tests assessing executive functions, attention, memory and visual perception. Performance was compared with 28 age- and education-matched controls as well as with standardized norms. The relation between neuropsychological outcome, demographical variables and disease-related parameters was assessed. Cognitive impairment affected only a subgroup of patients and mostly concerned attentional and executive functions. Good cognitive performance was associated with a later disease onset, shorter GAA repeat length and lower burden of disease. Age at disease onset has been found to be a good predictor when a cut-off of 14 years was chosen. No correlation was found between cognitive performance and education, age or disease duration. The present study extends earlier findings in FRDA showing that performance in attentional and executive function tasks is best predicted by the age at disease onset. Moreover, executive functions show a clear relationship to disease severity and repeat size of the shorter GAA allele. These findings therefore have important implications for patient counselling regarding education and career choices.
Collapse
|
19
|
Lavecchia A, Di Giovanni C, Cerchia C, Russo A, Russo G, Novellino E. Discovery of a novel small molecule inhibitor targeting the frataxin/ubiquitin interaction via structure-based virtual screening and bioassays. J Med Chem 2013; 56:2861-73. [PMID: 23506486 DOI: 10.1021/jm3017199] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive neuro- and cardiodegenerative disorder for which there are no proven effective treatments. FRDA is caused by decreased expression and/or function of the mitochondrial protein frataxin. Here, we report findings that frataxin is degraded via the ubiquitin-proteasomal pathway and that it is ubiquitinated at residue K(147) in Calu-6 cells. A theoretical model of the frataxin-K(147)/Ub complex, constructed by combining bioinformatics interface predictions with information-driven docking, revealed a hitherto unnoticed, potential ubiquitin-binding domain in frataxin. Through structure-based virtual screening and cell-based assays, we discovered a novel small molecule (compound (+)-11) able to prevent frataxin ubiquitination and degradation. (+)-11 was synthesized and tested for specific binding to frataxin by an UF-LC/MS based ligand-binding assay. Follow-up scaffold-based searches resulted in the identification of a lead series with micromolar activity in disrupting the frataxin/Ub interaction. This study also suggests that frataxin could be a potential target for FRDA drug development.
Collapse
Affiliation(s)
- Antonio Lavecchia
- Dipartimento di Chimica Farmaceutica e Tossicologica, Drug Discovery Laboratory, Università di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy.
| | | | | | | | | | | |
Collapse
|
20
|
Roman EA, Faraj SE, Gallo M, Salvay AG, Ferreiro DU, Santos J. Protein stability and dynamics modulation: the case of human frataxin. PLoS One 2012; 7:e45743. [PMID: 23049850 PMCID: PMC3458073 DOI: 10.1371/journal.pone.0045743] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 08/24/2012] [Indexed: 01/06/2023] Open
Abstract
Frataxin (FXN) is an α/β protein that plays an essential role in iron homeostasis. Apparently, the function of human FXN (hFXN) depends on the cooperative formation of crucial interactions between helix α1, helix α2, and the C-terminal region (CTR) of the protein. In this work we quantitatively explore these relationships using a purified recombinant fragment hFXN90-195. This variant shows the hydrodynamic behavior expected for a monomeric globular domain. Circular dichroism, fluorescence, and NMR spectroscopies show that hFXN90-195 presents native-like secondary and tertiary structure. However, chemical and temperature induced denaturation show that CTR truncation significantly destabilizes the overall hFXN fold. Accordingly, limited proteolysis experiments suggest that the native-state dynamics of hFXN90-195 and hFXN90-210 are indeed different, being the former form much more sensitive to the protease at specific sites. The overall folding dynamics of hFXN fold was further explored with structure-based protein folding simulations. These suggest that the native ensemble of hFXN can be decomposed in at least two substates, one with consolidation of the CTR and the other without consolidation of the CTR. Explicit-solvent all atom simulations identify some of the proteolytic target sites as flexible regions of the protein. We propose that the local unfolding of CTR may be a critical step for the global unfolding of hFXN, and that modulation of the CTR interactions may strongly affect hFXN physiological function.
Collapse
Affiliation(s)
- Ernesto A. Roman
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
- Protein Physiology Laboratory, Departamento de Química Biológica-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago E. Faraj
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana Gallo
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Andres G. Salvay
- Instituto de Física de Líquidos y Sistemas Biológicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- Departamento de Ciencia y Tecnología, Universidad Nacional Quilmes, Bernal, Provincia de Buenos Aires, Argentina
| | - Diego U. Ferreiro
- Protein Physiology Laboratory, Departamento de Química Biológica-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Javier Santos
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
21
|
Abstract
Friedreich ataxia is the most common human ataxia and results from inadequate production of the frataxin protein, most often the result of a triplet expansion in the nuclear FXN gene. The gene cannot be transcribed to generate the messenger ribonucleic acid for frataxin. Frataxin is an iron-binding protein targeted to the mitochondrial matrix. In its absence, multiple iron-sulfur-dependent proteins in mitochondria and the cytosol lack proper assembly, destroying mitochondrial and nuclear function. Mitochondrial oxidant stress may also participate in ongoing cellular injury. Although progressive and debilitative ataxia is the most prominent clinical finding, hypertrophic cardiomyopathy with heart failure is the most common cause of early death in this disease. There is no cure. In this review the authors cover recent basic and clinical findings regarding the heart in Friedreich ataxia, offer recommendations for clinical management of the cardiomyopathy in this disease, and point out new research directions to advance the field.
Collapse
Affiliation(s)
- R Mark Payne
- Department of Medical & Molecular Genetics, Riley Heart Research Center, Wells Center for Pediatric Research, Indianapolis, IN 46202, USA.
| | | |
Collapse
|
22
|
The ataxias. Neurogenetics 2012. [DOI: 10.1017/cbo9781139087711.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
23
|
Teixeira PF, Glaser E. Processing peptidases in mitochondria and chloroplasts. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:360-70. [PMID: 22495024 DOI: 10.1016/j.bbamcr.2012.03.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/21/2012] [Accepted: 03/22/2012] [Indexed: 12/12/2022]
Abstract
Most of the mitochondrial and chloroplastic proteins are nuclear encoded and synthesized in the cytosol as precursor proteins with N-terminal extensions called targeting peptides. Targeting peptides function as organellar import signals, they are recognized by the import receptors and route precursors through the protein translocons across the organellar membranes. After the fulfilled function, targeting peptides are proteolytically cleaved off inside the organelles by different processing peptidases. The processing of mitochondrial precursors is catalyzed in the matrix by the Mitochondrial Processing Peptidase, MPP, the Mitochondrial Intermediate Peptidase, MIP (recently called Octapeptidyl aminopeptidase 1, Oct1) and the Intermediate cleaving peptidase of 55kDa, Icp55. Furthermore, different inner membrane peptidases (Inner Membrane Proteases, IMPs, Atp23, rhomboids and AAA proteases) catalyze additional processing functions, resulting in intra-mitochondrial sorting of proteins, the targeting to the intermembrane space or in the assembly of proteins into inner membrane complexes. Chloroplast targeting peptides are cleaved off in the stroma by the Stromal Processing Peptidase, SPP. If the protein is further translocated to the thylakoid lumen, an additional thylakoid-transfer sequence is removed by the Thylakoidal Processing Peptidase, TPP. Proper function of the D1 protein of Photosystem II reaction center requires its C-terminal processing by Carboxy-terminal processing protease, CtpA. Both in mitochondria and in chloroplasts, the cleaved targeting peptides are finally degraded by the Presequence Protease, PreP. The organellar proteases involved in precursor processing and targeting peptide degradation constitute themselves a quality control system ensuring the correct maturation and localization of proteins as well as assembly of protein complexes, contributing to sustenance of organelle functions. Dysfunctions of several mitochondrial processing proteases have been shown to be associated with human diseases. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
Collapse
Affiliation(s)
- Pedro Filipe Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-106 91 Stockholm, Sweden
| | | |
Collapse
|
24
|
Vyas PM, Tomamichel WJ, Pride PM, Babbey CM, Wang Q, Mercier J, Martin EM, Payne RM. A TAT-frataxin fusion protein increases lifespan and cardiac function in a conditional Friedreich's ataxia mouse model. Hum Mol Genet 2012; 21:1230-47. [PMID: 22113996 PMCID: PMC3284115 DOI: 10.1093/hmg/ddr554] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 11/21/2011] [Indexed: 11/14/2022] Open
Abstract
Friedreich's ataxia (FRDA) is the most common inherited human ataxia and results from a deficiency of the mitochondrial protein, frataxin (FXN), which is encoded in the nucleus. This deficiency is associated with an iron-sulfur (Fe-S) cluster enzyme deficit leading to progressive ataxia and a frequently fatal cardiomyopathy. There is no cure. To determine whether exogenous replacement of the missing FXN protein in mitochondria would repair the defect, we used the transactivator of transcription (TAT) protein transduction domain to deliver human FXN protein to mitochondria in both cultured patient cells and a severe mouse model of FRDA. A TAT-FXN fusion protein bound iron in vitro, transduced into mitochondria of FRDA deficient fibroblasts and reduced caspase-3 activation in response to an exogenous iron-oxidant stress. Injection of TAT-FXN protein into mice with a conditional loss of FXN increased their growth velocity and mean lifespan by 53% increased their mean heart rate and cardiac output, increased activity of aconitase and reversed abnormal mitochondrial proliferation and ultrastructure in heart. These results show that a cell-penetrant peptide is capable of delivering a functional mitochondrial protein in vivo to rescue a very severe disease phenotype, and present the possibility of TAT-FXN as a protein replacement therapy.
Collapse
Affiliation(s)
- Piyush M. Vyas
- Riley Heart Research Center, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wendy J. Tomamichel
- Riley Heart Research Center, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - P. Melanie Pride
- Riley Heart Research Center, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Clifford M. Babbey
- Riley Heart Research Center, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Qiujuan Wang
- Riley Heart Research Center, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jennifer Mercier
- Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Elizabeth M. Martin
- Riley Heart Research Center, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - R. Mark Payne
- Riley Heart Research Center, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| |
Collapse
|
25
|
Bulteau AL, Planamente S, Jornea L, Dur A, Lesuisse E, Camadro JM, Auchère F. Changes in mitochondrial glutathione levels and protein thiol oxidation in ∆yfh1 yeast cells and the lymphoblasts of patients with Friedreich's ataxia. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1822:212-25. [PMID: 22200491 DOI: 10.1016/j.bbadis.2011.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 10/05/2011] [Accepted: 11/03/2011] [Indexed: 11/28/2022]
Abstract
Friedreich's ataxia (FRDA) is a neurodegenerative disease caused by low levels of the mitochondrial protein frataxin. The main phenotypic features of frataxin-deficient human and yeast cells include iron accumulation in mitochondria, iron-sulfur cluster defects and high sensitivity to oxidative stress. Frataxin deficiency is also associated with severe impairment of glutathione homeostasis and changes in glutathione-dependent antioxidant defenses. The potential biological consequences of oxidative stress and changes in glutathione levels associated with frataxin deficiency include the oxidation of susceptible protein thiols and reversible binding of glutathione to the SH of proteins by S-glutathionylation. In this study, we isolated mitochondria from frataxin-deficient ∆yfh1 yeast cells and lymphoblasts of FRDA patients, and show evidence for a severe mitochondrial glutathione-dependent oxidative stress, with a low GSH/GSSG ratio, and thiol modifications of key mitochondrial enzymes. Both yeast and human frataxin-deficient cells had abnormally high levels of mitochondrial proteins binding an anti-glutathione antibody. Moreover, proteomics and immunodetection experiments provided evidence of thiol oxidation in α-ketoglutarate dehydrogenase (KGDH) or subunits of respiratory chain complexes III and IV. We also found dramatic changes in GSH/GSSG ratio and thiol modifications on aconitase and KGDH in the lymphoblasts of FRDA patients. Our data for yeast cells also confirm the existence of a signaling and/or regulatory process involving both iron and glutathione.
Collapse
Affiliation(s)
- A L Bulteau
- CRICM-INSERM-UMRS975, CNRS UMR 7225-UPMC, Hôpital de la Salpétrière, Physiopathologie cellulaire et moléculaire des maladies mitochondriales, 91, bd de l'hôpital, salle 336, 75651 Paris Cedex 13, France
| | | | | | | | | | | | | |
Collapse
|
26
|
Kirches E, Andrae N, Hoefer A, Kehler B, Zarse K, Leverkus M, Keilhoff G, Schonfeld P, Schneider T, Wilisch-Neumann A, Mawrin C. Dual role of the mitochondrial protein frataxin in astrocytic tumors. J Transl Med 2011; 91:1766-76. [PMID: 21863062 DOI: 10.1038/labinvest.2011.130] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The mitochondrial protein frataxin (FXN) is known to be involved in mitochondrial iron homeostasis and iron-sulfur cluster biogenesis. It is discussed to modulate function of the electron transport chain and production of reactive oxygen species (ROS). FXN loss in neurons and heart muscle cells causes an autosomal-dominant mitochondrial disorder, Friedreich's ataxia. Recently, tumor induction after targeted FXN deletion in liver and reversal of the tumorigenic phenotype of colonic carcinoma cells following FXN overexpression were described in the literature, suggesting a tumor suppressor function. We hypothesized that a partial reversal of the malignant phenotype of glioma cells should occur after FXN transfection, if the mitochondrial protein has tumor suppressor functions in these brain tumors. In astrocytic brain tumors and tumor cell lines, we observed reduced FXN levels compared with non-neoplastic astrocytes. Mitochondrial content (citrate synthase activity) was not significantly altered in U87MG glioblastoma cells stably overexpressing FXN (U87-FXN). Surprisingly, U87-FXN cells exhibited increased cytoplasmic ROS levels, although mitochondrial ROS release was attenuated by FXN, as expected. Higher cytoplasmic ROS levels corresponded to reduced activities of glutathione peroxidase and catalase, and lower glutathione content. The defect of antioxidative capacity resulted in increased susceptibility of U87-FXN cells against oxidative stress induced by H(2)O(2) or buthionine sulfoximine. These characteristics may explain a higher sensitivity toward staurosporine and alkylating drugs, at least in part. On the other hand, U87-FXN cells exhibited enhanced growth rates in vitro under growth factor-restricted and hypoxic conditions and in vivo using tumor xenografts in nude mice. These data contrast to a general tumor suppressor function of FXN but suggest a dual, pro-proliferative but chemosensitizing role in astrocytic tumors.
Collapse
Affiliation(s)
- Elmar Kirches
- Department of Neuropathology, Otto-von-Guericke University, Magdeburg, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Swarup V, Srivastava AK, Padma MV, Rajeswari MR. Quantification of Circulating Plasma DNA in Friedreich's Ataxia and Spinocerebellar Ataxia Types 2 and 12. DNA Cell Biol 2011; 30:389-94. [DOI: 10.1089/dna.2010.1165] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Vishnu Swarup
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Achal K. Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Madakasira V. Padma
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Moganty R. Rajeswari
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
28
|
Abstract
Friedreich's Ataxia is the most common inherited ataxia in man. It is a mitochondrial disease caused by severely reduced expression of the iron binding protein, frataxin. A large GAA triplet expansion in the human FRDA gene encoding this protein inhibits expression of this gene. It is inherited in an autosomal recessive pattern and typically diagnosed in childhood. The primary symptoms include severe and progressive neuropathy, and a hypertrophic cardiomyopathy that may cause death. The cardiomyopathy is difficult to treat and is frequently associated with arrhythmias, heart failure, and intolerance of cardiovascular stress, such as surgeries. Innovative approaches to therapy, such as histone deacetylase inhibitors, and enzyme replacement with cell penetrant peptide fusion proteins, hold promise for this and other similar mitochondrial disorders. This review will focus on the basic findings of this disease, and the cardiomyopathy associated with its diagnosis.
Collapse
Affiliation(s)
- R Mark Payne
- Riley Heart Research Center, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202
| |
Collapse
|
29
|
Payne RM, Pride PM, Babbey CM. Cardiomyopathy of Friedreich's ataxia: use of mouse models to understand human disease and guide therapeutic development. Pediatr Cardiol 2011; 32:366-78. [PMID: 21360265 PMCID: PMC3097037 DOI: 10.1007/s00246-011-9943-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 02/11/2011] [Indexed: 01/02/2023]
Abstract
Friedreich's ataxia is a multisystem disorder of mitochondrial function affecting primarily the heart and brain. Patients experience a severe cardiomyopathy that can progress to heart failure and death. Although the gene defect is known, the precise function of the deficient mitochondrial protein, frataxin, is not known and limits therapeutic development. Animal models have been valuable for understanding the basic events of this disease. A significant need exists to focus greater attention on the heart disease in Friedreich's ataxia, to understand its long-term outcome, and to develop new therapeutic strategies using existing medications and approaches. This review discusses some key features of the cardiomyopathy in Friedreich's ataxia and potential therapeutic developments.
Collapse
Affiliation(s)
- R Mark Payne
- Riley Heart Research Center, Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut, R4302, Indianapolis, IN 46202, USA.
| | | | | |
Collapse
|
30
|
Kell DB. Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples. Arch Toxicol 2010; 84:825-89. [PMID: 20967426 PMCID: PMC2988997 DOI: 10.1007/s00204-010-0577-x] [Citation(s) in RCA: 286] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 07/14/2010] [Indexed: 12/11/2022]
Abstract
Exposure to a variety of toxins and/or infectious agents leads to disease, degeneration and death, often characterised by circumstances in which cells or tissues do not merely die and cease to function but may be more or less entirely obliterated. It is then legitimate to ask the question as to whether, despite the many kinds of agent involved, there may be at least some unifying mechanisms of such cell death and destruction. I summarise the evidence that in a great many cases, one underlying mechanism, providing major stresses of this type, entails continuing and autocatalytic production (based on positive feedback mechanisms) of hydroxyl radicals via Fenton chemistry involving poorly liganded iron, leading to cell death via apoptosis (probably including via pathways induced by changes in the NF-κB system). While every pathway is in some sense connected to every other one, I highlight the literature evidence suggesting that the degenerative effects of many diseases and toxicological insults converge on iron dysregulation. This highlights specifically the role of iron metabolism, and the detailed speciation of iron, in chemical and other toxicology, and has significant implications for the use of iron chelating substances (probably in partnership with appropriate anti-oxidants) as nutritional or therapeutic agents in inhibiting both the progression of these mainly degenerative diseases and the sequelae of both chronic and acute toxin exposure. The complexity of biochemical networks, especially those involving autocatalytic behaviour and positive feedbacks, means that multiple interventions (e.g. of iron chelators plus antioxidants) are likely to prove most effective. A variety of systems biology approaches, that I summarise, can predict both the mechanisms involved in these cell death pathways and the optimal sites of action for nutritional or pharmacological interventions.
Collapse
Affiliation(s)
- Douglas B Kell
- School of Chemistry and the Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK.
| |
Collapse
|
31
|
Morello N, Tonoli E, Logrand F, Fiorito V, Fagoonee S, Turco E, Silengo L, Vercelli A, Altruda F, Tolosano E. Haemopexin affects iron distribution and ferritin expression in mouse brain. J Cell Mol Med 2010; 13:4192-204. [PMID: 19120692 PMCID: PMC4496126 DOI: 10.1111/j.1582-4934.2008.00611.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Haemopexin (Hx) is an acute phase plasma glycoprotein, mainly produced by the liver and released into plasma where it binds heme with high affinity and delivers it to the liver. This system provides protection against free heme-mediated oxidative stress, limits access by pathogens to heme and contributes to iron homeostasis by recycling heme iron. Hx protein has been found in the sciatic nerve, skeletal muscle, retina, brain and cerebrospinal fluid (CSF). Recently, a comparative proteomic analysis has shown an increase of Hx in CSF from patients with Alzheimer’s disease, thus suggesting its involvement in heme detoxification in brain. Here, we report that Hx is synthesised in brain by the ventricular ependymal cells. To verify whether Hx is involved in heme scavenging in brain, and consequently, in the control of iron level, iron deposits and ferritin expression were analysed in cerebral regions known for iron accumulation. We show a twofold increase in the number of iron-loaded oligodendrocytes in the basal ganglia and thalamus of Hx-null mice compared to wild-type controls. Interestingly, there was no increase in H- and L-ferritin expression in these regions. This condition is common to several human neurological disorders such as Alzheimer’s disease and Parkinson’s disease in which iron loading is not associated with an adequate increase in ferritin expression. However, a strong reduction in the number of ferritin-positive cells was observed in the cerebral cortex of Hx-null animals. Consistent with increased iron deposits and inadequate ferritin expression, malondialdehyde level and Cu–Zn superoxide dismutase-1 expression were higher in the brain of Hx-null mice than in that of wild-type controls. These data demonstrate that Hx plays an important role in controlling iron distribution within brain, thus suggesting its involvement in iron-related neurodegenerative diseases.
Collapse
Affiliation(s)
- Noemi Morello
- Molecular Biotechnology Center, University of Torino, Torino, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Defects in mitochondrial axonal transport and membrane potential without increased reactive oxygen species production in a Drosophila model of Friedreich ataxia. J Neurosci 2010; 30:11369-78. [PMID: 20739558 DOI: 10.1523/jneurosci.0529-10.2010] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Friedreich ataxia, a neurodegenerative disorder resulting from frataxin deficiency, is thought to involve progressive cellular damage from oxidative stress. In Drosophila larvae with reduced frataxin expression (DfhIR), we evaluated possible mechanisms of cellular neuropathology by quantifying mitochondrial axonal transport, membrane potential (MMP), and reactive oxygen species (ROS) production in the DfhIR versus wild-type nervous system throughout development. Although dying-back neuropathy in DfhIR larvae did not occur until late third instar, reduced MMP was already apparent at second instar in the cell bodies, axons and neuromuscular junctions (NMJs) of segmental nerves. Defects in axonal transport of mitochondria appeared late in development in distal nerve of DfhIR larvae, with retrograde movement preferentially affected. As a result, by late third instar the neuromuscular junctions (NMJs) of DfhIR larvae accumulated a higher density of mitochondria, many of which were depolarized. Notably, increased ROS production was not detected in any neuronal region or developmental stage in DfhIR larvae. However, when challenged with antimycin A, neurons did respond with a larger increase in ROS. We propose that pathology in the frataxin-deficient nervous system involves decreased MMP and ATP production followed by failures of mitochondrial transport and NMJ function.
Collapse
|
33
|
Pérez-Luz S, Díaz-Nido J. Prospects for the use of artificial chromosomes and minichromosome-like episomes in gene therapy. J Biomed Biotechnol 2010; 2010:642804. [PMID: 20862363 PMCID: PMC2938438 DOI: 10.1155/2010/642804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 06/02/2010] [Accepted: 07/05/2010] [Indexed: 01/19/2023] Open
Abstract
Artificial chromosomes and minichromosome-like episomes are large DNA molecules capable of containing whole genomic loci, and be maintained as nonintegrating, replicating molecules in proliferating human somatic cells. Authentic human artificial chromosomes are very difficult to engineer because of the difficulties associated with centromere structure, so they are not widely used for gene-therapy applications. However, OriP/EBNA1-based episomes, which they lack true centromeres, can be maintained stably in dividing cells as they bind to mitotic chromosomes and segregate into daughter cells. These episomes are more easily engineered than true human artificial chromosomes and can carry entire genes along with all their regulatory sequences. Thus, these constructs may facilitate the long-term persistence and physiological regulation of the expression of therapeutic genes, which is crucial for some gene therapy applications. In particular, they are promising vectors for gene therapy in inherited diseases that are caused by recessive mutations, for example haemophilia A and Friedreich's ataxia. Interestingly, the episome carrying the frataxin gene (deficient in Friedreich's ataxia) has been demonstrated to rescue the susceptibility to oxidative stress which is typical of fibroblasts from Friedreich's ataxia patients. This provides evidence of their potential to treat genetic diseases linked to recessive mutations through gene therapy.
Collapse
Affiliation(s)
- Sara Pérez-Luz
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | | |
Collapse
|
34
|
Huang J, Wu X, Montenegro G, Price J, Wang G, Vance JM, Shy ME, Züchner S. Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease. J Neurol 2009; 257:735-41. [PMID: 19949810 DOI: 10.1007/s00415-009-5401-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/12/2009] [Accepted: 11/13/2009] [Indexed: 11/28/2022]
Abstract
Hereditary peripheral neuropathies present a group of clinically and genetically heterogeneous entities. All known forms, including the various forms of Charcot-Marie-Tooth disease (CMT) are characterized as Mendelian traits and over 35 genes have been identified thus far. The mutational mechanism of the most common CMT type, CMT1A, is a 1.5 Mb chromosomal duplication at 17p12 that contains the gene PMP22. Only recently it has been realized that such copy number variants (CNV) are a widespread phenomenon and important for disease. However, it is not known whether CNVs play a wider role in hereditary peripheral neuropathies outside of CMT1A. In a phenotypically heterogeneous sample of 97 patients, we performed the first high-density CNV study of 34 genomic regions harboring known genes for hereditary peripheral neuropathies including the 17p12 duplication region, with comparative genomic hybridization (CGH) microarrays. We identified three CNVs that affected coding exons. A novel shorter form of a PMP22 duplication was detected in a CMT1A family previously tested negative in a commercial test. Two other CNVs in MTMR2 and ARHGEF10 are likely not disease associated. Our results indicate that CNVs are a rare cause for non-CMT1A CMT. Their potential relevance as disease modifiers remains to be evaluated. The present study design cannot rule out that specific CMT forms exist where CNVs play a larger role.
Collapse
Affiliation(s)
- Jia Huang
- Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136,, USA
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Pan X, Ding Y, Shi L. The roles of SbcCD and RNaseE in the transcription of GAA x TTC repeats in Escherichia coli. DNA Repair (Amst) 2009; 8:1321-7. [PMID: 19733517 DOI: 10.1016/j.dnarep.2009.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 07/24/2009] [Accepted: 08/09/2009] [Indexed: 10/20/2022]
Abstract
Expansion of GAA x TTC repeats in FXN gene is associated with decreased frataxin production in Frederich's ataxia patients. To study this effect, we have engineered a set of GAA x TTC repeats in the EcoRI site of lacZ gene of plasmid pUC18 as part of the transcription template of the lacZ gene, while keeping its ORF unchanged. The effects of the GAA x TTC repeats on the lacZ expression were investigated in Escherichia coli JM83 and its mutants deficiency in RNA processing, homologous recombination and DNA repair. We found that transcriptions of the GAA strand with different sizes and organizations displayed normal alpha-complementation when RNase E was functional. By contrast, transcriptions of TTC repeats containing more than 13 triplets failed to support alpha-complementation, showing RNase-independent but length-dependent effects of TTC repeats on lacZ expression. In addition, we also found that functions of SbcCD, a DNA structure specific nuclease, were needed in the RNase E-dependent lacZ expression of the GAA repeats. These suggested that processing of DNA and RNA is essential to the transcription of the repeats-carrying gene in vivo.
Collapse
Affiliation(s)
- Xuefeng Pan
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | | | | |
Collapse
|
36
|
Scott LE, Orvig C. Medicinal Inorganic Chemistry Approaches to Passivation and Removal of Aberrant Metal Ions in Disease. Chem Rev 2009; 109:4885-910. [DOI: 10.1021/cr9000176] [Citation(s) in RCA: 266] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lauren E. Scott
- Medicinal Inorganic Chemistry Group, Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Chris Orvig
- Medicinal Inorganic Chemistry Group, Department of Chemistry, University of British Columbia, Vancouver, Canada
| |
Collapse
|
37
|
Shishkin AA, Voineagu I, Matera R, Cherng N, Chernet BT, Krasilnikova MM, Narayanan V, Lobachev KS, Mirkin SM. Large-scale expansions of Friedreich's ataxia GAA repeats in yeast. Mol Cell 2009; 35:82-92. [PMID: 19595718 PMCID: PMC2722067 DOI: 10.1016/j.molcel.2009.06.017] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 01/07/2009] [Accepted: 06/18/2009] [Indexed: 12/12/2022]
Abstract
Large-scale expansions of DNA repeats are implicated in numerous hereditary disorders in humans. We describe a yeast experimental system to analyze large-scale expansions of triplet GAA repeats responsible for the human disease Friedreich's ataxia. When GAA repeats were placed into an intron of the chimeric URA3 gene, their expansions caused gene inactivation, which was detected on the selective media. We found that the rates of expansions of GAA repeats increased exponentially with their lengths. These rates were only mildly dependent on the repeat's orientation within the replicon, whereas the repeat-mediated replication fork stalling was exquisitely orientation dependent. Expansion rates were significantly elevated upon inactivation of the replication fork stabilizers, Tof1 and Csm3, but decreased in the knockouts of postreplication DNA repair proteins, Rad6 and Rad5, and the DNA helicase Sgs1. We propose a model for large-scale repeat expansions based on template switching during replication fork progression through repetitive DNA.
Collapse
Affiliation(s)
| | - Irina Voineagu
- Department of Biology, Tufts University, Medford, MA 02155
| | - Robert Matera
- Department of Biology, Tufts University, Medford, MA 02155
| | - Nicole Cherng
- Department of Biology, Tufts University, Medford, MA 02155
| | | | - Maria M. Krasilnikova
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802
| | - Vidhya Narayanan
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | | |
Collapse
|
38
|
Bolognin S, Drago D, Messori L, Zatta P. Chelation therapy for neurodegenerative diseases. Med Res Rev 2009; 29:547-70. [DOI: 10.1002/med.20148] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
39
|
Kell DB. Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genomics 2009; 2:2. [PMID: 19133145 PMCID: PMC2672098 DOI: 10.1186/1755-8794-2-2] [Citation(s) in RCA: 359] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 01/08/2009] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular 'reactive oxygen species' (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. REVIEW We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation).The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible.This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, since in some circumstances (especially the presence of poorly liganded iron) molecules that are nominally antioxidants can actually act as pro-oxidants. The reduction of redox stress thus requires suitable levels of both antioxidants and effective iron chelators. Some polyphenolic antioxidants may serve both roles.Understanding the exact speciation and liganding of iron in all its states is thus crucial to separating its various pro- and anti-inflammatory activities. Redox stress, innate immunity and pro- (and some anti-)inflammatory cytokines are linked in particular via signalling pathways involving NF-kappaB and p38, with the oxidative roles of iron here seemingly involved upstream of the IkappaB kinase (IKK) reaction. In a number of cases it is possible to identify mechanisms by which ROSs and poorly liganded iron act synergistically and autocatalytically, leading to 'runaway' reactions that are hard to control unless one tackles multiple sites of action simultaneously. Some molecules such as statins and erythropoietin, not traditionally associated with anti-inflammatory activity, do indeed have 'pleiotropic' anti-inflammatory effects that may be of benefit here. CONCLUSION Overall we argue, by synthesising a widely dispersed literature, that the role of poorly liganded iron has been rather underappreciated in the past, and that in combination with peroxide and superoxide its activity underpins the behaviour of a great many physiological processes that degrade over time. Understanding these requires an integrative, systems-level approach that may lead to novel therapeutic targets.
Collapse
Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.
| |
Collapse
|
40
|
Kakhlon O, Manning H, Breuer W, Melamed-Book N, Lu C, Cortopassi G, Munnich A, Cabantchik ZI. Cell functions impaired by frataxin deficiency are restored by drug-mediated iron relocation. Blood 2008; 112:5219-27. [PMID: 18796625 DOI: 10.1182/blood-2008-06-161919] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Various human disorders are associated with misdistribution of iron within or across cells. Friedreich ataxia (FRDA), a deficiency in the mitochondrial iron-chaperone frataxin, results in defective use of iron and its misdistribution between mitochondria and cytosol. We assessed the possibility of functionally correcting the cellular properties affected by frataxin deficiency with a siderophore capable of relocating iron and facilitating its metabolic use. Adding the chelator deferiprone at clinical concentrations to inducibly frataxin-deficient HEK-293 cells resulted in chelation of mitochondrial labile iron involved in oxidative stress and in reactivation of iron-depleted aconitase. These led to (1) restoration of impaired mitochondrial membrane and redox potentials, (2) increased adenosine triphosphate production and oxygen consumption, and (3) attenuation of mitochondrial DNA damage and reversal of hypersensitivity to staurosporine-induced apoptosis. Permeant chelators of higher affinity than deferiprone were not as efficient in restoring affected functions. Thus, although iron chelation might protect cells from iron toxicity, rendering the chelated iron bioavailable might underlie the capacity of deferiprone to restore cell functions affected by frataxin deficiency, as also observed in FRDA patients. The siderophore-like properties of deferiprone provide a rational basis for treating diseases of iron misdistribution, such as FRDA, anemia of chronic disease, and X-linked sideroblastic anemia with ataxia.
Collapse
Affiliation(s)
- Or Kakhlon
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Willis JH, Isaya G, Gakh O, Capaldi RA, Marusich MF. Lateral-flow immunoassay for the frataxin protein in Friedreich's ataxia patients and carriers. Mol Genet Metab 2008; 94:491-497. [PMID: 18485778 PMCID: PMC2692602 DOI: 10.1016/j.ymgme.2008.03.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Accepted: 03/29/2008] [Indexed: 11/18/2022]
Abstract
Friedreich's Ataxia (FA) is an inherited neurodegenerative disease caused by reduction in levels of the mitochondrial protein frataxin. Currently there are no simple, reliable methods to accurately measure the concentrations of frataxin protein. We designed a lateral-flow immunoassay that quantifies frataxin protein levels in a variety of sample materials. Using recombinant frataxin we evaluated the accuracy and reproducibility of the assay. The assay measured recombinant human frataxin concentrations between 40 and 4000 pg/test or approximately 0.1-10 nM of sample. The intra and inter-assay error was <10% throughout the working range. To evaluate clinical utility of the assay we used genetically defined lymphoblastoid cells derived from FA patients, FA carriers and controls. Mean frataxin concentrations in FA patients and carriers were significantly different from controls and from one another (p=0.0001, p=0.003, p=0.005, respectively) with levels, on average, 29% (patients) and 64% (carriers) of the control group. As predicted, we observed an inverse relationship between GAA repeat number and frataxin protein concentrations within the FA patient cohort. The lateral flow immunoassay provides a simple, accurate and reproducible method to quantify frataxin protein in whole cell and tissue extracts, including primary samples obtained by non-invasive means, such as cheek swabs and whole blood. The assay is a novel tool for FA research that may facilitate improved diagnostic and prognostic evaluation of FA patients and could also be used to evaluate efficacy of therapies designed to cure FA by increasing frataxin protein levels.
Collapse
Affiliation(s)
| | - Grazia Isaya
- Mayo Clinic College of Medicine, Rochester, MN 55905
| | | | | | | |
Collapse
|
42
|
Friedman LS, Schadt KA, Wilson RB, Lynch DR. Efficacy and safety of idebenone in the treatment of Friedreich ataxia: a review of early results and future prospects. FUTURE NEUROLOGY 2008. [DOI: 10.2217/14796708.3.4.375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Friedreich ataxia (FRDA) is an autosomal-recessive neurodegenerative disorder characterized by difficulty walking, dysarthria and absent reflexes. At present, no treatment or cure exists, but the pathophysiology of FRDA suggests that antioxidants and related compounds may be efficacious. Research in the field has focused on idebenone, a lipid-soluble synthetic short-chain analogue of the quinone coenzyme Q10. Idebenone protects mitochondrial membranes from oxidative damage in vitro and may facilitate electron transport within the mitochondrial electron transport chain. In FRDA, idebenone decreases cardiac hypertrophy, but the clinical significance of this finding remains unknown. Recent Phase II trials using higher doses of idebenone have suggested a dose-dependent improvement in neurologic symptoms. To confirm these results, a Phase III trial has begun in the USA with the goal of assessing the efficacy of idebenone for the treatment of neurologic dysfunction in FRDA.
Collapse
Affiliation(s)
- Lisa S Friedman
- University of Pennsylvania School of Medicine, Departments of Neurology & Pediatrics and, The Children’s Hospital of Philadelphia, PA 19104, USA
| | - Kimberly A Schadt
- University of Pennsylvania School of Medicine, Departments of Neurology & Pediatrics and, The Children’s Hospital of Philadelphia, PA 19104, USA
| | - Robert B Wilson
- University of Pennsylvania School of Medicine, Department of Pathology & Laboratory Medicine, PA, USA
| | - David R Lynch
- Children’s Hospital of Philadelphia, Department of Neurology, Abramson Research Center, Room 502, 3615 Civic Center Blvd, PA 19104, USA
| |
Collapse
|
43
|
Abstract
Friedreich ataxia, the most common inherited ataxia, is caused by the transcriptional silencing of the FXN gene, which codes for the 210 amino acid frataxin, a mitochondrial protein involved in iron-sulfur cluster biosynthesis. The expansion of the GAA x TTC tract in intron 1 to as many as 1700 repeats elicits the transcriptional silencing by the formation of non-B DNA structures (triplexes or sticky DNA), the formation of a persistent DNA x RNA hybrid, or heterochromatin formation. The triplex (sticky DNA) adopted by the long repeat sequence also elicits profound mutagenic, genetic instability, and recombination behaviors. Early stage therapeutic investigations involving polyamides or histone deacetylase inhibitors are being pursued. Friedreich ataxia may be one of the most thoroughly studied hereditary neurological disease from a pathophysiological standpoint.
Collapse
Affiliation(s)
- Robert D Wells
- Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, The Texas Medical Center, 2121 W. Holcombe Blvd., Houston, TX 77030-3303, USA.
| |
Collapse
|
44
|
Rea SL, Ventura N, Johnson TE. Relationship between mitochondrial electron transport chain dysfunction, development, and life extension in Caenorhabditis elegans. PLoS Biol 2008; 5:e259. [PMID: 17914900 PMCID: PMC1994989 DOI: 10.1371/journal.pbio.0050259] [Citation(s) in RCA: 293] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Accepted: 08/03/2007] [Indexed: 01/19/2023] Open
Abstract
Prior studies have shown that disruption of mitochondrial electron transport chain (ETC) function in the nematode Caenorhabditis elegans can result in life extension. Counter to these findings, many mutations that disrupt ETC function in humans are known to be pathologically life-shortening. In this study, we have undertaken the first formal investigation of the role of partial mitochondrial ETC inhibition and its contribution to the life-extension phenotype of C. elegans. We have developed a novel RNA interference (RNAi) dilution strategy to incrementally reduce the expression level of five genes encoding mitochondrial proteins in C. elegans: atp-3, nuo-2, isp-1, cco-1, and frataxin (frh-1). We observed that each RNAi treatment led to marked alterations in multiple ETC components. Using this dilution technique, we observed a consistent, three-phase lifespan response to increasingly greater inhibition by RNAi: at low levels of inhibition, there was no response, then as inhibition increased, lifespan responded by monotonically lengthening. Finally, at the highest levels of RNAi inhibition, lifespan began to shorten. Indirect measurements of whole-animal oxidative stress showed no correlation with life extension. Instead, larval development, fertility, and adult size all became coordinately affected at the same point at which lifespan began to increase. We show that a specific signal, initiated during the L3/L4 larval stage of development, is sufficient for initiating mitochondrial dysfunction–dependent life extension in C. elegans. This stage of development is characterized by the last somatic cell divisions normally undertaken by C. elegans and also by massive mitochondrial DNA expansion. The coordinate effects of mitochondrial dysfunction on several cell cycle–dependent phenotypes, coupled with recent findings directly linking cell cycle progression with mitochondrial activity in C. elegans, lead us to propose that cell cycle checkpoint control plays a key role in specifying longevity of mitochondrial mutants. The worm Caenorhabditis elegans has afforded major advances in our understanding of aging, in part because a limited number of genetic pathways appear to govern aging in this organism. In this study, we explore one class of long-lived C. elegans, the Mit mutants, which are characterized by defective mitochondrial electron transport chain activity and, hence, ATP production. How disruption of mitochondrial function could lead to life extension has remained a mystery, especially because some of the same genes that cause life extension in worms (including nuo-2 and frh-1), result in pathology in people. Here, we resolve this paradox by showing that life extension of the Mit mutants is limited to a discrete window of electron transport chain dysfunction. We show that the onset of life extension correlates with the disruption of several cell cycle–related phenomena, including larval development, adult size, and fertility and fecundity. We find no overt correlation between levels of oxidative stress and longevity. We propose that life extension in the Mit mutants is intimately connected to DNA checkpoint signaling and that the Mit mutants provide a powerful model for studying human mitochondrial disorders and aging. Previous publications showed that the inhibition of the mitochondrial electron transport in C. elegans both extended and decreased lifespan. Here this paradox is resolved by showing that the fate depends on the degree of inhibition.
Collapse
Affiliation(s)
- Shane L Rea
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, Colorado, [corrected] United States of America. [corrected]
| | | | | |
Collapse
|
45
|
Anderson PR, Kirby K, Orr WC, Hilliker AJ, Phillips JP. Hydrogen peroxide scavenging rescues frataxin deficiency in a Drosophila model of Friedreich's ataxia. Proc Natl Acad Sci U S A 2008; 105:611-6. [PMID: 18184803 PMCID: PMC2206584 DOI: 10.1073/pnas.0709691105] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Indexed: 11/18/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a neurodegenerative disorder arising from a deficit of the mitochondrial iron chaperone, frataxin. Evidence primarily from yeast and mammalian cells is consistent with the hypothesis that a toxic hydroxyl radical generated from hydrogen peroxide (H2O2) via iron-catalyzed Fenton chemistry at least partially underlies the pathology associated with this disease. However, no whole-organism studies have been presented that directly test this hypothesis. We recently developed a Drosophila model that recapitulates the principal hallmarks of FRDA [Anderson PR, Kirby K, Hilliker A, Phillips JP (2005) Hum Mol Genet 14:3397-3405]. Using the Drosophila FRDA model, we now report that ectopic expression of enzymes that scavenge H2O2 suppresses the deleterious phenotypes associated with frataxin deficiency. In contrast, genetic augmentation with enzymes that scavenge superoxide is without effect. Augmentation of endogenous catalase restores the activity of the reactive oxygen species (ROS)-sensitive mitochondrial enzyme, aconitase and enhances resistance to H2O2 exposure, both of which are diminished by frataxin deficiency. Collectively, these data argue that H2O2 is an important pathogenic substrate underlying the phenotypes arising from frataxin deficiency in Drosophila and that interventions that reduce this specific ROS can effectively ameliorate these phenotypes. The therapeutic implications of these findings are clear and we believe warrant immediate clinical investigation.
Collapse
Affiliation(s)
- Peter R. Anderson
- *Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Kim Kirby
- *Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - William C. Orr
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75205; and
| | | | - John P. Phillips
- *Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
| |
Collapse
|
46
|
Yoon T, Dizin E, Cowan JA. N-terminal iron-mediated self-cleavage of human frataxin: regulation of iron binding and complex formation with target proteins. J Biol Inorg Chem 2007; 12:535-42. [PMID: 17285345 DOI: 10.1007/s00775-007-0205-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Accepted: 01/05/2007] [Indexed: 12/21/2022]
Abstract
Frataxin is an iron-binding mitochondrial matrix protein that has been shown to mediate iron delivery during iron-sulfur cluster and heme biosynthesis. Mitochondrial processing peptidase (MPP) yields a form of human frataxin corresponding to residues 56-210. However, structural and functional studies have focused on a core structure that results from an ill-defined cleavage event at the N-terminus. Herein we show that the N-terminus of MPP-processed frataxin shows a unique high-affinity iron site and that this iron center appears to mediate a self-cleavage reaction. Moreover, the N-terminus appears to block previously defined iron-binding sites located on the carboxylate-rich surface defined by the helix (alpha1) and the beta-sheet (beta1), most likely through electrostatic contact with the carboxylate-rich surface on the core protein, as well as inhibiting iron-promoted binding of the iron-sulfur cluster assembly scaffold partner protein, ISU. The physiological significance of iron-mediated release of the N-terminal residues from this anionic surface is discussed.
Collapse
Affiliation(s)
- Taejin Yoon
- Evans Laboratory of Chemistry, Ohio State University, Columbus, OH 43210, USA
| | | | | |
Collapse
|
47
|
Cooper JM, Schapira AHV. Friedreich's ataxia: coenzyme Q10 and vitamin E therapy. Mitochondrion 2007; 7 Suppl:S127-35. [PMID: 17485244 DOI: 10.1016/j.mito.2007.04.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 03/30/2007] [Accepted: 04/01/2007] [Indexed: 11/29/2022]
Abstract
Since the identification of the genetic mutation causing Friedreich's ataxia (FRDA) our understanding of the mechanisms underlying disease pathogenesis have improved markedly. The genetic abnormality results in the deficiency of frataxin, a protein targeted to the mitochondrion. There is extensive evidence that mitochondrial respiratory chain dysfunction, oxidative damage and iron accumulation play significant roles in the disease mechanism. There remains considerable debate as to the normal function of frataxin, but it is likely to be involved in mitochondrial iron handling, antioxidant regulation, and/or iron sulphur centre regulation. Therapeutic avenues for patients with FRDA are beginning to be explored in particular targeting antioxidant protection, enhancement of mitochondrial oxidative phosphorylation, iron chelation and more recently increasing FRDA transcription. The use of quinone therapy has been the most extensively studied to date with clear benefits demonstrated using evaluations of both disease biomarkers and clinical symptoms, and this is the topic that will be covered in this review.
Collapse
Affiliation(s)
- J M Cooper
- University Department of Clinical Neurosciences, Royal Free and University College Medical School, University College London, Rowland Hill Street, London NW3 2PF, UK.
| | | |
Collapse
|
48
|
Ding H, Yang J, Coleman LC, Yeung S. Distinct iron binding property of two putative iron donors for the iron-sulfur cluster assembly: IscA and the bacterial frataxin ortholog CyaY under physiological and oxidative stress conditions. J Biol Chem 2007; 282:7997-8004. [PMID: 17244611 DOI: 10.1074/jbc.m609665200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Frataxin, a small mitochondrial protein linked to the neurodegenerative disease Friedreich ataxia, has recently been proposed as an iron donor for the iron-sulfur cluster assembly. An analogous function has also been attributed to IscA, a key member of the iron-sulfur cluster assembly machinery found in bacteria, yeast, and humans. Here we have compared the iron binding property of IscA and the frataxin ortholog CyaY from Escherichia coli under physiological and oxidative stress conditions. In the presence of the thioredoxin reductase system, which emulates the intracellular redox potential, CyaY fails to bind any iron even at a 10-fold excess of iron in the incubation solution. Under the same physiologically relevant conditions, IscA efficiently recruits iron and transfers the iron for the iron-sulfur cluster assembly in a proposed scaffold IscU. In the presence of hydrogen peroxide, however, IscA completely loses its iron binding activity, whereas CyaY becomes a competent iron-binding protein and attenuates the iron-mediated production of hydroxyl free radicals. Hydrogen peroxide appears to oxidize the iron binding thiol groups in IscA, thus blocking the iron binding in the protein. Once the oxidized thiol groups in IscA are re-reduced with the thioredoxin reductase system, the iron binding activity of IscA is fully restored. On the other hand, hydrogen peroxide has no effect on the iron binding carboxyl groups in CyaY, allowing the protein to bind iron under oxidative stress conditions. The results suggest that IscA is capable of recruiting intracellular iron for the iron-sulfur cluster assembly under normal physiological conditions, whereas CyaY may serve as an iron chaperon to sequester redox active free iron and alleviate cellular oxidative damage under oxidative stress conditions.
Collapse
Affiliation(s)
- Huangen Ding
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
| | | | | | | |
Collapse
|
49
|
Fogel BL, Perlman S. Clinical features and molecular genetics of autosomal recessive cerebellar ataxias. Lancet Neurol 2007; 6:245-57. [PMID: 17303531 DOI: 10.1016/s1474-4422(07)70054-6] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Among the hereditary ataxias, autosomal recessive spinocerebellar ataxias comprise a diverse group of neurodegenerative disorders. Clinical phenotypes vary from predominantly cerebellar syndromes to sensorimotor neuropathy, ophthalmological disturbances, involuntary movements, seizures, cognitive dysfunction, skeletal anomalies, and cutaneous disorders, among others. Molecular pathogenesis also ranges from disorders of mitochondrial or cellular metabolism to impairments of DNA repair or RNA processing functions. Diagnosis can be improved by a systematic approach to the categorisation of these disorders, which is used to direct further, more specific, biochemical and genetic investigations. In this Review, we discuss the clinical characteristics and molecular genetics of the more common autosomal recessive ataxias and provide a framework for assessment and differential diagnosis of patients with these disorders.
Collapse
Affiliation(s)
- Brent L Fogel
- Department of Neurology, David Geffen School of Medicine at UCLA, University of California at Los Angeles, 90095, USA
| | | |
Collapse
|
50
|
Reisch AS, Elpeleg O. Biochemical assays for mitochondrial activity: assays of TCA cycle enzymes and PDHc. Methods Cell Biol 2007; 80:199-222. [PMID: 17445696 DOI: 10.1016/s0091-679x(06)80010-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ann Saada Reisch
- The Metabolic Disease Unit, Hadassah-Hebrew University Medical Centre, Jerusalem 91120, Israel
| | | |
Collapse
|